diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index fe30ca56..baaa0461 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -46,7 +46,6 @@ jobs:
               "cosmic_username": "${{ secrets.cosmic_username }}",
               "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
               "all": true,
-              "build_references": true
             }
           profiles: test_full,aws_tower
       - uses: actions/upload-artifact@v4
@@ -55,19 +54,3 @@ jobs:
           path: |
             seqera_platform_action_*.log
             seqera_platform_action_*.json
-      - name: Launch run workflow via tower
-        uses: seqeralabs/action-tower-launch@v2
-        with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
-          parameters: |
-            {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
-              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
-              "cosmic_username": "${{ secrets.cosmic_username }}",
-              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
-              "all": true,
-            }
-          profiles: test_full,aws_tower
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 8f6bfb01..977adb49 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -26,8 +26,7 @@ jobs:
               "cosmic_username": "${{ secrets.cosmic_username }}",
               "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
               "all": true,
-              "stub": true,
-              "build_references": true
+              "stub": true
             }
           profiles: test,aws_tower
       - uses: actions/upload-artifact@v4
@@ -36,27 +35,3 @@ jobs:
           path: |
             tower_action_*.log
             tower_action_*.json
-
-      - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v2
-        with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
-          parameters: |
-            {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
-              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
-              "cosmic_username": "${{ secrets.cosmic_username }}",
-              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
-              "all": true,
-              "stub": true
-            }
-          profiles: test,aws_tower
-      - uses: actions/upload-artifact@v4
-        with:
-          name: Seqera Platform debug log file
-          path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 71ff7245..a510d72d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -39,7 +39,6 @@ jobs:
           - "latest-stable"
         test_profile:
           - "test_stub"
-          - "test_build"
         compute_profile:
           - "docker"
           - "singularity"
diff --git a/CHANGELOG.md b/CHANGELOG.md
index c75b3bf3..d947b900 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add nf-test to local module: `STARFUSION_BUILD`. [#585](https://github.com/nf-core/rnafusion/pull/585)
 - Add nf-test to local module: `STARFUSION_DETECT`. [#586](https://github.com/nf-core/rnafusion/pull/586)
 - Added a new module `CTATSPLICING_STARTOCANCERINTRONS` and a new parameter `--ctatsplicing`. This options creates reports on cancer splicing abberations and requires one or both of `--arriba` and `--starfusion` to be given. [#587](https://github.com/nf-core/rnafusion/pull/587)
+- Add parameter `--references_only` when no data should be analysed, but only the references should be built [#505](https://github.com/nf-core/rnafusion/pull/505)
 
 ### Changed
 
@@ -34,6 +35,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Remove double nested folder introduced in [#577](https://github.com/nf-core/rnafusion/pull/577), [#581](https://github.com/nf-core/rnafusion/pull/581)
 - Use docker.io and galaxy containers for fusioncatcher and starfusion (incl. fusioninspector) instead of wave as they are not functional on wave [#588](https://github.com/nf-core/rnafusion/pull/588)
 - Update STAR-Fusion to 1.14 [#588](https://github.com/nf-core/rnafusion/pull/588)
+- Use "-genePredExt -geneNameAsName2 -ignoreGroupsWithoutExons" (to mimic gms/tomte) for GTF_TO_REFFLAT [#505](https://github.com/nf-core/rnafusion/pull/505)
+- Integrate reference building in the main workflow [#505](https://github.com/nf-core/rnafusion/pull/505)
+- Move from ensembl to gencode base [#505](https://github.com/nf-core/rnafusion/pull/505)
+- Update from ensembl 102 to gencode 46 default references [#505](https://github.com/nf-core/rnafusion/pull/505)
 
 ### Fixed
 
@@ -48,12 +53,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Removed
 
 - Remove fusionGDB from documentation and fusion-report download stubs [#503](https://github.com/nf-core/rnafusion/pull/503)
+- Removed test-build as reference building gets integrated in the main workflow [#505](https://github.com/nf-core/rnafusion/pull/505)
+- Removed parameter `--build_references`
 
 ### Parameters
 
-| Old parameter | New parameter |
-| ------------- | ------------- |
-|               | `--no_cosmic` |
+| Old parameter        | New parameter       |
+| -------------------- | ------------------- |
+|                      | `--no_cosmic`       |
+| `--build_references` | `--references_only` |
 
 ## v3.0.2 - [2024-04-10]
 
diff --git a/README.md b/README.md
index 41e2bc96..809de85f 100644
--- a/README.md
+++ b/README.md
@@ -19,7 +19,7 @@
 
 ## Introduction
 
-**nf-core/rnafusion** is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes. Results from up to 5 fusion callers tools are created, and are also aggregated, most notably in a pdf visualiation document, a vcf data collection file, and html and tsv reports.
+**nf-core/rnafusion** is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes. Results from up to 5 fusion callers tools are created, and are also aggregated, most notably in a pdf visualisation document, a vcf data collection file, and html and tsv reports.
 
 On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/rnafusion/results).
 
@@ -31,9 +31,9 @@ In rnafusion the full-sized test includes reference building and fusion detectio
 
 ### Build references
 
-`--build_references` triggers a parallel workflow to build references, which is a prerequisite to running the pipeline:
+`--references_only` triggers a workflow to ONLY build references, otherwise the references are build when the analysis is run:
 
-1. Download ensembl fasta and gtf files
+1. Download gencode fasta and gtf files
 2. Create [STAR](https://github.com/alexdobin/STAR) index
 3. Download [Arriba](https://github.com/suhrig/arriba) references
 4. Download [FusionCatcher](https://github.com/ndaniel/fusioncatcher) references
@@ -78,7 +78,7 @@ First, build the references:
 nextflow run nf-core/rnafusion \
    -profile test,<docker/singularity/.../institute> \
    --outdir <OUTDIR>\
-   --build_references \
+   --references_only \
    -stub
 ```
 
diff --git a/conf/modules.config b/conf/modules.config
index 1730b17b..b3643f48 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -18,10 +18,6 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: GFFREAD {
-        ext.args = '-w -S'
-    }
-
     withName: 'ARRIBA_ARRIBA' {
         publishDir = [
             path: { "${params.outdir}/arriba" },
@@ -40,7 +36,7 @@ process {
     }
 
     withName: 'ARRIBA_VISUALISATION' {
-        ext.when   = { !params.fusioninspector_only && (params.starfusion || params.all) }
+        ext.when   = { {!params.fusioninspector_only} && ({params.starfusion} || {params.all}) }
         ext.prefix = { "${meta.id}_combined_fusions_arriba_visualisation" }
         publishDir = [
             path: { "${params.outdir}/arriba_visualisation" },
@@ -73,9 +69,9 @@ process {
         ]
     }
 
-    withName: 'ENSEMBL_DOWNLOAD' {
+    withName: 'GENCODE_DOWNLOAD' {
         publishDir = [
-            path: { "${params.genomes_base}/ensembl" },
+            path: { "${params.genomes_base}/gencode" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -87,7 +83,7 @@ process {
 
     withName: 'FASTQC' {
         ext.args = '--quiet'
-        ext.when         = { !params.skip_qc }
+        ext.when = {!params.skip_qc}
         publishDir = [
             path: { "${params.outdir}/fastqc" },
             mode: params.publish_dir_mode,
@@ -97,6 +93,7 @@ process {
 
     withName: 'FASTQC_FOR_FASTP' {
         ext.args = '--quiet'
+        ext.when = { !params.skip_qc }
         ext.prefix = { "${meta.id}_trimmed" }
         publishDir = [
             path: { "${params.outdir}/fastqc_for_fastp" },
@@ -119,7 +116,7 @@ process {
 
     withName: 'FUSIONINSPECTOR' {
         ext.when = { !params.skip_vis }
-        ext.args = { params.fusioninspector_limitSjdbInsertNsj != 1000000 ? "--STAR_xtra_params \"--limitSjdbInsertNsj ${params.fusioninspector_limitSjdbInsertNsj}\"" : '' }
+        ext.args = { ${params.fusioninspector_limitSjdbInsertNsj} != 1000000 ? "--STAR_xtra_params \"--limitSjdbInsertNsj ${params.fusioninspector_limitSjdbInsertNsj}\"" : '' }
         ext.args2 = '--annotate --examine_coding_effect'
     }
 
@@ -146,12 +143,39 @@ process {
 
     withName: 'GATK4_BEDTOINTERVALLIST' {
         publishDir = [
-            path: { "${params.genomes_base}/ensembl" },
+            path: { "${params.genomes_base}/gencode" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
+    withName: 'GATK4_MARKDUPLICATES' {
+        ext.when         = { {!params.skip_qc} && {!params.fusioninspector_only} && ( {params.starfusion}|| {params.all}) }
+        publishDir = [
+            path: { "${params.outdir}/picard" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: 'GFFREAD' {
+        ext.args = { '-w -S' }
+        publishDir = [
+            path: { "${params.genomes_base}/gffread" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: 'GTF_TO_REFFLAT' {
+        ext.args = "-genePredExt -geneNameAsName2 -ignoreGroupsWithoutExons"
+        publishDir = [
+            path: { "${params.genomes_base}/gencode" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
     withName: 'HGNC_DOWNLOAD' {
         publishDir = [
             path: { "${params.genomes_base}/hgnc" },
@@ -161,7 +185,7 @@ process {
     }
     withName: 'MULTIQC' {
         ext.when         = { !params.skip_qc }
-        ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
+        ext.args   = {params.multiqc_title} ? "--title \"$params.multiqc_title\"" : ''
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
@@ -170,21 +194,12 @@ process {
     }
 
     withName: 'PICARD_COLLECTRNASEQMETRICS' {
-        ext.when         = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all) }
+        ext.when         = { {!params.skip_qc} && {!params.fusioninspector_only} && ( {params.starfusion} || {params.all}) }
 
     }
 
-    withName: 'GATK4_MARKDUPLICATES' {
-        ext.when         = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all) }
-        publishDir = [
-            path: { "${params.outdir}/picard" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
     withName: 'PICARD_COLLECTINSERTSIZEMETRICS' {
-        ext.when         = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all) }
+        ext.when         = { ${!params.skip_qc} && ${!params.fusioninspector_only} && (${params.starfusion} || ${params.all}) }
         ext.prefix       = { "${meta.id}_collectinsertsize"}
         publishDir = [
             path: { "${params.outdir}/picard" },
@@ -215,7 +230,7 @@ process {
 
     withName: 'SAMTOOLS_FAIDX' {
         publishDir = [
-            path: { "${params.genomes_base}/ensembl" },
+            path: { "${params.genomes_base}/gencode" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
@@ -375,16 +390,11 @@ process {
         ]
     }
 
-    withName: 'UCSC_GTFTOGENEPRED' {
-        ext.args   = "-genePredExt -geneNameAsName2"
-        publishDir = [
-            path: { "${params.genomes_base}/ensembl" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
     withName: 'VCF_COLLECT' {
         ext.when = { {!params.fusioninspector_only} && {!params.skip_vcf} }
     }
+
+    withName: '.*' {
+            ext.when = { !params.references_only || task.process.contains('BUILD_REFERENCES') }
+        }
 }
diff --git a/conf/test.config b/conf/test.config
index b3d32585..2d403c75 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -16,6 +16,8 @@ params {
 
     // Input data
     input                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv'
+    all                    = true
+    no_cosmic              = true
 }
 
 // Limit and standardize resources for github actions and reproducibility
diff --git a/conf/test_build.config b/conf/test_build.config
index cce3196e..e577ada5 100644
--- a/conf/test_build.config
+++ b/conf/test_build.config
@@ -15,7 +15,7 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    build_references           = true
+    references_only            = true
     input                      = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv'
     no_cosmic                  = true
     all                        = true
diff --git a/docs/usage.md b/docs/usage.md
index 1bddcf71..b3942057 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -10,7 +10,7 @@ The pipeline is divided into two parts:
 
 1. Download and build references
 
-- specified with `--build_references` parameter
+- specified with `--references_only` parameter
 - required only once before running the pipeline
 - **Important**: has to be run with each new release
 
@@ -32,7 +32,7 @@ The rnafusion pipeline needs references for the fusion detection tools, so downl
 ```bash
 nextflow run nf-core/rnafusion \
   -profile <docker/singularity/.../institute> \
-  --build_references --all \
+  --references_only --all \
   --cosmic_username <EMAIL> --cosmic_passwd <PASSWORD> \
   --genomes_base <PATH/TO/REFERENCES> \
   --outdir <PATH/TO/REFERENCES>
@@ -43,7 +43,7 @@ References for each tools can also be downloaded separately with:
 ```bash
 nextflow run nf-core/rnafusion \
   -profile <docker/singularity/.../institute> \
-  --build_references --<tool1> --<tool2> ... \
+  --references_only --<tool1> --<tool2> ... \
   --cosmic_username <EMAIL> --cosmic_passwd <PASSWORD> \
   --genomes_base <PATH/TO/REFERENCES> \
   --outdir <OUTPUT/PATH>
@@ -64,7 +64,7 @@ Use credentials from QIAGEN and add `--qiagen`
 ```bash
 nextflow run nf-core/rnafusion \
   -profile <docker/singularity/.../institute> \
-  --build_references --<tool1> --<tool2> ... \
+  --references_only --<tool1> --<tool2> ... \
   --cosmic_username <EMAIL> --cosmic_passwd <PASSWORD> \
   --genomes_base <PATH/TO/REFERENCES> \
   --outdir <OUTPUT/PATH> --qiagen
@@ -81,7 +81,7 @@ If process `FUSIONREPORT_DOWNLOAD` times out, it could be due to network restric
 ```bash
 nextflow run nf-core/rnafusion  \
   -profile <docker/singularity/.../institute> \
-  --build_references \
+  --references_only \
   --cosmic_username <EMAIL> --cosmic_passwd <PASSWORD> \
   --fusionreport \
   --genomes_base <PATH/TO/REFERENCES> \
@@ -93,7 +93,7 @@ Where the custom configuration could look like (adaptation to local machine nece
 
 ```text
 process {
-  withName:  'NFCORE_RNAFUSION:BUILD_REFERENCES:FUSIONREPORT_DOWNLOAD' {
+  withName:  'NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:FUSIONREPORT_DOWNLOAD' {
     memory = '8.GB'
     cpus = 4
   }
@@ -162,7 +162,7 @@ If you are not covered by the research COSMIC license and want to avoid using CO
 
 > **IMPORTANT: Either `--all` or `--<tool>`** is necessary to run detection tools
 
-`--genomes_base` should be the path to the directory containing the folder `references/` that was built with `--build_references`.
+`--genomes_base` should be the path to the directory containing the folder `references/` that was built with `--references_only`.
 
 Note that the pipeline will create the following files in your working directory:
 
@@ -397,7 +397,6 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `test`
   - A profile with a complete configuration for automated testing
   - Includes links to test data so needs no other parameters
-  - Needs to run in two steps: with `--build_references` first and then without `--build_references` to run the analysis
   - !!!! Run with `-stub` as all references need to be downloaded otherwise !!!!
 
 ### `-resume`
diff --git a/main.nf b/main.nf
index ced04ca9..78781bed 100644
--- a/main.nf
+++ b/main.nf
@@ -18,7 +18,6 @@
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_rnafusion_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_rnafusion_pipeline'
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_rnafusion_pipeline'
-include { BUILD_REFERENCES        } from './workflows/build_references'
 include { RNAFUSION               } from './workflows/rnafusion'
 
 
@@ -51,12 +50,10 @@ workflow NFCORE_RNAFUSION {
     // WORKFLOW: Run pipeline
     //
 
-    if (params.build_references) {
-        BUILD_REFERENCES ()
-    } else {
-        RNAFUSION(samplesheet)
-    }
+    RNAFUSION(samplesheet)
 
+    emit:
+    multiqc_report = RNAFUSION.out.multiqc_report
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -73,18 +70,14 @@ workflow {
     PIPELINE_INITIALISATION (
         params.version,
         params.validate_params,
-        params.monochrome_logs,
         args,
         params.outdir,
-        params.input
     )
 
     //
     // WORKFLOW: Run main workflow
     //
-    NFCORE_RNAFUSION (
-        PIPELINE_INITIALISATION.out.samplesheet
-    )
+    NFCORE_RNAFUSION (PIPELINE_INITIALISATION.out.samplesheet)
 
     //
     // SUBWORKFLOW: Run completion tasks
@@ -96,6 +89,7 @@ workflow {
         params.outdir,
         params.monochrome_logs,
         params.hook_url,
+        NFCORE_RNAFUSION.out.multiqc_report,
     )
 }
 
diff --git a/modules.json b/modules.json
index f8ae46ae..b41d5fa5 100644
--- a/modules.json
+++ b/modules.json
@@ -17,7 +17,7 @@
                     },
                     "arriba/download": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "467c202a876d26af544fa8c4b22a050a535462a7",
                         "installed_by": ["modules"]
                     },
                     "bedops/convert2bed": {
@@ -32,7 +32,7 @@
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
                         "installed_by": ["modules"]
                     },
                     "fastp": {
@@ -42,27 +42,27 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164",
                         "installed_by": ["modules"]
                     },
                     "gatk4/bedtointervallist": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "1999eff2c530b2b185a25cc42117a1686f09b685",
                         "installed_by": ["modules"]
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "1999eff2c530b2b185a25cc42117a1686f09b685",
                         "installed_by": ["modules"]
                     },
                     "gatk4/markduplicates": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "1999eff2c530b2b185a25cc42117a1686f09b685",
                         "installed_by": ["modules"]
                     },
                     "gffread": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "bd5f75ccaf2345269810e66e85de8a70e4de8764",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -72,7 +72,7 @@
                     },
                     "picard/collectinsertsizemetrics": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
                         "installed_by": ["modules"]
                     },
                     "picard/collectrnaseqmetrics": {
@@ -82,7 +82,7 @@
                     },
                     "picard/collectwgsmetrics": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
                         "installed_by": ["modules"]
                     },
                     "rrnatranscripts": {
@@ -93,12 +93,12 @@
                     },
                     "salmon/index": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
                         "installed_by": ["modules"]
                     },
                     "salmon/quant": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
@@ -113,22 +113,22 @@
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["modules"]
                     },
                     "star/align": {
                         "branch": "master",
-                        "git_sha": "30a97c755895b7dfe40a730b0695c554a10f1cdd",
+                        "git_sha": "a5ad53288c79fa52c5ae708c317e09ec2dd149ab",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "a5ad53288c79fa52c5ae708c317e09ec2dd149ab",
                         "installed_by": ["modules"]
                     },
                     "stringtie/merge": {
@@ -138,7 +138,7 @@
                     },
                     "stringtie/stringtie": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
                         "installed_by": ["modules"]
                     },
                     "ucsc/gtftogenepred": {
@@ -152,17 +152,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
+                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/local/arriba/visualisation/main.nf b/modules/local/arriba/visualisation/main.nf
index cc120119..f1aa097b 100644
--- a/modules/local/arriba/visualisation/main.nf
+++ b/modules/local/arriba/visualisation/main.nf
@@ -22,17 +22,17 @@ process ARRIBA_VISUALISATION {
 
     script:
     def args = task.ext.args ?: ''
-    def cytobands = cytobands ? " --cytobands=$cytobands" : ""
+    def arg_cytobands = cytobands ? " --cytobands=$cytobands" : ""
+    def arg_protein_domains = protein_domains ? "--proteinDomains=$protein_domains" : ""
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def protein_domains = protein_domains ? "--proteinDomains=$protein_domains" : ""
     """
     draw_fusions.R \\
         --fusions=$fusions \\
         --alignments=$bam \\
         --output=${prefix}.pdf \\
         --annotation=${gtf} \\
-        $cytobands \\
-        $protein_domains \\
+        $arg_cytobands \\
+        $arg_protein_domains \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/local/ensembl/main.nf b/modules/local/ensembl/main.nf
deleted file mode 100644
index 8f708fc2..00000000
--- a/modules/local/ensembl/main.nf
+++ /dev/null
@@ -1,53 +0,0 @@
-process ENSEMBL_DOWNLOAD {
-    tag "ensembl"
-    label 'process_low'
-
-    conda "bioconda::gnu-wget=1.18"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h5bf99c6_5' :
-        'biocontainers/gnu-wget:1.18--h5bf99c6_5' }"
-
-    input:
-    val ensembl_version
-    val genome
-    val meta
-
-    output:
-    tuple val(meta), path("Homo_sapiens.${genome}.${ensembl_version}.gtf")                       , emit: gtf
-    tuple val(meta), path("Homo_sapiens.${genome}.${ensembl_version}.dna.primary_assembly.fa")   , emit: primary_assembly
-    tuple val(meta), path("Homo_sapiens.${genome}.${ensembl_version}.chr.gtf")                   , emit: chrgtf
-    path "versions.yml"                                                                          , emit: versions
-
-
-    script:
-    """
-    wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/gtf/homo_sapiens/Homo_sapiens.${params.genome}.${ensembl_version}.gtf.gz
-    wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/fasta/homo_sapiens/dna/Homo_sapiens.${params.genome}.dna.primary_assembly.fa.gz -O Homo_sapiens.${params.genome}.${ensembl_version}.dna.primary_assembly.fa.gz
-    wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/gtf/homo_sapiens/Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf.gz
-
-    gunzip Homo_sapiens.${params.genome}.${ensembl_version}.gtf.gz
-    gunzip Homo_sapiens.${params.genome}.${ensembl_version}.dna.primary_assembly.fa.gz
-    gunzip Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        wget: \$(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3)
-        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
-
-    END_VERSIONS
-    """
-
-    stub:
-    """
-    touch "Homo_sapiens.${genome}.${ensembl_version}.gtf"
-    touch "Homo_sapiens.${params.genome}.${ensembl_version}.dna.primary_assembly.fa"
-    touch "Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf"
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        wget: \$(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3)
-        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
-    END_VERSIONS
-    """
-
-}
diff --git a/modules/local/ensembl/tests/main.nf.test b/modules/local/ensembl/tests/main.nf.test
deleted file mode 100644
index e30a826f..00000000
--- a/modules/local/ensembl/tests/main.nf.test
+++ /dev/null
@@ -1,37 +0,0 @@
-nextflow_process {
-
-    name "Test Process ENSEMBL_DOWNLOAD"
-    script "../main.nf"
-    process "ENSEMBL_DOWNLOAD"
-
-    test("Should download Ensembl files") {
-
-        when {
-            params {
-                outdir = "tests/results"
-                genome = "GRCh38"
-            }
-            process {
-                """
-                input[0] = "102"
-                input[1] = "GRCh38"
-                input[2] = "GRCh38"
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    file(process.out.gtf[0][1]).name,
-                    file(process.out.primary_assembly[0][1]).name,
-                    file(process.out.chrgtf[0][1]).name,
-                    process.out.versions
-                ).match() }
-            )
-        }
-
-    }
-
-}
diff --git a/modules/local/ensembl/tests/main.nf.test.snap b/modules/local/ensembl/tests/main.nf.test.snap
deleted file mode 100644
index a6eb2971..00000000
--- a/modules/local/ensembl/tests/main.nf.test.snap
+++ /dev/null
@@ -1,17 +0,0 @@
-{
-    "Should download Ensembl files": {
-        "content": [
-            "Homo_sapiens.GRCh38.102.gtf",
-            "Homo_sapiens.GRCh38.102.dna.primary_assembly.fa",
-            "Homo_sapiens.GRCh38.102.chr.gtf",
-            [
-                "versions.yml:md5,efb55665a151fe2b4d9eac70c0e01bb0"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
-        },
-        "timestamp": "2024-11-26T14:06:24.319131837"
-    }
-}
\ No newline at end of file
diff --git a/modules/local/fusioncatcher/build/main.nf b/modules/local/fusioncatcher/build/main.nf
new file mode 100644
index 00000000..4aaaf504
--- /dev/null
+++ b/modules/local/fusioncatcher/build/main.nf
@@ -0,0 +1,41 @@
+process FUSIONCATCHER_BUILD {
+    tag "fusioncatcher_build"
+    label 'process_medium'
+
+    container "docker.io/rannickscilifelab/fusioncatcher:1.34"
+
+    input:
+    val genome_gencode_version
+
+    output:
+    path "human_v${genome_gencode_version}"  , emit: reference
+    path "versions.yml"                      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+
+    def args = task.ext.args ?: ''
+    """
+    fusioncatcher-build.py \\
+        -g homo_sapiens \\
+        -o human_v${genome_gencode_version} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fusioncatcher: \$(echo \$(fusioncatcher --version 2>&1))
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir human_v${genome_gencode_version}
+    touch human_v${genome_gencode_version}/ensembl_fully_overlapping_genes.txt
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fusioncatcher: \$(echo \$(fusioncatcher --version 2>&1))
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/fusioncatcher/build/meta.yml b/modules/local/fusioncatcher/build/meta.yml
new file mode 100644
index 00000000..202be7e1
--- /dev/null
+++ b/modules/local/fusioncatcher/build/meta.yml
@@ -0,0 +1,24 @@
+name: fusioncatcher_build
+description: Build genome for fusioncatcher
+keywords:
+  - sort
+tools:
+  - fusioncatcher:
+      description: Build genome for fusioncatcher
+      homepage: https://github.com/ndaniel/fusioncatcher/
+      documentation: https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md
+      tool_dev_url: https://github.com/ndaniel/fusioncatcher/
+      doi: "10.1101/011650"
+      licence: ["GPL v3"]
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - reference:
+      type: directory
+      description: Path to fusioncatcher references
+
+authors:
+  - "@praveenraj2018, @rannick"
diff --git a/modules/local/fusioncatcher/download/main.nf b/modules/local/fusioncatcher/download/main.nf
index f11491b9..c7ea28ec 100644
--- a/modules/local/fusioncatcher/download/main.nf
+++ b/modules/local/fusioncatcher/download/main.nf
@@ -4,8 +4,13 @@ process FUSIONCATCHER_DOWNLOAD {
 
     container "docker.io/rannickscilifelab/fusioncatcher:1.34"
 
+
+    input:
+    val genome_gencode_version
+
+
     output:
-    path "*"                , emit: reference
+    path "human_v${genome_gencode_version}"                , emit: reference
     path "versions.yml"     , emit: versions
 
     when:
@@ -14,23 +19,16 @@ process FUSIONCATCHER_DOWNLOAD {
     script:
 
     def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
-    def human_version = "v102"
-    def url = "http://sourceforge.net/projects/fusioncatcher/files/data/human_${human_version}.tar.gz.aa"
+        // TODO: move to S3
+
+    // def url =
     """
-    if wget --spider "$url" 2>/dev/null; then
-        wget $args $url
-        wget $args http://sourceforge.net/projects/fusioncatcher/files/data/human_${human_version}.tar.gz.ab
-        wget $args http://sourceforge.net/projects/fusioncatcher/files/data/human_${human_version}.tar.gz.ac
-        wget $args http://sourceforge.net/projects/fusioncatcher/files/data/human_${human_version}.tar.gz.ad
-        cat human_${human_version}.tar.gz.* | tar xz
-        rm human_${human_version}.tar*
-    else
-        fusioncatcher-build \\
-            -g homo_sapiens \\
-            -o human_${human_version} \\
-            $args2
-    fi
+    wget $args http://sourceforge.net/projects/fusioncatcher/files/data/human_${genome_gencode_version}.tar.gz.aa
+    wget $args http://sourceforge.net/projects/fusioncatcher/files/data/human_${genome_gencode_version}.tar.gz.ab
+    wget $args http://sourceforge.net/projects/fusioncatcher/files/data/human_${genome_gencode_version}.tar.gz.ac
+    wget $args http://sourceforge.net/projects/fusioncatcher/files/data/human_${genome_gencode_version}.tar.gz.ad
+    cat human_${genome_gencode_version}.tar.gz.* | tar xz
+    rm human_${genome_gencode_version}.tar*
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -39,9 +37,9 @@ process FUSIONCATCHER_DOWNLOAD {
     """
 
     stub:
-    def human_version = "v102"
     """
-    mkdir human_${human_version}
+    mkdir human_v${genome_gencode_version}
+    touch human_v${genome_gencode_version}/ensembl_fully_overlapping_genes.txt
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         fusioncatcher: \$(echo \$(fusioncatcher --version 2>&1))
diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf
index 8981e601..56a29ab4 100644
--- a/modules/local/fusionreport/detect/main.nf
+++ b/modules/local/fusionreport/detect/main.nf
@@ -11,13 +11,13 @@ process FUSIONREPORT {
     val(tools_cutoff)
 
     output:
-    path "versions.yml"                                                 , emit: versions
     tuple val(meta), path("*fusionreport.tsv")                          , emit: fusion_list
     tuple val(meta), path("*fusionreport_filtered.tsv")                 , emit: fusion_list_filtered
-    tuple val(meta), path("*index.html")                                 , emit: report
+    tuple val(meta), path("*index.html")                                , emit: report
     tuple val(meta), path("*_*.html")                    , optional:true, emit: html
     tuple val(meta), path("*.csv")                       , optional:true, emit: csv
     tuple val(meta), path("*.json")                      , optional:true, emit: json
+    path "versions.yml"                                                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/gencode_download/main.nf b/modules/local/gencode_download/main.nf
new file mode 100644
index 00000000..1f466d26
--- /dev/null
+++ b/modules/local/gencode_download/main.nf
@@ -0,0 +1,49 @@
+process GENCODE_DOWNLOAD {
+    tag "gencode_download"
+    label 'process_low'
+
+    conda "bioconda::gnu-wget=1.18"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h5bf99c6_5' :
+        'quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5' }"
+
+    input:
+    val genome_gencode_version
+    val genome
+
+    output:
+    path "*.fa"        , emit: fasta
+    path "*.gtf"       , emit: gtf
+    path "versions.yml", emit: versions
+
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def folder_gencode = genome.contains("38") ? "" : "/${genome}_mapping"
+    def gtf_file_name = genome.contains("38") ? "gencode.v${genome_gencode_version}.primary_assembly.annotation.gtf.gz" : "gencode.v${genome_gencode_version}lift${genome_gencode_version}.annotation.gtf.gz"
+    """
+    wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_${genome_gencode_version}/${folder_gencode}${genome}.primary_assembly.genome.fa.gz -O Homo_sapiens_${genome}_${genome_gencode_version}_dna_primary_assembly.fa.gz
+    gunzip Homo_sapiens_${genome}_${genome_gencode_version}_dna_primary_assembly.fa.gz
+    wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_${genome_gencode_version}/${folder_gencode}${gtf_file_name} -O Homo_sapiens_${genome}_${genome_gencode_version}.gtf.gz
+    gunzip  Homo_sapiens_${genome}_${genome_gencode_version}.gtf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wget: \$(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3)
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch Homo_sapiens.${genome}.${genome_gencode_version}_dna_primary_assembly.fa
+    touch Homo_sapiens.${genome}.${genome_gencode_version}.gtf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wget: \$(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3)
+    END_VERSIONS
+    """
+
+}
diff --git a/modules/local/get_rrna_transcript/environment.yml b/modules/local/get_rrna_transcript/environment.yml
new file mode 100644
index 00000000..66b65c3a
--- /dev/null
+++ b/modules/local/get_rrna_transcript/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::pirate=1.0.5
+  - bioconda::perl-bioperl=1.7.8
diff --git a/modules/local/get_rrna_transcript/main.nf b/modules/local/get_rrna_transcript/main.nf
new file mode 100644
index 00000000..5331f534
--- /dev/null
+++ b/modules/local/get_rrna_transcript/main.nf
@@ -0,0 +1,43 @@
+process GET_RRNA_TRANSCRIPTS {
+    tag 'get_rrna_bed'
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pirate:1.0.5--hdfd78af_0' :
+        'biocontainers/pirate:1.0.5--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(gtf)
+
+    output:
+    tuple val(meta), path('rrna.gtf')    , emit: rrnagtf
+    tuple val(meta), path('rrna.bed')    , emit: bed
+    path "versions.yml" , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+    $baseDir/bin/get_rrna_transcripts.py --gtf ${gtf} --output rrna.gtf
+
+    $baseDir/bin/gtf2bed rrna.gtf > rrna.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        get_rrna_transcripts: v1.0
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch rrna.gtf
+    touch rrna.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        get_rrna_transcripts: v1.0
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/hgnc/main.nf b/modules/local/hgnc/main.nf
index a3559726..aa5c077c 100644
--- a/modules/local/hgnc/main.nf
+++ b/modules/local/hgnc/main.nf
@@ -7,12 +7,9 @@ process HGNC_DOWNLOAD {
         'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h5bf99c6_5' :
         'biocontainers/gnu-wget:1.18--h5bf99c6_5' }"
 
-    input:
-
     output:
     path "hgnc_complete_set.txt"        , emit: hgnc_ref
     path "HGNC-DB-timestamp.txt"        , emit: hgnc_date
-
     path "versions.yml"   , emit: versions
 
 
diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
index f1239789..fcd9cf80 100644
--- a/modules/local/starfusion/build/main.nf
+++ b/modules/local/starfusion/build/main.nf
@@ -15,6 +15,7 @@ process STARFUSION_BUILD {
 
     output:
     tuple val(meta), path("ctat_genome_lib_build_dir"), emit: reference
+    path "versions.yml"   , emit: versions
 
     script:
     def args = task.ext.args ?: ''
@@ -25,8 +26,8 @@ process STARFUSION_BUILD {
         --dfam_db ${dfam_species} \\
         --pfam_db current \\
         --fusion_annot_lib $fusion_annot_lib \\
-        ${args} \\
-        --CPU $task.cpus
+        --CPU $task.cpus \\
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/starfusion/download/main.nf b/modules/local/starfusion/download/main.nf
index 989c2420..ace18a9e 100644
--- a/modules/local/starfusion/download/main.nf
+++ b/modules/local/starfusion/download/main.nf
@@ -8,9 +8,9 @@ process STARFUSION_DOWNLOAD {
 
     output:
     path "ctat_genome_lib_build_dir/*"            , emit: reference
-    path "ctat_genome_lib_build_dir/ref_annot.gtf", emit: chrgtf
 
 
+    // TODO: move to S3
     script:
     """
     wget https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz --no-check-certificate
diff --git a/modules/local/uscs/custom_gtftogenepred/main.nf b/modules/local/uscs/custom_gtftogenepred/main.nf
new file mode 100644
index 00000000..9cc15765
--- /dev/null
+++ b/modules/local/uscs/custom_gtftogenepred/main.nf
@@ -0,0 +1,39 @@
+process GTF_TO_REFFLAT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "bioconda::ucsc-gtftogenepred=377"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ucsc-gtftogenepred:377--ha8a8165_5' :
+        'quay.io/biocontainers/ucsc-gtftogenepred:377--ha8a8165_5' }"
+
+    input:
+    tuple val(meta), path (gtf)
+
+    output:
+    path('*.refflat')    , emit: refflat
+    path "versions.yml"  , emit: versions
+
+    script:
+    def genepred = gtf + '.genepred'
+    def refflat = gtf + '.refflat'
+    """
+    gtfToGenePred -genePredExt -geneNameAsName2 ${gtf} ${genepred}
+    paste ${genepred} ${genepred} | cut -f12,16-25 > ${refflat}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gtfToGenePred: 377
+    END_VERSIONS
+    """
+
+    stub:
+    def refflat = gtf + '.refflat'
+    """
+    touch ${refflat}
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gtfToGenePred: 377
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/arriba/download/main.nf b/modules/nf-core/arriba/download/main.nf
index 96a4e336..c45120ad 100644
--- a/modules/nf-core/arriba/download/main.nf
+++ b/modules/nf-core/arriba/download/main.nf
@@ -8,17 +8,21 @@ process ARRIBA_DOWNLOAD {
         'biocontainers/arriba:2.4.0--h0033a41_2' }"
 
     input:
+    val(genome)
 
     output:
-    path "*"              , emit: reference
-    path "versions.yml"           , emit: versions
+    path "blacklist*${genome}*.tsv.gz"       , emit: blacklist
+    path "cytobands*${genome}*.tsv"          , emit: cytobands
+    path "protein_domains*${genome}*.gff3"   , emit: protein_domains
+    path "known_fusions*${genome}*.tsv.gz"   , emit: known_fusions
+    path "versions.yml"                      , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     """
-    wget https://github.com/suhrig/arriba/releases/download/v2.4.0/arriba_v2.4.0.tar.gz -O arriba_v2.4.0.tar.gz
+    wget https://github.com/suhrig/arriba/releases/download/v2.4.0/arriba_v2.4.0.tar.gz -O arriba_v2.4.0.tar.gz --no-check-certificate
     tar -xzvf arriba_v2.4.0.tar.gz
     rm arriba_v2.4.0.tar.gz
     mv arriba_v2.4.0/database/* .
@@ -36,7 +40,6 @@ process ARRIBA_DOWNLOAD {
     touch protein_domains_hg38_GRCh38_v2.4.0.gff3
     touch cytobands_hg38_GRCh38_v2.4.0.tsv
     touch known_fusions_hg38_GRCh38_v2.4.0.tsv.gz
-    touch protein_domains_hg38_GRCh38_v2.4.0.gff3
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/arriba/download/meta.yml b/modules/nf-core/arriba/download/meta.yml
index 531c66c2..bdf542eb 100644
--- a/modules/nf-core/arriba/download/meta.yml
+++ b/modules/nf-core/arriba/download/meta.yml
@@ -15,12 +15,34 @@ tools:
       licence: ["MIT"]
       identifier: biotools:Arriba
 
+input:
+  - - genome:
+        type: string
+        description: hg38, hg19, GRCh38, GRCh37 for humans are accepted
 output:
-  - reference:
-      - "*":
-          type: directory
-          description: Folder with arriba references
-          pattern: "*"
+  - blacklist:
+      - blacklist*${genome}*.tsv.gz:
+          type: string
+          description: The blacklist removes recurrent alignment artifacts and transcripts
+            which are present in healthy tissue
+          pattern: ".tsv.gz"
+  - cytobands:
+      - cytobands*${genome}*.tsv:
+          type: file
+          description: Coordinates of the Giemsa staining bands. This information is used
+            to draw ideograms
+          pattern: ".tsv"
+  - protein_domains:
+      - protein_domains*${genome}*.gff3:
+          type: file
+          description: Protein domain annotations
+          patter: "*.gff3"
+  - known_fusions:
+      - known_fusions*${genome}*.tsv.gz:
+          type: file
+          description: Arriba is more sensitive to those fusions to improve the detection
+            rate of expected or highly relevant events, such as recurrent fusions
+          patter: "*.tsv.gz"
   - versions:
       - versions.yml:
           type: file
diff --git a/modules/nf-core/arriba/download/tests/main.nf.test b/modules/nf-core/arriba/download/tests/main.nf.test
index cccc95db..2c32c7a0 100644
--- a/modules/nf-core/arriba/download/tests/main.nf.test
+++ b/modules/nf-core/arriba/download/tests/main.nf.test
@@ -11,11 +11,10 @@ nextflow_process {
     tag "arriba/download"
 
     test("test-arriba-download") {
-
         when {
             process {
                 """
-
+                input[0] = 'GRCh38'
                 """
             }
         }
@@ -23,11 +22,27 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.reference[0].collect { file(it).name }.toSorted(),
-                    process.out.versions
-                    ).match()
-                }
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("download - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = 'GRCh38'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success }
             )
         }
     }
diff --git a/modules/nf-core/arriba/download/tests/main.nf.test.snap b/modules/nf-core/arriba/download/tests/main.nf.test.snap
index eda3f706..fe9b18b9 100644
--- a/modules/nf-core/arriba/download/tests/main.nf.test.snap
+++ b/modules/nf-core/arriba/download/tests/main.nf.test.snap
@@ -1,35 +1,43 @@
 {
-    "test-arriba-download": {
+    "download": {
         "content": [
-            [
-                "CREDITS",
-                "RefSeq_viral_genomes_v2.4.0.fa.gz",
-                "blacklist_hg19_hs37d5_GRCh37_v2.4.0.tsv.gz",
-                "blacklist_hg38_GRCh38_v2.4.0.tsv.gz",
-                "blacklist_mm10_GRCm38_v2.4.0.tsv.gz",
-                "blacklist_mm39_GRCm39_v2.4.0.tsv.gz",
-                "cytobands_hg19_hs37d5_GRCh37_v2.4.0.tsv",
-                "cytobands_hg38_GRCh38_v2.4.0.tsv",
-                "cytobands_mm10_GRCm38_v2.4.0.tsv",
-                "cytobands_mm39_GRCm39_v2.4.0.tsv",
-                "known_fusions_hg19_hs37d5_GRCh37_v2.4.0.tsv.gz",
-                "known_fusions_hg38_GRCh38_v2.4.0.tsv.gz",
-                "known_fusions_mm10_GRCm38_v2.4.0.tsv.gz",
-                "known_fusions_mm39_GRCm39_v2.4.0.tsv.gz",
-                "protein_domains_hg19_hs37d5_GRCh37_v2.4.0.gff3",
-                "protein_domains_hg38_GRCh38_v2.4.0.gff3",
-                "protein_domains_mm10_GRCm38_v2.4.0.gff3",
-                "protein_domains_mm39_GRCm39_v2.4.0.gff3",
-                "versions.yml"
-            ],
-            [
-                "versions.yml:md5,98c69df5eaea5caf0b4af7b8d7af4893"
-            ]
+            {
+                "0": [
+                    "blacklist_hg38_GRCh38_v2.4.0.tsv.gz:md5,e3098a4be51aece78aede64b55c39318"
+                ],
+                "1": [
+                    "cytobands_hg38_GRCh38_v2.4.0.tsv:md5,7bd504feefb33fcfc9be0517439a423c"
+                ],
+                "2": [
+                    "protein_domains_hg38_GRCh38_v2.4.0.gff3:md5,43c387a784ebeed71b4147076cebf978"
+                ],
+                "3": [
+                    "known_fusions_hg38_GRCh38_v2.4.0.tsv.gz:md5,4f00f81ccb5f4db283f1a22b8b0da67c"
+                ],
+                "4": [
+                    "versions.yml:md5,98c69df5eaea5caf0b4af7b8d7af4893"
+                ],
+                "blacklist": [
+                    "blacklist_hg38_GRCh38_v2.4.0.tsv.gz:md5,e3098a4be51aece78aede64b55c39318"
+                ],
+                "cytobands": [
+                    "cytobands_hg38_GRCh38_v2.4.0.tsv:md5,7bd504feefb33fcfc9be0517439a423c"
+                ],
+                "known_fusions": [
+                    "known_fusions_hg38_GRCh38_v2.4.0.tsv.gz:md5,4f00f81ccb5f4db283f1a22b8b0da67c"
+                ],
+                "protein_domains": [
+                    "protein_domains_hg38_GRCh38_v2.4.0.gff3:md5,43c387a784ebeed71b4147076cebf978"
+                ],
+                "versions": [
+                    "versions.yml:md5,98c69df5eaea5caf0b4af7b8d7af4893"
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-22T17:00:38.086459"
+        "timestamp": "2024-10-08T11:12:17.010496"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/arriba/download/tests/tags.yml b/modules/nf-core/arriba/download/tests/tags.yml
new file mode 100644
index 00000000..f510bbf1
--- /dev/null
+++ b/modules/nf-core/arriba/download/tests/tags.yml
@@ -0,0 +1,2 @@
+arriba/download:
+  - "modules/nf-core/arriba/download/**"
diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml
index c7eb9bd1..71e04c3d 100644
--- a/modules/nf-core/cat/fastq/environment.yml
+++ b/modules/nf-core/cat/fastq/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::coreutils=8.30
+  - conda-forge::coreutils=9.5
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
index b68e5f91..4364a389 100644
--- a/modules/nf-core/cat/fastq/main.nf
+++ b/modules/nf-core/cat/fastq/main.nf
@@ -4,8 +4,8 @@ process CAT_FASTQ {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'nf-core/ubuntu:20.04' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' :
+        'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }"
 
     input:
     tuple val(meta), path(reads, stageAs: "input*/*")
diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap
index aec119a9..f8689a1c 100644
--- a/modules/nf-core/cat/fastq/tests/main.nf.test.snap
+++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-01-17T17:30:39.816981"
+        "timestamp": "2024-10-19T20:02:07.519211144"
     },
     "test_cat_fastq_single_end_same_name": {
         "content": [
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -59,15 +59,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-01-17T17:32:35.229332"
+        "timestamp": "2024-10-19T20:02:31.618628921"
     },
     "test_cat_fastq_single_end_single_file": {
         "content": [
@@ -82,7 +82,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -94,15 +94,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-01-17T17:34:00.058829"
+        "timestamp": "2024-10-19T20:02:57.904149581"
     },
     "test_cat_fastq_paired_end_same_name": {
         "content": [
@@ -120,7 +120,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -135,15 +135,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-01-17T17:33:33.031555"
+        "timestamp": "2024-10-19T20:02:44.577183829"
     },
     "test_cat_fastq_single_end - stub": {
         "content": [
@@ -158,7 +158,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -170,15 +170,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-05T12:07:28.244999"
+        "timestamp": "2024-10-19T20:03:10.603734777"
     },
     "test_cat_fastq_paired_end_same_name - stub": {
         "content": [
@@ -196,7 +196,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -211,15 +211,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-05T12:07:57.070911"
+        "timestamp": "2024-10-19T20:03:46.041808828"
     },
     "test_cat_fastq_single_end_same_name - stub": {
         "content": [
@@ -234,7 +234,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -246,15 +246,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-05T12:07:46.796254"
+        "timestamp": "2024-10-19T20:03:34.13865402"
     },
     "test_cat_fastq_paired_end": {
         "content": [
@@ -272,7 +272,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -287,15 +287,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-01-17T17:32:02.270935"
+        "timestamp": "2024-10-19T20:02:19.64383573"
     },
     "test_cat_fastq_paired_end - stub": {
         "content": [
@@ -313,7 +313,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -328,15 +328,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-05T12:07:37.807553"
+        "timestamp": "2024-10-19T20:03:22.597246066"
     },
     "test_cat_fastq_single_end_single_file - stub": {
         "content": [
@@ -351,7 +351,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -363,14 +363,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-05T12:14:51.861264"
+        "timestamp": "2024-10-19T20:03:58.44849001"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d8989f48..752c3a10 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -24,7 +24,7 @@ process FASTQC {
     // Make list of old name and new name pairs to use for renaming in the bash while loop
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
     def rename_to = old_new_pairs*.join(' ').join(' ')
-    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+    def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ')
 
     // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
     // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 4827da7a..2b2e62b8 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -11,6 +11,7 @@ tools:
         FastQC gives general quality metrics about your reads.
         It provides information about the quality score distribution
         across your reads, the per base sequence content (%A/C/G/T).
+
         You get information about adapter contamination and other
         overrepresented sequences.
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml
index 55993f44..1f7d0824 100644
--- a/modules/nf-core/gatk4/bedtointervallist/environment.yml
+++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml
@@ -1,5 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::gatk4=4.5.0.0
+  # renovate: datasource=conda depName=bioconda/gatk4
+  - bioconda::gatk4=4.6.1.0
+  # renovate: datasource=conda depName=bioconda/gcnvkernel
+  - bioconda::gcnvkernel=0.9
diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf
index 68863d67..89960e04 100644
--- a/modules/nf-core/gatk4/bedtointervallist/main.nf
+++ b/modules/nf-core/gatk4/bedtointervallist/main.nf
@@ -1,11 +1,11 @@
 process GATK4_BEDTOINTERVALLIST {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_single'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data':
+        'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }"
 
     input:
     tuple val(meta), path(bed)
diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap
index 48c322fd..6936cf97 100644
--- a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap
+++ b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b"
+                    "versions.yml:md5,6b3aa4d49cc3ba433ecf92e31f155d00"
                 ],
                 "interval_list": [
                     [
@@ -22,14 +22,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b"
+                    "versions.yml:md5,6b3aa4d49cc3ba433ecf92e31f155d00"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-03-19T14:20:12.168775"
+        "timestamp": "2024-10-31T10:37:25.720782902"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml
index 55993f44..1f7d0824 100644
--- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml
+++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml
@@ -1,5 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::gatk4=4.5.0.0
+  # renovate: datasource=conda depName=bioconda/gatk4
+  - bioconda::gatk4=4.6.1.0
+  # renovate: datasource=conda depName=bioconda/gcnvkernel
+  - bioconda::gcnvkernel=0.9
diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf
index c7f1d75b..998622a0 100644
--- a/modules/nf-core/gatk4/createsequencedictionary/main.nf
+++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf
@@ -1,11 +1,11 @@
 process GATK4_CREATESEQUENCEDICTIONARY {
     tag "$fasta"
-    label 'process_medium'
+    label 'process_single'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data':
+        'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap
index 16735f95..e8a600fd 100644
--- a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap
+++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6"
+                    "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439"
                 ],
                 "dict": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6"
+                    "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-16T10:16:16.34453"
+        "timestamp": "2024-10-31T10:51:56.155954077"
     },
     "sarscov2 - fasta": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6"
+                    "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439"
                 ],
                 "dict": [
                     [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6"
+                    "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-16T13:58:25.822068"
+        "timestamp": "2024-10-31T10:51:45.562993875"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml
index 3c73c17e..ec65c32d 100644
--- a/modules/nf-core/gatk4/markduplicates/environment.yml
+++ b/modules/nf-core/gatk4/markduplicates/environment.yml
@@ -1,8 +1,15 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 
 dependencies:
-  - bioconda::gatk4=4.5.0.0
+  # renovate: datasource=conda depName=bioconda/gatk4
+  - bioconda::gatk4=4.6.1.0
+  # renovate: datasource=conda depName=bioconda/gcnvkernel
+  - bioconda::gcnvkernel=0.9
+  # renovate: datasource=conda depName=bioconda/htslib
   - bioconda::htslib=1.19.1
+  # renovate: datasource=conda depName=bioconda/samtools
   - bioconda::samtools=1.19.2
diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf
index baadefef..cf770308 100644
--- a/modules/nf-core/gatk4/markduplicates/main.nf
+++ b/modules/nf-core/gatk4/markduplicates/main.nf
@@ -1,6 +1,6 @@
 process GATK4_MARKDUPLICATES {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test
index 4cd13dcd..d039f367 100644
--- a/modules/nf-core/gffread/tests/main.nf.test
+++ b/modules/nf-core/gffread/tests/main.nf.test
@@ -23,6 +23,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true)
                 ]
                 input[1] = []
+
                 """
             }
         }
@@ -220,4 +221,4 @@ nextflow_process {
 
     }
 
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml
index ff4a85ed..1d715d56 100644
--- a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml
+++ b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::picard=3.2.0
+  - bioconda::picard=3.3.0
diff --git a/modules/nf-core/picard/collectinsertsizemetrics/main.nf b/modules/nf-core/picard/collectinsertsizemetrics/main.nf
index 1a49a7f0..c3014d80 100644
--- a/modules/nf-core/picard/collectinsertsizemetrics/main.nf
+++ b/modules/nf-core/picard/collectinsertsizemetrics/main.nf
@@ -4,8 +4,8 @@ process PICARD_COLLECTINSERTSIZEMETRICS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
-        'biocontainers/picard:3.2.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' :
+        'biocontainers/picard:3.3.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test.snap
index bcb5b455..cbe9329d 100644
--- a/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test.snap
+++ b/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test.snap
@@ -9,14 +9,14 @@
             ],
             "test.pdf",
             [
-                "versions.yml:md5,4423bfe2194f61d919c382d2225b0835"
+                "versions.yml:md5,38d39e9882afe7ac015213c286745056"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-30T12:23:29.392944"
+        "timestamp": "2024-10-18T10:55:45.769771444"
     },
     "test-picard-collectinsertsizemetrics-stub": {
         "content": [
@@ -40,7 +40,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,4423bfe2194f61d919c382d2225b0835"
+                    "versions.yml:md5,38d39e9882afe7ac015213c286745056"
                 ],
                 "histogram": [
                     [
@@ -61,14 +61,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,4423bfe2194f61d919c382d2225b0835"
+                    "versions.yml:md5,38d39e9882afe7ac015213c286745056"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-30T12:20:03.841884"
+        "timestamp": "2024-10-18T10:56:09.914953495"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/picard/collectwgsmetrics/environment.yml b/modules/nf-core/picard/collectwgsmetrics/environment.yml
index 58d52581..13265842 100644
--- a/modules/nf-core/picard/collectwgsmetrics/environment.yml
+++ b/modules/nf-core/picard/collectwgsmetrics/environment.yml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::picard=3.2.0
-  - r::r-base
+  - bioconda::picard=3.3.0
+  - conda-forge::r-base=4.4.1
diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf
index 6002a7ca..39cf7d2b 100644
--- a/modules/nf-core/picard/collectwgsmetrics/main.nf
+++ b/modules/nf-core/picard/collectwgsmetrics/main.nf
@@ -4,8 +4,8 @@ process PICARD_COLLECTWGSMETRICS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
-        'biocontainers/picard:3.2.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' :
+        'biocontainers/picard:3.3.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap
index f188382b..1958fcde 100644
--- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap
+++ b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap
@@ -3,26 +3,26 @@
         "content": [
             true,
             [
-                "versions.yml:md5,06b5898fb06823b736c90e1dcebe75fe"
+                "versions.yml:md5,9927db69fdd55176be5cdbd427d000c2"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-23T11:02:46.301176"
+        "timestamp": "2024-10-18T10:15:18.13771243"
     },
     "test-picard-collectwgsmetrics": {
         "content": [
             true,
             [
-                "versions.yml:md5,06b5898fb06823b736c90e1dcebe75fe"
+                "versions.yml:md5,9927db69fdd55176be5cdbd427d000c2"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-23T11:02:25.132069"
+        "timestamp": "2024-10-18T10:14:57.786056996"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml
index 471164fa..b3f75777 100644
--- a/modules/nf-core/salmon/index/environment.yml
+++ b/modules/nf-core/salmon/index/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::salmon=1.10.1
+  - bioconda::salmon=1.10.3
diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf
index e755d9a3..3d653c0d 100644
--- a/modules/nf-core/salmon/index/main.nf
+++ b/modules/nf-core/salmon/index/main.nf
@@ -4,8 +4,8 @@ process SALMON_INDEX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0' :
-        'biocontainers/salmon:1.10.1--h7e5ed60_0' }"
+        'https://depot.galaxyproject.org/singularity/salmon:1.10.3--h6dccd9a_2' :
+        'biocontainers/salmon:1.10.3--h6dccd9a_2' }"
 
     input:
     path genome_fasta
diff --git a/modules/nf-core/salmon/index/tests/main.nf.test.snap b/modules/nf-core/salmon/index/tests/main.nf.test.snap
index 703e455c..e5899b51 100644
--- a/modules/nf-core/salmon/index/tests/main.nf.test.snap
+++ b/modules/nf-core/salmon/index/tests/main.nf.test.snap
@@ -2,25 +2,25 @@
     "versions": {
         "content": [
             [
-                "versions.yml:md5,563eeafb4577be0b13801d7021c0bf42"
+                "versions.yml:md5,85337fa0a286ea35073ee5260974e307"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2023-11-22T14:26:33.32036"
+        "timestamp": "2024-10-18T10:00:47.087293189"
     },
     "versions stub": {
         "content": [
             [
-                "versions.yml:md5,563eeafb4577be0b13801d7021c0bf42"
+                "versions.yml:md5,85337fa0a286ea35073ee5260974e307"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-04-23T09:47:58.828124"
+        "timestamp": "2024-10-18T10:01:03.89824494"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml
index 471164fa..b3f75777 100644
--- a/modules/nf-core/salmon/quant/environment.yml
+++ b/modules/nf-core/salmon/quant/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::salmon=1.10.1
+  - bioconda::salmon=1.10.3
diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf
index 6c528b24..f1e3b5cd 100644
--- a/modules/nf-core/salmon/quant/main.nf
+++ b/modules/nf-core/salmon/quant/main.nf
@@ -4,8 +4,8 @@ process SALMON_QUANT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0' :
-        'biocontainers/salmon:1.10.1--h7e5ed60_0' }"
+        'https://depot.galaxyproject.org/singularity/salmon:1.10.3--h6dccd9a_2' :
+        'biocontainers/salmon:1.10.3--h6dccd9a_2' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/salmon/quant/tests/main.nf.test.snap b/modules/nf-core/salmon/quant/tests/main.nf.test.snap
index 547ce2de..ea22a80c 100644
--- a/modules/nf-core/salmon/quant/tests/main.nf.test.snap
+++ b/modules/nf-core/salmon/quant/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "sarscov2 - single_end": {
         "content": [
             [
-                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+                "versions.yml:md5,0d510d5db6398e2c8ca9443330740607"
             ],
             [
                 [
@@ -15,15 +15,15 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-14T09:51:22.424672"
+        "timestamp": "2024-10-18T10:01:16.989080539"
     },
     "sarscov2 - single_end stub": {
         "content": [
             [
-                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+                "versions.yml:md5,0d510d5db6398e2c8ca9443330740607"
             ],
             [
                 [
@@ -36,15 +36,15 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-14T09:51:32.292277"
+        "timestamp": "2024-10-18T10:01:29.340996235"
     },
     "sarscov2 - single_end lib type A": {
         "content": [
             [
-                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+                "versions.yml:md5,0d510d5db6398e2c8ca9443330740607"
             ],
             [
                 [
@@ -57,15 +57,15 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-14T09:51:42.656382"
+        "timestamp": "2024-10-18T10:01:43.056167576"
     },
     "sarscov2 - pair_end multiple": {
         "content": [
             [
-                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+                "versions.yml:md5,0d510d5db6398e2c8ca9443330740607"
             ],
             [
                 [
@@ -78,15 +78,15 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-14T09:52:33.03647"
+        "timestamp": "2024-10-18T10:03:05.500792631"
     },
     "sarscov2 - pair_end multiple stub": {
         "content": [
             [
-                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+                "versions.yml:md5,0d510d5db6398e2c8ca9443330740607"
             ],
             [
                 [
@@ -99,15 +99,15 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-14T09:52:43.388379"
+        "timestamp": "2024-10-18T10:03:26.428959203"
     },
     "sarscov2 - single_end lib type A stub": {
         "content": [
             [
-                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+                "versions.yml:md5,0d510d5db6398e2c8ca9443330740607"
             ],
             [
                 [
@@ -120,15 +120,15 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-14T09:51:52.612664"
+        "timestamp": "2024-10-18T10:02:03.420850208"
     },
     "sarscov2 - pair_end": {
         "content": [
             [
-                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+                "versions.yml:md5,0d510d5db6398e2c8ca9443330740607"
             ],
             [
                 [
@@ -141,15 +141,15 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-14T09:52:05.577881"
+        "timestamp": "2024-10-18T10:02:16.130074696"
     },
     "sarscov2 - pair_end stub": {
         "content": [
             [
-                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+                "versions.yml:md5,0d510d5db6398e2c8ca9443330740607"
             ],
             [
                 [
@@ -162,9 +162,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-14T09:52:15.286461"
+        "timestamp": "2024-10-18T10:02:39.470004547"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index acfd9252..caf3c61a 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -12,11 +12,11 @@ process SAMTOOLS_SORT {
     tuple val(meta2), path(fasta)
 
     output:
-    tuple val(meta), path("*.bam"),     emit: bam,  optional: true
-    tuple val(meta), path("*.cram"),    emit: cram, optional: true
-    tuple val(meta), path("*.crai"),    emit: crai, optional: true
-    tuple val(meta), path("*.csi"),     emit: csi,  optional: true
-    path  "versions.yml"          , emit: versions
+    tuple val(meta), path("*.bam"),  emit: bam,  optional: true
+    tuple val(meta), path("*.cram"), emit: cram, optional: true
+    tuple val(meta), path("*.crai"), emit: crai, optional: true
+    tuple val(meta), path("*.csi"),  emit: csi,  optional: true
+    path  "versions.yml",            emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test
index c2ea9c72..b05e6691 100644
--- a/modules/nf-core/samtools/sort/tests/main.nf.test
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test
@@ -39,6 +39,40 @@ nextflow_process {
         }
     }
 
+    test("multiple bam") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true)
+                    ]
+                ])
+                input[1] = Channel.of([
+                    [ id:'fasta' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                        process.out.bam,
+                        process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } },
+                        process.out.versions
+                ).match()}
+            )
+        }
+    }
+
     test("cram") {
 
         config "./nextflow_cram.config"
@@ -98,6 +132,36 @@ nextflow_process {
         }
     }
 
+    test("multiple bam - stub") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true)
+                    ]
+                ])
+                input[1] = Channel.of([
+                    [ id:'fasta' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
     test("cram - stub") {
 
         options "-stub"
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
index 2d6b2900..469891fe 100644
--- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
@@ -159,6 +159,101 @@
         },
         "timestamp": "2024-09-16T08:50:19.061912443"
     },
+    "multiple bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam.csi"
+                ]
+            ],
+            [
+                "versions.yml:md5,2659b187d681241451539d4c53500b9f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-08T11:59:55.479443"
+    },
+    "multiple bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-08T11:36:13.781404"
+    },
     "bam": {
         "content": [
             [
@@ -185,8 +280,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-09-16T08:49:43.971158333"
+        "timestamp": "2024-10-08T11:59:46.372244"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml
index 62054fc9..02cda6e6 100644
--- a/modules/nf-core/samtools/view/environment.yml
+++ b/modules/nf-core/samtools/view/environment.yml
@@ -4,5 +4,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  # renovate: datasource=conda depName=bioconda/htslib
   - bioconda::htslib=1.21
+  # renovate: datasource=conda depName=bioconda/samtools
   - bioconda::samtools=1.21
diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
index 37e05cec..a6941e63 100644
--- a/modules/nf-core/samtools/view/main.nf
+++ b/modules/nf-core/samtools/view/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_VIEW {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
-        'biocontainers/samtools:1.21--h50ea8bc_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9edc2564215d5cd137a8b25ca8a311600987186d406b092022444adf3c4447f7/data' :
+        'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' }"
 
     input:
     tuple val(meta), path(input), path(index)
@@ -63,7 +63,7 @@ process SAMTOOLS_VIEW {
                 input.getExtension()
     if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
 
-    def index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.csi" : ""
+    index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.csi" : ""
 
     """
     touch ${prefix}.${file_type}
diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml
index 1debc4c9..7c57530a 100644
--- a/modules/nf-core/star/align/environment.yml
+++ b/modules/nf-core/star/align/environment.yml
@@ -3,7 +3,7 @@ channels:
   - bioconda
 
 dependencies:
-  - bioconda::htslib=1.18
-  - bioconda::samtools=1.18
-  - bioconda::star=2.7.10a
+  - bioconda::htslib=1.20
+  - bioconda::samtools=1.20
+  - bioconda::star=2.7.11b
   - conda-forge::gawk=5.1.0
diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf
index b5bc9ddf..417071ba 100644
--- a/modules/nf-core/star/align/main.nf
+++ b/modules/nf-core/star/align/main.nf
@@ -4,8 +4,8 @@ process STAR_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' :
-        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' :
+        'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }"
 
     input:
     tuple val(meta), path(reads, stageAs: "input*/*")
diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml
index d9cba2aa..5cfe763e 100644
--- a/modules/nf-core/star/align/meta.yml
+++ b/modules/nf-core/star/align/meta.yml
@@ -56,27 +56,30 @@ input:
 output:
   - log_final:
       - meta:
-          type: file
-          description: STAR final log file
-          pattern: "*Log.final.out"
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - "*Log.final.out":
           type: file
           description: STAR final log file
           pattern: "*Log.final.out"
   - log_out:
       - meta:
-          type: file
-          description: STAR lot out file
-          pattern: "*Log.out"
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - "*Log.out":
           type: file
           description: STAR lot out file
           pattern: "*Log.out"
   - log_progress:
       - meta:
-          type: file
-          description: STAR log progress file
-          pattern: "*Log.progress.out"
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - "*Log.progress.out":
           type: file
           description: STAR log progress file
@@ -88,57 +91,70 @@ output:
           pattern: "versions.yml"
   - bam:
       - meta:
-          type: file
-          description: Output BAM file containing read alignments
-          pattern: "*.{bam}"
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - "*d.out.bam":
           type: file
           description: Output BAM file containing read alignments
           pattern: "*.{bam}"
   - bam_sorted:
       - meta:
-          type: file
-          description: Sorted BAM file of read alignments (optional)
-          pattern: "*sortedByCoord.out.bam"
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - ${prefix}.sortedByCoord.out.bam:
           type: file
           description: Sorted BAM file of read alignments (optional)
           pattern: "*sortedByCoord.out.bam"
   - bam_sorted_aligned:
-      - meta: {}
-      - ${prefix}.Aligned.sortedByCoord.out.bam: {}
-  - bam_transcript:
       - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.Aligned.sortedByCoord.out.bam:
           type: file
-          description: Output BAM file of transcriptome alignment (optional)
-          pattern: "*toTranscriptome.out.bam"
+          description: Sorted BAM file of read alignments (optional)
+          pattern: "*.Aligned.sortedByCoord.out.bam"
+  - bam_transcript:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - "*toTranscriptome.out.bam":
           type: file
           description: Output BAM file of transcriptome alignment (optional)
           pattern: "*toTranscriptome.out.bam"
   - bam_unsorted:
       - meta:
-          type: file
-          description: Unsorted BAM file of read alignments (optional)
-          pattern: "*Aligned.unsort.out.bam"
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - "*Aligned.unsort.out.bam":
           type: file
           description: Unsorted BAM file of read alignments (optional)
           pattern: "*Aligned.unsort.out.bam"
   - fastq:
       - meta:
-          type: file
-          description: Unmapped FastQ files (optional)
-          pattern: "*fastq.gz"
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - "*fastq.gz":
           type: file
           description: Unmapped FastQ files (optional)
           pattern: "*fastq.gz"
   - tab:
       - meta:
-          type: file
-          description: STAR output tab file(s) (optional)
-          pattern: "*.tab"
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - "*.tab":
           type: file
           description: STAR output tab file(s) (optional)
@@ -149,12 +165,9 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-          pattern: "*.SJ.out.tab"
       - "*.SJ.out.tab":
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+          type: file
+          description: STAR output splice junction tab file
           pattern: "*.SJ.out.tab"
   - read_per_gene_tab:
       - meta:
@@ -162,18 +175,16 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-          pattern: "*.ReadsPerGene.out.tab"
       - "*.ReadsPerGene.out.tab":
+          type: file
+          description: STAR output read per gene tab file
+          pattern: "*.ReadsPerGene.out.tab"
+  - junction:
+      - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-          pattern: "*.ReadsPerGene.out.tab"
-  - junction:
-      - meta:
-          type: file
-          description: STAR chimeric junction output file (optional)
-          pattern: "*.out.junction"
       - "*.out.junction":
           type: file
           description: STAR chimeric junction output file (optional)
@@ -186,25 +197,25 @@ output:
             e.g. [ id:'test', single_end:false ]
           pattern: "*.out.sam"
       - "*.out.sam":
+          type: file
+          description: STAR output SAM file(s) (optional)
+          pattern: "*.out.sam"
+  - wig:
+      - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-          pattern: "*.out.sam"
-  - wig:
-      - meta:
-          type: file
-          description: STAR output wiggle format file(s) (optional)
-          pattern: "*.wig"
       - "*.wig":
           type: file
           description: STAR output wiggle format file(s) (optional)
           pattern: "*.wig"
   - bedgraph:
       - meta:
-          type: file
-          description: STAR output bedGraph format file(s) (optional)
-          pattern: "*.bg"
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - "*.bg":
           type: file
           description: STAR output bedGraph format file(s) (optional)
diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test
index 2d9f72dd..a62c17db 100644
--- a/modules/nf-core/star/align/tests/main.nf.test
+++ b/modules/nf-core/star/align/tests/main.nf.test
@@ -56,13 +56,10 @@ nextflow_process {
                     file(process.out.log_final[0][1]).name,
                     file(process.out.log_out[0][1]).name,
                     file(process.out.log_progress[0][1]).name,
-                    process.out.bam,
-                    process.out.bam_sorted,
-                    process.out.bam_transcript,
-                    process.out.bam_unsorted,
+                    bam(process.out.bam[0][1]).getReadsMD5(),
+                    bam(process.out.bam_sorted_aligned[0][1]).getReadsMD5(),
                     process.out.bedgraph,
                     process.out.fastq,
-                    process.out.junction,
                     process.out.read_per_gene_tab,
                     process.out.sam,
                     process.out.spl_junc_tab,
@@ -124,13 +121,10 @@ nextflow_process {
                     file(process.out.log_final[0][1]).name,
                     file(process.out.log_out[0][1]).name,
                     file(process.out.log_progress[0][1]).name,
-                    process.out.bam,
-                    process.out.bam_sorted,
-                    process.out.bam_transcript,
-                    process.out.bam_unsorted,
+                    bam(process.out.bam[0][1]).getReadsMD5(),
+                    bam(process.out.bam_sorted_aligned[0][1]).getReadsMD5(),
                     process.out.bedgraph,
                     process.out.fastq,
-                    process.out.junction,
                     process.out.read_per_gene_tab,
                     process.out.sam,
                     process.out.spl_junc_tab,
@@ -192,13 +186,9 @@ nextflow_process {
                     file(process.out.log_final[0][1]).name,
                     file(process.out.log_out[0][1]).name,
                     file(process.out.log_progress[0][1]).name,
-                    process.out.bam,
-                    process.out.bam_sorted,
-                    process.out.bam_transcript,
-                    process.out.bam_unsorted,
+                    bam(process.out.bam[0][1]).getReadsMD5(),
                     process.out.bedgraph,
                     process.out.fastq,
-                    process.out.junction,
                     process.out.read_per_gene_tab,
                     process.out.sam,
                     process.out.spl_junc_tab,
@@ -260,13 +250,10 @@ nextflow_process {
                     file(process.out.log_final[0][1]).name,
                     file(process.out.log_out[0][1]).name,
                     file(process.out.log_progress[0][1]).name,
-                    process.out.bam,
-                    process.out.bam_sorted,
-                    process.out.bam_transcript,
-                    process.out.bam_unsorted,
+                    file(process.out.junction[0][1]).name,
+                    bam(process.out.bam[0][1]).getReadsMD5(),
                     process.out.bedgraph,
                     process.out.fastq,
-                    process.out.junction,
                     process.out.read_per_gene_tab,
                     process.out.sam,
                     process.out.spl_junc_tab,
@@ -330,13 +317,10 @@ nextflow_process {
                     file(process.out.log_final[0][1]).name,
                     file(process.out.log_out[0][1]).name,
                     file(process.out.log_progress[0][1]).name,
-                    process.out.bam,
-                    process.out.bam_sorted,
-                    process.out.bam_transcript,
-                    process.out.bam_unsorted,
+                    bam(process.out.bam[0][1]).getReadsMD5(),
+                    bam(process.out.bam_sorted_aligned[0][1]).getReadsMD5(),
                     process.out.bedgraph,
                     process.out.fastq,
-                    process.out.junction,
                     process.out.read_per_gene_tab,
                     process.out.sam,
                     process.out.spl_junc_tab,
@@ -606,4 +590,4 @@ nextflow_process {
             )
         }
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap
index 0da28d37..b533fb8b 100644
--- a/modules/nf-core/star/align/tests/main.nf.test.snap
+++ b/modules/nf-core/star/align/tests/main.nf.test.snap
@@ -97,7 +97,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                    "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
                 ],
                 "4": [
                     [
@@ -307,7 +307,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                    "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
                 ],
                 "wig": [
                     [
@@ -322,9 +322,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-01T11:39:15.440397"
+        "timestamp": "2024-10-20T17:09:08.738074176"
     },
     "homo_sapiens - paired_end - arriba - stub": {
         "content": [
@@ -424,7 +424,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                    "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
                 ],
                 "4": [
                     [
@@ -634,7 +634,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                    "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
                 ],
                 "wig": [
                     [
@@ -649,33 +649,17 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-01T11:40:15.472109"
+        "timestamp": "2024-10-20T17:09:36.122131869"
     },
     "homo_sapiens - single_end": {
         "content": [
             "test.Log.final.out",
             "test.Log.out",
             "test.Log.progress.out",
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": true
-                    },
-                    "test.Aligned.sortedByCoord.out.bam:md5,c6cfaccaf91bc7fdabed3cfe236d4535"
-                ]
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
+            "9f76be49a6607613a64f760101bdddce",
+            "9f76be49a6607613a64f760101bdddce",
             [
                 [
                     {
@@ -696,9 +680,6 @@
             ],
             [
                 
-            ],
-            [
-                
             ],
             [
                 [
@@ -722,38 +703,22 @@
                 
             ],
             [
-                "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-01T11:23:08.001162"
+        "timestamp": "2024-10-20T17:01:22.197991909"
     },
     "homo_sapiens - paired_end": {
         "content": [
             "test.Log.final.out",
             "test.Log.out",
             "test.Log.progress.out",
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f"
-                ]
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
+            "db9a8324b5163b025bcc0c33e848486",
+            "db9a8324b5163b025bcc0c33e848486",
             [
                 [
                     {
@@ -774,9 +739,6 @@
             ],
             [
                 
-            ],
-            [
-                
             ],
             [
                 [
@@ -800,14 +762,14 @@
                 
             ],
             [
-                "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-01T11:24:46.295219"
+        "timestamp": "2024-10-20T17:02:06.988663857"
     },
     "homo_sapiens - paired_end - multiple - stub": {
         "content": [
@@ -907,7 +869,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                    "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
                 ],
                 "4": [
                     [
@@ -1117,7 +1079,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                    "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
                 ],
                 "wig": [
                     [
@@ -1132,33 +1094,17 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-01T11:41:07.310866"
+        "timestamp": "2024-10-20T17:10:12.005468781"
     },
     "homo_sapiens - paired_end - multiple": {
         "content": [
             "test.Log.final.out",
             "test.Log.out",
             "test.Log.progress.out",
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a"
-                ]
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
+            "3e54e45f5dc3e9c1f2fc55bc41531a87",
+            "3e54e45f5dc3e9c1f2fc55bc41531a87",
             [
                 [
                     {
@@ -1179,9 +1125,6 @@
             ],
             [
                 
-            ],
-            [
-                
             ],
             [
                 [
@@ -1205,14 +1148,14 @@
                 
             ],
             [
-                "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-01T11:38:46.605044"
+        "timestamp": "2024-10-20T17:08:54.877286681"
     },
     "homo_sapiens - paired_end - stub": {
         "content": [
@@ -1312,7 +1255,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                    "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
                 ],
                 "4": [
                     [
@@ -1522,7 +1465,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                    "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
                 ],
                 "wig": [
                     [
@@ -1537,24 +1480,17 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-01T11:39:51.595873"
+        "timestamp": "2024-10-20T17:09:20.911466345"
     },
     "homo_sapiens - paired_end - starfusion": {
         "content": [
             "test.Log.final.out",
             "test.Log.out",
             "test.Log.progress.out",
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.Aligned.out.bam:md5,bcad07b838f6762fc01eea52b5cd3f84"
-                ]
-            ],
+            "test.Chimeric.out.junction",
+            "caee9dcda13882d4913456973c25b57a",
             [
                 
             ],
@@ -1566,24 +1502,6 @@
             ],
             [
                 
-            ],
-            [
-                
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.Chimeric.out.junction:md5,c10ef219f4a30e83711b995bc5e40dba"
-                ]
-            ],
-            [
-                
-            ],
-            [
-                
             ],
             [
                 [
@@ -1607,41 +1525,21 @@
                 
             ],
             [
-                "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-01T11:35:43.874508"
+        "timestamp": "2024-10-20T17:07:25.0639914"
     },
     "homo_sapiens - paired_end - arriba": {
         "content": [
             "test.Log.final.out",
             "test.Log.out",
             "test.Log.progress.out",
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.Aligned.out.bam:md5,c1b1747f5873f2d17762725636e891d5"
-                ]
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
+            "1a3abe88fb2490589c58497d39921bcc",
             [
                 
             ],
@@ -1676,14 +1574,14 @@
                 
             ],
             [
-                "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-01T11:28:32.599223"
+        "timestamp": "2024-10-20T17:04:00.685784211"
     },
     "homo_sapiens - paired_end - starfusion - stub": {
         "content": [
@@ -1783,7 +1681,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                    "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
                 ],
                 "4": [
                     [
@@ -1993,7 +1891,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                    "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3"
                 ],
                 "wig": [
                     [
@@ -2008,8 +1906,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-01T11:40:42.29249"
+        "timestamp": "2024-10-20T17:09:53.173671551"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml
index 1debc4c9..7c57530a 100644
--- a/modules/nf-core/star/genomegenerate/environment.yml
+++ b/modules/nf-core/star/genomegenerate/environment.yml
@@ -3,7 +3,7 @@ channels:
   - bioconda
 
 dependencies:
-  - bioconda::htslib=1.18
-  - bioconda::samtools=1.18
-  - bioconda::star=2.7.10a
+  - bioconda::htslib=1.20
+  - bioconda::samtools=1.20
+  - bioconda::star=2.7.11b
   - conda-forge::gawk=5.1.0
diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf
index b8855715..8f0c67e7 100644
--- a/modules/nf-core/star/genomegenerate/main.nf
+++ b/modules/nf-core/star/genomegenerate/main.nf
@@ -4,8 +4,8 @@ process STAR_GENOMEGENERATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' :
-        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' :
+        'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap
index 207f4b4f..3db25678 100644
--- a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap
+++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap
@@ -3,14 +3,14 @@
         "content": [
             "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]",
             [
-                "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+                "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T14:55:35.478401"
+        "timestamp": "2024-10-19T20:37:47.410432728"
     },
     "fasta_gtf_stub": {
         "content": [
@@ -41,7 +41,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+                    "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6"
                 ],
                 "index": [
                     [
@@ -69,15 +69,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+                    "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T14:55:57.247585"
+        "timestamp": "2024-10-19T20:38:09.165234795"
     },
     "fasta_stub": {
         "content": [
@@ -101,7 +101,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+                    "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6"
                 ],
                 "index": [
                     [
@@ -122,27 +122,27 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+                    "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T14:56:07.01742"
+        "timestamp": "2024-10-19T20:38:19.530862664"
     },
     "fasta": {
         "content": [
             "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]",
             [
-                "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+                "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T14:55:45.48784"
+        "timestamp": "2024-10-19T20:37:58.667436398"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml
index 0556de41..906b7486 100644
--- a/modules/nf-core/stringtie/stringtie/environment.yml
+++ b/modules/nf-core/stringtie/stringtie/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::stringtie=2.2.1
+  - bioconda::stringtie=2.2.3
diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf
index 6e25ba27..4635c8c5 100644
--- a/modules/nf-core/stringtie/stringtie/main.nf
+++ b/modules/nf-core/stringtie/stringtie/main.nf
@@ -4,8 +4,8 @@ process STRINGTIE_STRINGTIE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
-        'biocontainers/stringtie:2.2.1--hecb563c_2' }"
+        'https://depot.galaxyproject.org/singularity/stringtie:2.2.3--h43eeafb_0' :
+        'biocontainers/stringtie:2.2.3--h43eeafb_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap
index 124dd4cb..d4645de3 100644
--- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap
+++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap
@@ -31,18 +31,18 @@
                         "id": "test",
                         "strandedness": "forward"
                     },
-                    "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04"
+                    "test.transcripts.gtf:md5,37154e7bda96544f24506ee902bb561d"
                 ]
             ],
             [
-                "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T12:33:44.299962"
+        "timestamp": "2024-10-18T09:56:50.294157199"
     },
     "sarscov2 [bam] - forward strandedness": {
         "content": [
@@ -61,18 +61,18 @@
                         "id": "test",
                         "strandedness": "forward"
                     },
-                    "test.transcripts.gtf:md5,569137af5be452413086b50653a97203"
+                    "test.transcripts.gtf:md5,6087dfc9700a52d9e4a1ae3fcd1d1dfd"
                 ]
             ],
             [
-                "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T12:33:35.177738"
+        "timestamp": "2024-10-18T09:56:39.4249133"
     },
     "sarscov2 [bam] - forward strandedness - stub": {
         "content": [
@@ -114,7 +114,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                    "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913"
                 ],
                 "abundance": [
                     [
@@ -153,15 +153,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                    "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T12:36:32.885078"
+        "timestamp": "2024-10-18T09:57:23.008470065"
     },
     "sarscov2 [bam] - forward strandedness + reference annotation - stub": {
         "content": [
@@ -203,7 +203,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                    "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913"
                 ],
                 "abundance": [
                     [
@@ -242,15 +242,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                    "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T12:36:43.325777"
+        "timestamp": "2024-10-18T09:57:33.622824981"
     },
     "sarscov2 [bam] - reverse strandedness + reference annotation - stub": {
         "content": [
@@ -292,7 +292,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                    "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913"
                 ],
                 "abundance": [
                     [
@@ -331,15 +331,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                    "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T12:37:06.085936"
+        "timestamp": "2024-10-18T09:57:55.803421433"
     },
     "sarscov2 [bam] - reverse strandedness - stub": {
         "content": [
@@ -381,7 +381,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                    "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913"
                 ],
                 "abundance": [
                     [
@@ -420,15 +420,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                    "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T12:36:53.837578"
+        "timestamp": "2024-10-18T09:57:44.825389635"
     },
     "sarscov2 [bam] - reverse strandedness + reference annotation": {
         "content": [
@@ -462,18 +462,18 @@
                         "id": "test",
                         "strandedness": "reverse"
                     },
-                    "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa"
+                    "test.transcripts.gtf:md5,fbabb4e3888bbede67f11f692e484880"
                 ]
             ],
             [
-                "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T12:34:03.114695"
+        "timestamp": "2024-10-18T09:57:11.793664242"
     },
     "sarscov2 [bam] - reverse strandedness": {
         "content": [
@@ -492,17 +492,17 @@
                         "id": "test",
                         "strandedness": "reverse"
                     },
-                    "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f"
+                    "test.transcripts.gtf:md5,01d6da00a3c458420841e57427297183"
                 ]
             ],
             [
-                "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T12:33:52.874479"
+        "timestamp": "2024-10-18T09:57:01.166309777"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index c4011d87..e9f2f6c4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -11,7 +11,7 @@ params {
 
     // Input options
     input                      = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv'
-    build_references           = false
+    references_only            = false
     cosmic_username            = null
     cosmic_passwd              = null
     qiagen                     = false
@@ -26,20 +26,12 @@ params {
     // Genome
     genome                     = 'GRCh38'
     genomes_base               = "${params.outdir}/references"
-    ensembl_version            = 102
+    genome_gencode_version     = 46
     read_length                = 100
     starfusion_build           = true
     genomes                    = [:]
     fusion_annot_lib           = "https://github.com/FusionAnnotator/CTAT_HumanFusionLib/releases/download/v0.3.0/fusion_lib.Mar2021.dat.gz" // path to  dat.gz CTAT genome lib // TODO: Update to latest with s3 link when available
-
-    // Genomes options
-    fasta          = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.all.fa"
-    fai            = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.all.fa.fai"
-    gtf            = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.gtf"
-    chrgtf         = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.chr.gtf"
-    transcript     = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.cdna.all.fa.gz"
-    refflat        = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.chr.gtf.refflat"
-    rrna_intervals = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.interval_list"
+    species                    = "human"
 
     // Filtering
     tools_cutoff               = 1
@@ -76,15 +68,22 @@ params {
     skip_vcf                   = false
     skip_salmon_index          = false
 
+    // Download references option
+    download_refs              = false
+
     // Path to references
+    fasta                         = "${params.genomes_base}/gencode/Homo_sapiens_${params.genome}_${params.genome_gencode_version}_dna_primary_assembly.fa"
+    fai                           = "${params.genomes_base}/gencode/Homo_sapiens_${params.genome}_${params.genome_gencode_version}_dna_primary_assembly.fa.fai"
+    gtf                           = "${params.genomes_base}/gencode/Homo_sapiens_${params.genome}_${params.genome_gencode_version}.gtf"
+    refflat                       = "${params.genomes_base}/gencode/Homo_sapiens_${params.genome}_${params.genome_gencode_version}.gtf.refflat"
+    rrna_intervals                = "${params.genomes_base}/gencode/Homo_sapiens_${params.genome}_${params.genome_gencode_version}.interval_list"
+    gencode_ref                   = "${params.genomes_base}/gencode"
     no_cosmic                     = false
-    ensembl_ref                   = "${params.genomes_base}/ensembl"
-    arriba_ref                    = "${params.genomes_base}/arriba"
     arriba_ref_blacklist          = "${params.genomes_base}/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz"
     arriba_ref_cytobands          = "${params.genomes_base}/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv"
     arriba_ref_known_fusions      = "${params.genomes_base}/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz"
     arriba_ref_protein_domains    = "${params.genomes_base}/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3"
-    fusioncatcher_ref             = "${params.genomes_base}/fusioncatcher/human_v102"
+    fusioncatcher_ref             = "${params.genomes_base}/fusioncatcher/human_v${params.genome_gencode_version}"
     hgnc_ref                      = "${params.genomes_base}/hgnc/hgnc_complete_set.txt"
     hgnc_date                     = "${params.genomes_base}/hgnc/HGNC-DB-timestamp.txt"
     salmon_index                  = "${params.genomes_base}/salmon/salmon"
@@ -93,6 +92,13 @@ params {
     fusionreport_ref              = "${params.genomes_base}/fusion_report_db"
 
 
+    // Internal file presence checks
+    salmon_index_stub_check       = "${params.genomes_base}/salmon/salmon/complete_ref_lens.bin"
+    starindex_ref_stub_check      = "${params.genomes_base}/star/star/Genome"
+    fusionreport_ref_stub_check   = "${params.genomes_base}/fusion_report_db/mitelman.db"
+    fusioncatcher_ref_stub_check  = "${params.genomes_base}/fusioncatcher/human_v${params.genome_gencode_version}/ensembl_fully_overlapping_genes.txt"
+    starfusion_ref_stub_check     = "${params.genomes_base}/starfusion/Pfam-A.hmm"
+
     // Path to fusion outputs
     arriba_fusions                = null
     starfusion_fusions            = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 03b2e149..3b54697c 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -15,13 +15,13 @@
                     "type": "boolean",
                     "description": "Skip QC steps"
                 },
-                "skip_vis": {
+                "skip_vcf": {
                     "type": "boolean",
-                    "description": "Skip visualisation steps"
+                    "description": "Skip vcf creation step"
                 },
-                "skip_vcf": {
+                "skip_vis": {
                     "type": "boolean",
-                    "description": "Skip vcf generation step"
+                    "description": "Skip visualisation steps"
                 },
                 "skip_salmon_index": {
                     "type": "boolean",
@@ -66,11 +66,6 @@
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                     "fa_icon": "fas fa-file-signature"
                 },
-                "build_references": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-file-code",
-                    "description": "Specifies which analysis type for the pipeline - either build references or analyse data"
-                },
                 "cosmic_username": {
                     "type": "string",
                     "fa_icon": "far fa-file-code",
@@ -86,11 +81,10 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to reference folder"
                 },
-                "ensembl_version": {
+                "genome_gencode_version": {
                     "type": "integer",
                     "fa_icon": "far fa-file-code",
-                    "description": "ensembl version",
-                    "default": 102
+                    "description": "gencode version"
                 },
                 "starfusion_build": {
                     "type": "boolean",
@@ -113,11 +107,6 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Build or run arriba references/analyses"
                 },
-                "arriba_ref": {
-                    "type": "string",
-                    "fa_icon": "far fa-file-code",
-                    "description": "Path to arriba references"
-                },
                 "arriba_ref_blacklist": {
                     "type": "string",
                     "fa_icon": "far fa-file-code",
@@ -143,15 +132,20 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to arriba output"
                 },
+                "download_refs": {
+                    "type": "boolean",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Download references instead of building them (for fusioncatcher and starfusion)"
+                },
                 "ctatsplicing": {
                     "type": "boolean",
                     "fa_icon": "far fa-file-code",
                     "description": "Run CTAT-splicing to detect abberant cancer splicing introns. Needs --arriba and/or --starfusion to run."
                 },
-                "ensembl_ref": {
+                "gencode_ref": {
                     "type": "string",
                     "fa_icon": "far fa-file-code",
-                    "description": "Path to ensembl references"
+                    "description": "Path to gencode references"
                 },
                 "fusioncatcher": {
                     "type": "boolean",
@@ -173,6 +167,11 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to fusioncatcher references"
                 },
+                "fusioncatcher_ref_stub_check": {
+                    "type": "string",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Path to file in fusioncatcher references"
+                },
                 "fusioninspector_limitSjdbInsertNsj": {
                     "type": "integer",
                     "fa_icon": "far fa-file-code",
@@ -198,6 +197,11 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to fusionreport references"
                 },
+                "fusionreport_ref_stub_check": {
+                    "type": "string",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Path to file in fusionreport references"
+                },
                 "hgnc_ref": {
                     "type": "string",
                     "fa_icon": "far fa-file-code",
@@ -218,6 +222,11 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to salmon index"
                 },
+                "salmon_index_stub_check": {
+                    "type": "string",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Path to file in salmon index"
+                },
                 "starfusion": {
                     "type": "boolean",
                     "fa_icon": "far fa-file-code",
@@ -233,6 +242,11 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to starfusion references"
                 },
+                "starfusion_ref_stub_check": {
+                    "type": "string",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Path to file in starfusion references"
+                },
                 "starindex": {
                     "type": "boolean",
                     "fa_icon": "far fa-file-code",
@@ -243,6 +257,11 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to starindex references"
                 },
+                "starindex_ref_stub_check": {
+                    "type": "string",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Path to file in starindex references"
+                },
                 "stringtie": {
                     "type": "boolean",
                     "fa_icon": "far fa-file-code",
@@ -302,9 +321,9 @@
             "fa_icon": "fas fa-dna",
             "description": "Reference genome related files and options required for the workflow.",
             "properties": {
-                "genome": {
-                    "type": "string",
-                    "description": "Name of iGenomes reference.",
+                "references_only": {
+                    "type": "boolean",
+                    "description": "Skip running the analysis, only builds the references",
                     "fa_icon": "fas fa-book"
                 },
                 "fasta": {
@@ -323,15 +342,12 @@
                     "description": "Path to FASTA genome index file.",
                     "fa_icon": "far fa-file-code"
                 },
-                "gtf": {
+                "genome": {
                     "type": "string",
-                    "format": "file-path",
-                    "mimetype": "text/plain",
-                    "pattern": "^\\S+\\.gtf?(\\.gz)?$",
-                    "description": "Path to GTF genome file.",
-                    "fa_icon": "far fa-file-code"
+                    "description": "Name of iGenomes reference.",
+                    "fa_icon": "fas fa-book"
                 },
-                "chrgtf": {
+                "gtf": {
                     "type": "string",
                     "format": "file-path",
                     "mimetype": "text/plain",
@@ -339,14 +355,6 @@
                     "description": "Path to GTF genome file.",
                     "fa_icon": "far fa-file-code"
                 },
-                "transcript": {
-                    "type": "string",
-                    "format": "file-path",
-                    "mimetype": "text/plain",
-                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
-                    "description": "Path to GTF genome file.",
-                    "fa_icon": "far fa-file-code"
-                },
                 "refflat": {
                     "type": "string",
                     "format": "file-path",
@@ -372,6 +380,11 @@
                     "type": "string",
                     "description": "Path to Fusion Annotation Library to be used in STARFUSION_BUILD.",
                     "fa_icon": "far fa-file-code"
+                },
+                "species": {
+                    "type": "string",
+                    "description": "Which species dfam should automatically download, default: human.",
+                    "fa_icon": "far fa-file-code"
                 }
             }
         },
diff --git a/subworkflows/local/arriba_workflow/main.nf b/subworkflows/local/arriba_workflow/main.nf
index c7089e85..84ba3604 100644
--- a/subworkflows/local/arriba_workflow/main.nf
+++ b/subworkflows/local/arriba_workflow/main.nf
@@ -8,14 +8,14 @@ include { CTATSPLICING_WORKFLOW         }   from '../ctatsplicing_workflow'
 
 workflow ARRIBA_WORKFLOW {
     take:
-        reads                           // channel [ meta, [ fastqs ]          ]
-        ch_gtf                          // channel [ meta, path_gtf            ]
-        ch_fasta                        // channel [ meta, path_fasta          ]
-        ch_starindex_ref                // channel [ meta, path_index          ]
-        ch_arriba_ref_blacklist         // channel [ meta, path_blacklist      ]
-        ch_arriba_ref_known_fusions     // channel [ meta, path_known_fusions  ]
-        ch_arriba_ref_cytobands         // channel [ meta, path_cytobands      ]
-        ch_arriba_ref_protein_domains   // channel [ meta, path_proteins       ]
+        reads                           // channel [ meta, [ fastqs ]         ]
+        ch_gtf                          // channel [ meta, path_gtf           ]
+        ch_fasta                        // channel [ meta, path_fasta         ]
+        ch_starindex_ref                // channel [ meta, path_index         ]
+        ch_arriba_ref_blacklist         // channel [ meta, path_blacklist     ]
+        ch_arriba_ref_cytobands         // channel [ meta, path_cytobands     ]
+        ch_arriba_ref_known_fusions     // channel [ meta, path_known_fusions ]
+        ch_arriba_ref_protein_domains   // channel [ meta, path_proteins      ]
         ch_starfusion_ref               // channel [ meta, path_starfusion_ref ]
         arriba                          // boolean
         all                             // boolean
@@ -27,6 +27,7 @@ workflow ARRIBA_WORKFLOW {
         cram                            // array
 
     main:
+
         def ch_versions   = Channel.empty()
         def ch_cram_index = Channel.empty()
         def ch_dummy_file = file("$projectDir/assets/dummy_file_arriba.txt", checkIfExists: true)
@@ -56,7 +57,7 @@ workflow ARRIBA_WORKFLOW {
             if ( arriba_fusions ) {
 
                 ch_arriba_fusions = reads.combine( Channel.value( file( arriba_fusions, checkIfExists: true ) ) )
-                    .map { meta, reads, fusions -> [ meta, fusions ] }
+                    .map { it -> [ it[0], it[2] ] }
                 ch_arriba_fusion_fail = ch_dummy_file
 
             } else {
@@ -65,16 +66,16 @@ workflow ARRIBA_WORKFLOW {
                     STAR_FOR_ARRIBA.out.bam,
                     ch_fasta,
                     ch_gtf,
-                    ch_arriba_ref_blacklist.map{ it[1] },
-                    ch_arriba_ref_known_fusions.map{ it[1] },
-                    ch_arriba_ref_cytobands.map{ it[1] },
-                    ch_arriba_ref_protein_domains.map{ it[1] }
+                    ch_arriba_ref_blacklist,
+                    ch_arriba_ref_known_fusions,
+                    ch_arriba_ref_cytobands,
+                    ch_arriba_ref_protein_domains
                 )
 
                 ch_versions = ch_versions.mix(ARRIBA_ARRIBA.out.versions)
 
                 ch_arriba_fusions     = ARRIBA_ARRIBA.out.fusions
-                ch_arriba_fusion_fail = ARRIBA_ARRIBA.out.fusions_fail.map{ meta, file -> return file }
+                ch_arriba_fusion_fail = ARRIBA_ARRIBA.out.fusions_fail.map{ it -> return it[1] }
             }
 
             if ( cram.contains('arriba') ) {
@@ -96,7 +97,7 @@ workflow ARRIBA_WORKFLOW {
 
             ch_arriba_fusions = reads
                 .combine(Channel.value( file(ch_dummy_file, checkIfExists: true ) ) )
-                .map { meta, reads, fusions -> [ meta, fusions ] }
+                .map { it -> [ it[0], it[2] ] }
 
             ch_arriba_fusion_fail = ch_dummy_file
         }
diff --git a/subworkflows/local/build_references.nf b/subworkflows/local/build_references.nf
new file mode 100644
index 00000000..56fd8eb2
--- /dev/null
+++ b/subworkflows/local/build_references.nf
@@ -0,0 +1,187 @@
+/*
+========================================================================================
+    IMPORT LOCAL MODULES/SUBWORKFLOWS
+========================================================================================
+*/
+
+include { GENCODE_DOWNLOAD }                from '../../modules/local/gencode_download/main'
+include { FUSIONCATCHER_BUILD }             from '../../modules/local/fusioncatcher/build/main'
+include { FUSIONREPORT_DOWNLOAD }           from '../../modules/local/fusionreport/download/main'
+include { HGNC_DOWNLOAD }                   from '../../modules/local/hgnc/main'
+include { STARFUSION_BUILD }                from '../../modules/local/starfusion/build/main'
+include { GTF_TO_REFFLAT }                  from '../../modules/local/uscs/custom_gtftogenepred/main'
+include { GET_RRNA_TRANSCRIPTS }            from '../../modules/local/get_rrna_transcript/main'
+
+/*
+========================================================================================
+    IMPORT NF-CORE MODULES/SUBWORKFLOWS
+========================================================================================
+*/
+include { ARRIBA_DOWNLOAD }                 from '../../modules/nf-core/arriba/download/main'
+include { SAMTOOLS_FAIDX }                  from '../../modules/nf-core/samtools/faidx/main'
+include { STAR_GENOMEGENERATE }             from '../../modules/nf-core/star/genomegenerate/main'
+include { GATK4_CREATESEQUENCEDICTIONARY }  from '../../modules/nf-core/gatk4/createsequencedictionary/main'
+include { GATK4_BEDTOINTERVALLIST }         from '../../modules/nf-core/gatk4/bedtointervallist/main'
+include { SALMON_INDEX }                    from '../../modules/nf-core/salmon/index/main'
+include { GFFREAD }                         from '../../modules/nf-core/gffread/main'
+
+/*
+========================================================================================
+    RUN MAIN WORKFLOW
+========================================================================================
+*/
+
+workflow BUILD_REFERENCES {
+
+    main:
+    ch_versions = Channel.empty()
+
+    if (!file(params.fasta).exists() || file(params.fasta).isEmpty() ||
+            !file(params.gtf).exists() || file(params.gtf).isEmpty()){
+        GENCODE_DOWNLOAD(params.genome_gencode_version, params.genome)
+        ch_versions = ch_versions.mix(GENCODE_DOWNLOAD.out.versions)
+        ch_fasta = GENCODE_DOWNLOAD.out.fasta.map { that -> [[id:that.Name], that] }
+        ch_gtf = GENCODE_DOWNLOAD.out.gtf.map { that -> [[id:that.Name], that] }
+    } else {
+        ch_fasta = Channel.fromPath(params.fasta).map { that -> [[id:that.Name], that] }
+        ch_gtf = Channel.fromPath(params.gtf).map { that -> [[id:that.Name], that] }
+    }
+
+    if (!file(params.fai).exists() || file(params.fai).isEmpty()){
+        SAMTOOLS_FAIDX(ch_fasta, [[],[]])
+        ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
+        ch_fai = SAMTOOLS_FAIDX.out.fai
+    } else {
+        ch_fai = Channel.fromPath(params.fai).map { that -> [[id:that.Name], that] }
+    }
+
+    if ((!file(params.hgnc_ref).exists() || file(params.hgnc_ref).isEmpty() ||
+            !file(params.hgnc_date).exists() || file(params.hgnc_date).isEmpty()) && !params.skip_vcf){
+        HGNC_DOWNLOAD( )
+        ch_versions = ch_versions.mix(HGNC_DOWNLOAD.out.versions)
+        ch_hgnc_ref = HGNC_DOWNLOAD.out.hgnc_ref
+        ch_hgnc_date = HGNC_DOWNLOAD.out.hgnc_date
+    } else {
+        ch_hgnc_ref = Channel.fromPath(params.hgnc_ref).map { that -> [[id:that.Name], that] }
+        ch_hgnc_date = Channel.fromPath(params.hgnc_date).map { that -> [[id:that.Name], that] }
+    }
+
+    if (!file(params.rrna_intervals).exists() || file(params.rrna_intervals).isEmpty()){
+        GATK4_CREATESEQUENCEDICTIONARY(ch_fasta)
+        ch_versions = ch_versions.mix(GATK4_CREATESEQUENCEDICTIONARY.out.versions)
+        GET_RRNA_TRANSCRIPTS(ch_gtf)
+        ch_versions = ch_versions.mix(GET_RRNA_TRANSCRIPTS.out.versions)
+        GATK4_BEDTOINTERVALLIST(GET_RRNA_TRANSCRIPTS.out.bed, GATK4_CREATESEQUENCEDICTIONARY.out.dict )
+        ch_versions = ch_versions.mix(GATK4_BEDTOINTERVALLIST.out.versions)
+        ch_rrna_interval = GATK4_BEDTOINTERVALLIST.out.interval_list
+    } else {
+        ch_rrna_interval = Channel.fromPath(params.rrna_intervals).map { that -> [[id:that.Name], that] }
+    }
+
+    if (!file(params.refflat).exists() || file(params.refflat).isEmpty()){
+        GTF_TO_REFFLAT(ch_gtf)
+        ch_versions = ch_versions.mix(GTF_TO_REFFLAT.out.versions)
+        ch_refflat = GTF_TO_REFFLAT.out.refflat.map { that -> [[id:that.Name], that] }
+    } else {
+        ch_refflat = Channel.fromPath(params.refflat).map { that -> [[id:that.Name], that] }
+    }
+
+    if (!file(params.salmon_index).exists() || file(params.salmon_index).isEmpty() ||
+        !file(params.salmon_index_stub_check).exists() || file(params.salmon_index_stub_check).isEmpty()){ // add condition for qc
+        GFFREAD(ch_gtf, ch_fasta.map{ it -> it[1] })
+        ch_versions = ch_versions.mix(GFFREAD.out.versions)
+        SALMON_INDEX(ch_fasta.map{ it -> it[1] }, GFFREAD.out.gffread_fasta.map{ it -> it[1] })
+        ch_versions = ch_versions.mix(SALMON_INDEX.out.versions)
+        ch_salmon_index = SALMON_INDEX.out.index
+    } else {
+        ch_salmon_index = Channel.fromPath({params.salmon_index})
+    }
+
+    if ((params.starindex || params.all || params.starfusion || params.arriba) &&
+            (!file(params.starindex_ref).exists() || file(params.starindex_ref).isEmpty() ||
+            !file(params.starindex_ref_stub_check).exists() || file(params.starindex_ref_stub_check).isEmpty() )) {
+        STAR_GENOMEGENERATE(ch_fasta, ch_gtf)
+        ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions)
+        ch_starindex_ref = STAR_GENOMEGENERATE.out.index
+    } else {
+        ch_starindex_ref = Channel.fromPath(params.starindex_ref).map { that -> [[id:that.Name], that] }
+    }
+
+    if ((params.arriba || params.all) &&
+            (!file(params.arriba_ref_blacklist).exists() || file(params.arriba_ref_blacklist).isEmpty() ||
+            !file(params.arriba_ref_known_fusions).exists() || file(params.arriba_ref_known_fusions).isEmpty() ||
+            !file(params.arriba_ref_protein_domains).exists() || file(params.arriba_ref_protein_domains).isEmpty())) {
+        ARRIBA_DOWNLOAD(params.genome)
+        ch_versions = ch_versions.mix(ARRIBA_DOWNLOAD.out.versions)
+        ch_arriba_ref_blacklist = ARRIBA_DOWNLOAD.out.blacklist
+        ch_arriba_ref_cytobands = ARRIBA_DOWNLOAD.out.cytobands
+        ch_arriba_ref_known_fusions = ARRIBA_DOWNLOAD.out.known_fusions
+        ch_arriba_ref_protein_domains = ARRIBA_DOWNLOAD.out.protein_domains
+    } else {
+        ch_arriba_ref_blacklist = Channel.fromPath(params.arriba_ref_blacklist)
+        ch_arriba_ref_cytobands = Channel.fromPath(params.arriba_ref_cytobands)
+        ch_arriba_ref_known_fusions = Channel.fromPath(params.arriba_ref_known_fusions)
+        ch_arriba_ref_protein_domains = Channel.fromPath(params.arriba_ref_protein_domains)
+    }
+
+
+    if ((params.fusioncatcher || params.all) &&
+            (!file(params.fusioncatcher_ref).exists() || file(params.fusioncatcher_ref).isEmpty() ||
+            !file(params.fusioncatcher_ref_stub_check).exists() || file(params.fusioncatcher_ref_stub_check).isEmpty() )) {
+            FUSIONCATCHER_BUILD(params.genome_gencode_version)
+            ch_versions = ch_versions.mix(FUSIONCATCHER_BUILD.out.versions)
+            ch_fusioncatcher_ref = FUSIONCATCHER_BUILD.out.reference
+    }
+    else {
+        ch_fusioncatcher_ref = Channel.fromPath(params.fusioncatcher_ref)
+    }
+
+
+    if ((params.starfusion || params.all) &&
+            (!file(params.starfusion_ref).exists() || file(params.starfusion_ref).isEmpty() ||
+            !file(params.starfusion_ref_stub_check).exists() || file(params.starfusion_ref_stub_check).isEmpty() )) {
+            STARFUSION_BUILD(ch_fasta, ch_gtf, params.fusion_annot_lib, params.species)
+            ch_versions = ch_versions.mix(STARFUSION_BUILD.out.versions)
+            ch_starfusion_ref = STARFUSION_BUILD.out.reference
+    }
+    else {
+        ch_starfusion_ref = Channel.fromPath(params.starfusion_ref)
+    }
+
+
+    if ((params.fusionreport || params.all) &&
+            (!file(params.fusionreport_ref).exists() || file(params.fusionreport_ref).isEmpty() ||
+            !file(params.fusionreport_ref_stub_check).exists() || file(params.fusionreport_ref_stub_check).isEmpty())) {
+        if (!params.no_cosmic && (!params.cosmic_username || !params.cosmic_passwd)) { exit 1, 'COSMIC username and/or password missing' }
+        FUSIONREPORT_DOWNLOAD()
+        ch_versions = ch_versions.mix(FUSIONREPORT_DOWNLOAD.out.versions)
+        ch_fusionreport_ref = FUSIONREPORT_DOWNLOAD.out.fusionreport_ref
+    } else {
+        ch_fusionreport_ref = Channel.fromPath(params.fusionreport_ref).map { that -> [[id:that.Name], that] }
+    }
+
+    emit:
+    ch_fasta
+    ch_gtf
+    ch_fai
+    ch_hgnc_ref
+    ch_hgnc_date
+    ch_rrna_interval
+    ch_refflat
+    ch_salmon_index
+    ch_starindex_ref
+    ch_arriba_ref_blacklist
+    ch_arriba_ref_cytobands
+    ch_arriba_ref_known_fusions
+    ch_arriba_ref_protein_domains
+    ch_fusioncatcher_ref
+    ch_starfusion_ref
+    ch_fusionreport_ref
+    versions        = ch_versions
+}
+
+/*
+========================================================================================
+    THE END
+========================================================================================
+*/
diff --git a/subworkflows/local/fusioncatcher_workflow.nf b/subworkflows/local/fusioncatcher_workflow.nf
index ebb09e60..97ed55de 100644
--- a/subworkflows/local/fusioncatcher_workflow.nf
+++ b/subworkflows/local/fusioncatcher_workflow.nf
@@ -12,7 +12,7 @@ workflow FUSIONCATCHER_WORKFLOW {
         if ((params.fusioncatcher || params.all) && !params.fusioninspector_only) {
             if (params.fusioncatcher_fusions){
                 ch_fusioncatcher_fusions = reads.combine(Channel.value(file(params.fusioncatcher_fusions, checkIfExists:true)))
-                                            .map { meta, reads, fusions -> [ meta, fusions ] }
+                                            .map { it -> [ it[0], it[1] ] }
             } else {
                 FUSIONCATCHER (
                     reads,
@@ -24,7 +24,7 @@ workflow FUSIONCATCHER_WORKFLOW {
         }
         else {
             ch_fusioncatcher_fusions = reads.combine(Channel.value(file(ch_dummy_file, checkIfExists:true)))
-                                        .map { meta, reads, fusions -> [ meta, fusions ] }
+                                        .map { it -> [ it[0], it[1] ] }
         }
 
     emit:
diff --git a/subworkflows/local/fusionreport_workflow.nf b/subworkflows/local/fusionreport_workflow.nf
index 6a87244f..04019e12 100644
--- a/subworkflows/local/fusionreport_workflow.nf
+++ b/subworkflows/local/fusionreport_workflow.nf
@@ -28,7 +28,7 @@ workflow FUSIONREPORT_WORKFLOW {
             ch_csv = FUSIONREPORT.out.csv
         } else {
             ch_fusion_list = reads.combine(Channel.value(file(params.fusioninspector_fusions, checkIfExists:true)))
-                            .map { meta, reads, fusions -> [ meta, fusions ] }
+                            .map { it -> [ it[0], it[1] ] }
 
             ch_fusion_list_filtered  = ch_fusion_list
         }
diff --git a/subworkflows/local/qc_workflow/main.nf b/subworkflows/local/qc_workflow/main.nf
index a0ad60b6..4b635242 100644
--- a/subworkflows/local/qc_workflow/main.nf
+++ b/subworkflows/local/qc_workflow/main.nf
@@ -9,7 +9,6 @@ include { PICARD_COLLECTINSERTSIZEMETRICS   } from '../../../modules/nf-core/pic
 workflow QC_WORKFLOW {
     take:
         ch_bam_sorted           // channel [ meta, bam        ]
-        ch_chrgtf               // channel [ meta, gtf        ]
         ch_refflat              // channel [ meta, refflat    ]
         ch_fasta                // channel [ meta, fasta      ]
         ch_fai                  // channel [ meta, fai        ]
diff --git a/subworkflows/local/starfusion_workflow.nf b/subworkflows/local/starfusion_workflow.nf
index 82ae6f76..7f12f08a 100644
--- a/subworkflows/local/starfusion_workflow.nf
+++ b/subworkflows/local/starfusion_workflow.nf
@@ -9,7 +9,7 @@ include { CTATSPLICING_WORKFLOW         }   from './ctatsplicing_workflow'
 workflow STARFUSION_WORKFLOW {
     take:
         reads
-        ch_chrgtf
+        ch_gtf
         ch_starindex_ref
         ch_fasta
         ch_starfusion_ref
@@ -25,9 +25,9 @@ workflow STARFUSION_WORKFLOW {
         if ((params.starfusion || params.all || params.stringtie) && !params.fusioninspector_only) {
             if (params.starfusion_fusions){
                 ch_starfusion_fusions = reads.combine(Channel.value(file(params.starfusion_fusions, checkIfExists:true)))
-                                        .map { meta, reads, fusions -> [ meta, fusions ] }
+                                        .map { it -> [ it[0], it[2] ] }
             } else {
-                STAR_FOR_STARFUSION( reads, ch_starindex_ref, ch_chrgtf, params.star_ignore_sjdbgtf, '', params.seq_center ?: '')
+                STAR_FOR_STARFUSION( reads, ch_starindex_ref, ch_gtf, params.star_ignore_sjdbgtf, '', params.seq_center ?: '')
                 ch_versions = ch_versions.mix(STAR_FOR_STARFUSION.out.versions)
                 ch_align = STAR_FOR_STARFUSION.out.bam_sorted
 
@@ -65,7 +65,7 @@ workflow STARFUSION_WORKFLOW {
         }
         else {
             ch_starfusion_fusions = reads.combine(Channel.value(file(ch_dummy_file, checkIfExists:true)))
-                                    .map { meta, reads, fusions -> [ meta, fusions ] }
+                                    .map { it -> [ it[0], it[2] ] }
             ch_star_stats = Channel.empty()
             ch_star_gene_count = Channel.empty()
         }
diff --git a/subworkflows/local/stringtie_workflow.nf b/subworkflows/local/stringtie_workflow.nf
index 60bd4f38..d66ec0ee 100644
--- a/subworkflows/local/stringtie_workflow.nf
+++ b/subworkflows/local/stringtie_workflow.nf
@@ -5,14 +5,14 @@ include { STRINGTIE_MERGE }        from '../../modules/nf-core/stringtie/merge/m
 workflow STRINGTIE_WORKFLOW {
     take:
         bam_sorted
-        ch_chrgtf
+        ch_gtf
 
     main:
         ch_versions = Channel.empty()
         ch_stringtie_gtf = Channel.empty()
 
         if ((params.stringtie || params.all) && !params.fusioninspector_only) {
-            STRINGTIE_STRINGTIE(bam_sorted, ch_chrgtf.map { meta, gtf -> [ gtf ]})
+            STRINGTIE_STRINGTIE(bam_sorted, ch_gtf.map { meta, gtf -> [ gtf ]})
             ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions)
 
             STRINGTIE_STRINGTIE
@@ -23,7 +23,7 @@ workflow STRINGTIE_WORKFLOW {
             ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions)
 
 
-            STRINGTIE_MERGE (stringtie_gtf, ch_chrgtf.map { meta, gtf -> [ gtf ]})
+            STRINGTIE_MERGE (stringtie_gtf, ch_gtf.map { meta, gtf -> [ gtf ]})
             ch_versions = ch_versions.mix(STRINGTIE_MERGE.out.versions)
             ch_stringtie_gtf = STRINGTIE_MERGE.out.gtf
         }
diff --git a/subworkflows/local/trim_workflow/main.nf b/subworkflows/local/trim_workflow/main.nf
index 2cbb8380..d548c8ae 100644
--- a/subworkflows/local/trim_workflow/main.nf
+++ b/subworkflows/local/trim_workflow/main.nf
@@ -6,7 +6,7 @@ include { FASTQC as FASTQC_FOR_FASTP } from '../../../modules/nf-core/fastqc/mai
 workflow TRIM_WORKFLOW {
 
     take:
-        reads           // channel [ meta, [ fastqs ] ]
+        reads           // channel [ meta, [ fastq files ] ]
         adapter_fasta   // channel [ path ]
         fastp_trim      // boolean
 
diff --git a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf
index ad97686a..96279699 100644
--- a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf
@@ -30,10 +30,8 @@ workflow PIPELINE_INITIALISATION {
     take:
     version           // boolean: Display version and exit
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
-    monochrome_logs   // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
     outdir            //  string: The output directory where the results will be saved
-    input             //  string: Path to input samplesheet
 
     main:
 
@@ -114,6 +112,7 @@ workflow PIPELINE_COMPLETION {
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
+    multiqc_report  //  string: Path to MultiQC report
 
     main:
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
@@ -157,8 +156,8 @@ workflow PIPELINE_COMPLETION {
 def validateInputParameters() {
     genomeExistsError()
 
-    if (params.build_references && params.no_cosmic) {
-            log.warn("No cosmic credentials were provided. Skipping COSMIC DB download from `FUSIONREPORT_DOWNLOAD`")
+    if (params.no_cosmic) {
+            log.warn("Skipping COSMIC DB download from `FUSIONREPORT_DOWNLOAD` and skip using it in `FUSIONREPORT`")
     }
 
     if (params.starfusion_build && !params.fusion_annot_lib) {
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index 0fcbf7b3..d6e593e8 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -92,10 +92,12 @@ def checkCondaChannels() {
         channels = config.channels
     }
     catch (NullPointerException e) {
+        log.debug(e)
         log.warn("Could not verify conda channel configuration.")
         return null
     }
     catch (IOException e) {
+        log.debug(e)
         log.warn("Could not verify conda channel configuration.")
         return null
     }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index ca964ce8..02dbf094 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -52,10 +52,12 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.stdout.contains("nextflow_workflow v9.9.9") }
-            )
+            expect {
+                with(workflow) {
+                    assert success
+                    assert "nextflow_workflow v9.9.9" in stdout
+                }
+            }
         }
     }
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 5cb7bafe..bfd25876 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -56,21 +56,6 @@ def checkProfileProvided(nextflow_cli_args) {
     }
 }
 
-//
-// Citation string for pipeline
-//
-def workflowCitation() {
-    def temp_doi_ref = ""
-    def manifest_doi = workflow.manifest.doi.tokenize(",")
-    // Handling multiple DOIs
-    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
-    // Removing ` ` since the manifest.doi is a string and not a proper list
-    manifest_doi.each { doi_ref ->
-        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
-    }
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + "  https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-}
-
 //
 // Generate workflow version string
 //
@@ -150,33 +135,6 @@ def paramsSummaryMultiqc(summary_params) {
     return yaml_file_text
 }
 
-//
-// nf-core logo
-//
-def nfCoreLogo(monochrome_logs=true) {
-    def colors = logColours(monochrome_logs) as Map
-    String.format(
-        """\n
-        ${dashedLine(monochrome_logs)}
-                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                ${colors.green}`._,._,\'${colors.reset}
-        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
-        ${dashedLine(monochrome_logs)}
-        """.stripIndent()
-    )
-}
-
-//
-// Return dashed line
-//
-def dashedLine(monochrome_logs=true) {
-    def colors = logColours(monochrome_logs) as Map
-    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-}
-
 //
 // ANSII colours used for terminal logging
 //
@@ -245,28 +203,24 @@ def logColours(monochrome_logs=true) {
     return colorcodes
 }
 
-//
-// Attach the multiqc report to email
-//
-def attachMultiqcReport(multiqc_report) {
-    def mqc_report = null
-    try {
-        if (workflow.success) {
-            mqc_report = multiqc_report.getVal()
-            if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
-                if (mqc_report.size() > 1) {
-                    log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
-                }
-                mqc_report = mqc_report[0]
-            }
+// Return a single report from an object that may be a Path or List
+//
+def getSingleReport(multiqc_reports) {
+    if (multiqc_reports instanceof Path) {
+        return multiqc_reports
+    } else if (multiqc_reports instanceof List) {
+        if (multiqc_reports.size() == 0) {
+            log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
+            return null
+        } else if (multiqc_reports.size() == 1) {
+            return multiqc_reports.first()
+        } else {
+            log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
+            return multiqc_reports.first()
         }
+    } else {
+        return null
     }
-    catch (Exception all) {
-        if (multiqc_report) {
-            log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
-        }
-    }
-    return mqc_report
 }
 
 //
@@ -320,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     email_fields['summary']      = summary << misc_fields
 
     // On success try attach the multiqc report
-    def mqc_report = attachMultiqcReport(multiqc_report)
+    def mqc_report = getSingleReport(multiqc_report)
 
     // Check if we are only sending emails on failure
     def email_address = email
@@ -340,7 +294,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def email_html    = html_template.toString()
 
     // Render the sendmail template
-    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
+    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit
     def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
     def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
     def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
@@ -351,14 +305,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     if (email_address) {
         try {
             if (plaintext_email) {
-new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')            }
+                new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')
+            }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
             ['sendmail', '-t'].execute() << sendmail_html
             log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
         }
-        catch (Exception all) {
+        catch (Exception msg) {
+            log.debug(msg.toString())
+            log.debug("Trying with mail instead of sendmail")
             // Catch failures and try with plaintext
             def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
             mail_cmd.execute() << email_html
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index 1dc317f8..f117040c 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -41,26 +41,14 @@ nextflow_function {
         }
     }
 
-    test("Test Function workflowCitation") {
-
-        function "workflowCitation"
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function nfCoreLogo") {
+    test("Test Function without logColours") {
 
-        function "nfCoreLogo"
+        function "logColours"
 
         when {
             function {
                 """
-                input[0] = false
+                input[0] = true
                 """
             }
         }
@@ -73,9 +61,8 @@ nextflow_function {
         }
     }
 
-    test("Test Function dashedLine") {
-
-        function "dashedLine"
+    test("Test Function with logColours") {
+        function "logColours"
 
         when {
             function {
@@ -93,14 +80,13 @@ nextflow_function {
         }
     }
 
-    test("Test Function without logColours") {
-
-        function "logColours"
+    test("Test Function getSingleReport with a single file") {
+        function "getSingleReport"
 
         when {
             function {
                 """
-                input[0] = true
+                input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true)
                 """
             }
         }
@@ -108,18 +94,22 @@ nextflow_function {
         then {
             assertAll(
                 { assert function.success },
-                { assert snapshot(function.result).match() }
+                { assert function.result.contains("test.tsv") }
             )
         }
     }
 
-    test("Test Function with logColours") {
-        function "logColours"
+    test("Test Function getSingleReport with multiple files") {
+        function "getSingleReport"
 
         when {
             function {
                 """
-                input[0] = false
+                input[0] = [
+                    file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true)
+                ]
                 """
             }
         }
@@ -127,7 +117,9 @@ nextflow_function {
         then {
             assertAll(
                 { assert function.success },
-                { assert snapshot(function.result).match() }
+                { assert function.result.contains("test.tsv") },
+                { assert !function.result.contains("network.tsv") },
+                { assert !function.result.contains("expression.tsv") }
             )
         }
     }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index 1037232c..02c67014 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -17,26 +17,6 @@
         },
         "timestamp": "2024-02-28T12:02:59.729647"
     },
-    "Test Function nfCoreLogo": {
-        "content": [
-            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:10.562934"
-    },
-    "Test Function workflowCitation": {
-        "content": [
-            "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:07.019761"
-    },
     "Test Function without logColours": {
         "content": [
             {
@@ -95,16 +75,6 @@
         },
         "timestamp": "2024-02-28T12:03:17.969323"
     },
-    "Test Function dashedLine": {
-        "content": [
-            "-\u001b[2m----------------------------------------------------\u001b[0m-"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:14.366181"
-    },
     "Test Function with logColours": {
         "content": [
             {
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 842dc432..8fb30164 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -42,7 +42,7 @@ nextflow_workflow {
 
             params {
                 test_data   = ''
-                outdir      = 1
+                outdir      = null
             }
 
             workflow {
@@ -94,7 +94,7 @@ nextflow_workflow {
 
             params {
                 test_data   = ''
-                outdir      = 1
+                outdir      = null
             }
 
             workflow {
diff --git a/tests/test_build.nf.test b/tests/test_build.nf.test
deleted file mode 100644
index 1999a3b4..00000000
--- a/tests/test_build.nf.test
+++ /dev/null
@@ -1,36 +0,0 @@
-nextflow_pipeline {
-
-    name "Test pipeline"
-    script "../main.nf"
-    profile "test_build"
-    tag "pipeline"
-    tag "pipeline_rnafusion"
-    tag "test_build"
-
-    test("test_build") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-                all    = false // Output files when running all are too big for CI
-            }
-        }
-
-        then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            // Ignore files with timestamps in their names
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
-            assertAll(
-                { assert workflow.success},
-                { assert snapshot(
-                    // All stable path name, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path
-                ).match() }
-            )
-        }
-    }
-}
diff --git a/tests/test_build.nf.test.snap b/tests/test_build.nf.test.snap
deleted file mode 100644
index 28c64818..00000000
--- a/tests/test_build.nf.test.snap
+++ /dev/null
@@ -1,47 +0,0 @@
-{
-    "test_build": {
-        "content": [
-            [
-                "bedops",
-                "bedops/Homo_sapiens.GRCh38.102_rrna_intervals.gtf.bed",
-                "gatk4",
-                "gatk4/Homo_sapiens.GRCh38.102.dna.primary_assembly.dict",
-                "gffread",
-                "gffread/Homo_sapiens.GRCh38.102.fasta",
-                "pipeline_info",
-                "references",
-                "references/ensembl",
-                "references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf",
-                "references/ensembl/Homo_sapiens.GRCh38.102.dna.primary_assembly.fa",
-                "references/ensembl/Homo_sapiens.GRCh38.102.dna.primary_assembly.fa.fai",
-                "references/ensembl/Homo_sapiens.GRCh38.102.genepred",
-                "references/ensembl/Homo_sapiens.GRCh38.102.gtf",
-                "references/ensembl/Homo_sapiens.GRCh38.102.refflat",
-                "references/ensembl/Homo_sapiens.GRCh38.102_rrna_intervals.gtf.interval_list",
-                "references/hgnc",
-                "references/hgnc/HGNC-DB-timestamp.txt",
-                "references/hgnc/hgnc_complete_set.txt",
-                "rrnatranscripts",
-                "rrnatranscripts/Homo_sapiens.GRCh38.102_rrna_intervals.gtf"
-            ],
-            [
-                "Homo_sapiens.GRCh38.102_rrna_intervals.gtf.bed:md5,5bc3ccc76735ae46699a75269f0ea65b",
-                "Homo_sapiens.GRCh38.102.dna.primary_assembly.dict:md5,092f1bf29fce906ff7b5ece02b4b21c8",
-                "Homo_sapiens.GRCh38.102.fasta:md5,d1f17b045dc60c49f2cc29e30006afc0",
-                "Homo_sapiens.GRCh38.102.chr.gtf:md5,0069687307852c63596b4d2ebdbbaf0c",
-                "Homo_sapiens.GRCh38.102.dna.primary_assembly.fa.fai:md5,d527f3eb6b664020cf4d882b5820056f",
-                "Homo_sapiens.GRCh38.102.genepred:md5,59c577ca4ab033c0ce1feac1e387bcab",
-                "Homo_sapiens.GRCh38.102.gtf:md5,defac755cd9aa4e82ec33398c27745ef",
-                "Homo_sapiens.GRCh38.102.refflat:md5,ef095e13743811c31d44752c32e9673e",
-                "Homo_sapiens.GRCh38.102_rrna_intervals.gtf.interval_list:md5,0abf61877f65247b15c438d605d85599",
-                "hgnc_complete_set.txt:md5,a563a2f8432ec0ab7d3dc74d769102b8",
-                "Homo_sapiens.GRCh38.102_rrna_intervals.gtf:md5,744bf505deb50837b15441e808cad345"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-09T18:20:09.914393513"
-    }
-}
\ No newline at end of file
diff --git a/tests/test_cosmic.nf.test.snap b/tests/test_cosmic.nf.test.snap
index e69de29b..b8e6d4a5 100644
--- a/tests/test_cosmic.nf.test.snap
+++ b/tests/test_cosmic.nf.test.snap
@@ -0,0 +1,58 @@
+{
+    "test cosmic no fastp trim build": {
+        "content": [
+            0,
+            {
+                "Workflow": {
+                    "nf-core/rnafusion": "v4.0.0dev"
+                }
+            },
+            [
+                "pipeline_info",
+                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml"
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T12:42:49.558429"
+    },
+    "test cosmic no fastp trim": {
+        "content": [
+            0,
+            null,
+            [
+                "pipeline_info"
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T15:09:53.130295"
+    },
+    "test cosmic with fastp trim": {
+        "content": [
+            0,
+            null,
+            [
+                "pipeline_info"
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T15:09:29.277399"
+    }
+}
\ No newline at end of file
diff --git a/tests/test_stub.nf.test.snap b/tests/test_stub.nf.test.snap
index 3b83c240..0ac620e7 100644
--- a/tests/test_stub.nf.test.snap
+++ b/tests/test_stub.nf.test.snap
@@ -1,22 +1,144 @@
 {
     "stub test no fastp trim": {
         "content": [
-            4,
+            31,
             {
+                "ARRIBA_ARRIBA": {
+                    "arriba": "2.4.0"
+                },
+                "ARRIBA_DOWNLOAD": {
+                    "arriba_download": "2.4.0"
+                },
+                "CTATSPLICING_STARTOCANCERINTRONS": {
+                    "ctat-splicing": "0.0.2"
+                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
+                "FUSIONCATCHER": {
+                    "fusioncatcher": 1.35
+                },
+                "FUSIONCATCHER_BUILD": {
+                    "fusioncatcher": "fusioncatcher.py 1.35"
+                },
                 "FUSIONREPORT": {
                     "fusion_report": "2.1.5"
                 },
+                "FUSIONREPORT_DOWNLOAD": {
+                    "fusion_report": "2.1.5"
+                },
+                "GATK4_BEDTOINTERVALLIST": {
+                    "gatk4": "4.6.1.0"
+                },
+                "GATK4_CREATESEQUENCEDICTIONARY": {
+                    "gatk4": "4.6.1.0"
+                },
+                "GATK4_MARKDUPLICATES": {
+                    "gatk4": "4.5.0.0",
+                    "samtools": "1.19.2"
+                },
+                "GENCODE_DOWNLOAD": {
+                    "wget": null
+                },
+                "GET_RRNA_TRANSCRIPTS": {
+                    "get_rrna_transcripts": "v1.0"
+                },
+                "GFFREAD": {
+                    "gffread": "0.12.7"
+                },
+                "GTF_TO_REFFLAT": {
+                    "gtfToGenePred": 377
+                },
+                "HGNC_DOWNLOAD": {
+                    "wget": null
+                },
+                "PICARD_COLLECTINSERTSIZEMETRICS": {
+                    "picard": "3.3.0"
+                },
+                "PICARD_COLLECTRNASEQMETRICS": {
+                    "picard": "3.3.0"
+                },
+                "SALMON_INDEX": {
+                    "salmon": "1.10.3"
+                },
+                "SALMON_QUANT": {
+                    "salmon": "1.10.3"
+                },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_INDEX_FOR_STARFUSION": {
+                    "samtools": 1.21
+                },
+                "STARFUSION": {
+                    "STAR-Fusion": "1.14.0"
+                },
+                "STARFUSION_BUILD": {
+                    "STAR-Fusion": "1.14.0"
+                },
+                "STAR_FOR_ARRIBA": {
+                    "star": "2.7.11b",
+                    "samtools": 1.2,
+                    "gawk": "5.1.0"
+                },
+                "STAR_FOR_STARFUSION": {
+                    "star": "2.7.11b",
+                    "samtools": 1.2,
+                    "gawk": "5.1.0"
+                },
+                "STAR_GENOMEGENERATE": {
+                    "star": "2.7.11b",
+                    "samtools": 1.2,
+                    "gawk": "5.1.0"
+                },
+                "STRINGTIE_MERGE": {
+                    "stringtie": "2.2.1"
+                },
+                "STRINGTIE_STRINGTIE": {
+                    "stringtie": "2.2.3"
+                },
                 "Workflow": {
                     "nf-core/rnafusion": "v4.0.0dev"
                 }
             },
             [
+                "arriba",
+                "arriba/test.arriba.fusions.discarded.tsv",
+                "arriba/test.arriba.fusions.tsv",
+                "ctatsplicing",
+                "ctatsplicing/arriba",
+                "ctatsplicing/arriba/test.cancer.introns",
+                "ctatsplicing/arriba/test.cancer.introns.prelim",
+                "ctatsplicing/arriba/test.cancer_intron_reads.sorted.bam",
+                "ctatsplicing/arriba/test.cancer_intron_reads.sorted.bam.bai",
+                "ctatsplicing/arriba/test.chckpts",
+                "ctatsplicing/arriba/test.ctat-splicing.igv.html",
+                "ctatsplicing/arriba/test.gene_reads.sorted.sifted.bam",
+                "ctatsplicing/arriba/test.gene_reads.sorted.sifted.bam.bai",
+                "ctatsplicing/arriba/test.igv.tracks",
+                "ctatsplicing/arriba/test.introns",
+                "ctatsplicing/arriba/test.introns.for_IGV.bed",
+                "ctatsplicing/starfusion",
+                "ctatsplicing/starfusion/test.cancer.introns",
+                "ctatsplicing/starfusion/test.cancer.introns.prelim",
+                "ctatsplicing/starfusion/test.cancer_intron_reads.sorted.bam",
+                "ctatsplicing/starfusion/test.cancer_intron_reads.sorted.bam.bai",
+                "ctatsplicing/starfusion/test.chckpts",
+                "ctatsplicing/starfusion/test.ctat-splicing.igv.html",
+                "ctatsplicing/starfusion/test.gene_reads.sorted.sifted.bam",
+                "ctatsplicing/starfusion/test.gene_reads.sorted.sifted.bam.bai",
+                "ctatsplicing/starfusion/test.igv.tracks",
+                "ctatsplicing/starfusion/test.introns",
+                "ctatsplicing/starfusion/test.introns.for_IGV.bed",
                 "fastqc",
                 "fastqc/test.html",
                 "fastqc/test.zip",
+                "fusioncatcher",
+                "fusioncatcher/human_v46",
+                "fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
+                "fusioncatcher/test.fusioncatcher.fusion-genes.txt",
+                "fusioncatcher/test.fusioncatcher.log",
+                "fusioncatcher/test.fusioncatcher.summary.txt",
                 "fusionreport",
                 "fusionreport/test",
                 "fusionreport/test/AAA_BBB.html",
@@ -25,28 +147,231 @@
                 "fusionreport/test/test.fusions.csv",
                 "fusionreport/test/test.fusions.json",
                 "fusionreport/test/test_fusionreport_index.html",
+                "gatk4",
+                "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict",
+                "get",
+                "get/rrna.bed",
+                "get/rrna.gtf",
                 "multiqc",
                 "multiqc/multiqc_data",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_report.html",
+                "picard",
+                "picard/test.bai",
+                "picard/test.bam",
+                "picard/test.bam.metrics",
+                "picard/test.cram",
+                "picard/test.cram.crai",
+                "picard/test.rna_metrics",
+                "picard/test_collectinsertsize.pdf",
+                "picard/test_collectinsertsize.txt",
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "references",
+                "references/arriba",
+                "references/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz",
+                "references/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv",
+                "references/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz",
+                "references/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3",
+                "references/fusion_report_db",
+                "references/fusion_report_db/DB-timestamp.txt",
+                "references/fusion_report_db/cosmic.db",
+                "references/fusion_report_db/fusion_report.log",
+                "references/fusion_report_db/fusiongdb2.db",
+                "references/fusion_report_db/mitelman.db",
+                "references/gencode",
+                "references/gencode/Homo_sapiens.GRCh38.46.gtf",
+                "references/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list",
+                "references/gencode/Homo_sapiens.GRCh38.46.gtf.refflat",
+                "references/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa",
+                "references/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai",
+                "references/gffread",
+                "references/gffread/Homo_sapiens.GRCh38.46.gtf.fasta",
+                "references/hgnc",
+                "references/hgnc/HGNC-DB-timestamp.txt",
+                "references/hgnc/hgnc_complete_set.txt",
+                "references/salmon",
+                "references/salmon/salmon",
+                "references/salmon/salmon/complete_ref_lens.bin",
+                "references/salmon/salmon/ctable.bin",
+                "references/salmon/salmon/ctg_offsets.bin",
+                "references/salmon/salmon/duplicate_clusters.tsv",
+                "references/salmon/salmon/info.json",
+                "references/salmon/salmon/mphf.bin",
+                "references/salmon/salmon/pos.bin",
+                "references/salmon/salmon/pre_indexing.log",
+                "references/salmon/salmon/rank.bin",
+                "references/salmon/salmon/refAccumLengths.bin",
+                "references/salmon/salmon/ref_indexing.log",
+                "references/salmon/salmon/reflengths.bin",
+                "references/salmon/salmon/refseq.bin",
+                "references/salmon/salmon/seq.bin",
+                "references/salmon/salmon/versionInfo.json",
+                "references/star",
+                "references/star/Genome",
+                "references/star/Log.out",
+                "references/star/SA",
+                "references/star/SAindex",
+                "references/star/chrLength.txt",
+                "references/star/chrName.txt",
+                "references/star/chrNameLength.txt",
+                "references/star/chrStart.txt",
+                "references/star/exonGeTrInfo.tab",
+                "references/star/exonInfo.tab",
+                "references/star/geneInfo.tab",
+                "references/star/genomeParameters.txt",
+                "references/star/sjdbInfo.txt",
+                "references/star/sjdbList.fromGTF.out.tab",
+                "references/star/sjdbList.out.tab",
+                "references/star/transcriptInfo.tab",
                 "salmon",
                 "salmon/test",
                 "salmon/test_lib_format_counts.json",
-                "salmon/test_meta_info.json"
+                "salmon/test_meta_info.json",
+                "star_for_arriba",
+                "star_for_arriba/test.Aligned.sortedByCoord.out.bam",
+                "star_for_arriba/test.Aligned.unsort.out.bam",
+                "star_for_arriba/test.Chimeric.out.junction",
+                "star_for_arriba/test.Log.final.out",
+                "star_for_arriba/test.Log.out",
+                "star_for_arriba/test.Log.progress.out",
+                "star_for_arriba/test.ReadsPerGene.out.tab",
+                "star_for_arriba/test.SJ.out.tab",
+                "star_for_arriba/test.Signal.UniqueMultiple.str1.out.bg",
+                "star_for_arriba/test.Signal.UniqueMultiple.str1.out.wig",
+                "star_for_arriba/test.out.sam",
+                "star_for_arriba/test.sortedByCoord.out.bam",
+                "star_for_arriba/test.tab",
+                "star_for_arriba/test.toTranscriptome.out.bam",
+                "star_for_arriba/test.unmapped_1.fastq.gz",
+                "star_for_arriba/test.unmapped_2.fastq.gz",
+                "star_for_arriba/testXd.out.bam",
+                "star_for_starfusion",
+                "star_for_starfusion/test.Aligned.sortedByCoord.out.bam",
+                "star_for_starfusion/test.Aligned.unsort.out.bam",
+                "star_for_starfusion/test.Chimeric.out.junction",
+                "star_for_starfusion/test.Log.final.out",
+                "star_for_starfusion/test.Log.out",
+                "star_for_starfusion/test.Log.progress.out",
+                "star_for_starfusion/test.ReadsPerGene.out.tab",
+                "star_for_starfusion/test.SJ.out.tab",
+                "star_for_starfusion/test.Signal.UniqueMultiple.str1.out.bg",
+                "star_for_starfusion/test.Signal.UniqueMultiple.str1.out.wig",
+                "star_for_starfusion/test.out.sam",
+                "star_for_starfusion/test.sortedByCoord.out.bam",
+                "star_for_starfusion/test.sortedByCoord.out.bam.bai",
+                "star_for_starfusion/test.tab",
+                "star_for_starfusion/test.toTranscriptome.out.bam",
+                "star_for_starfusion/test.unmapped_1.fastq.gz",
+                "star_for_starfusion/test.unmapped_2.fastq.gz",
+                "star_for_starfusion/testXd.out.bam",
+                "starfusion",
+                "starfusion/ctat_genome_lib_build_dir",
+                "starfusion/ctat_genome_lib_build_dir/AnnotFilterRule.pm",
+                "starfusion/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/_fusion_annot_lib.idx.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/_prot_info_db.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/annotfiltrule_cp.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/blast_pairs.idx.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/cp_gene_blast_pairs.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/cp_pfam_dat.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/cp_ref_annot_cdna.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/fusion_annot_lib.cp.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/index_pfam_hits.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/index_ref_annot_cdna.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/makeblastdb.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/mm2.splice_bed.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/mm2_genome_idx.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.cp.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.idx.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.gene_spans.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.mini.sortu.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_genome.fa.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_genome_fai.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/trans.blast.dat.cp.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/trans.blast.dat.index.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/validate_ctat_genome_lib.ok",
+                "starfusion/ctat_genome_lib_build_dir/blast_pairs.dat.gz",
+                "starfusion/ctat_genome_lib_build_dir/blast_pairs.idx",
+                "starfusion/ctat_genome_lib_build_dir/fusion_annot_lib.gz",
+                "starfusion/ctat_genome_lib_build_dir/fusion_annot_lib.idx",
+                "starfusion/ctat_genome_lib_build_dir/pfam_domains.dbm",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.cdna.fa",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.cdna.fa.idx",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.cds",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa.idx",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.gtf",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.gtf.mm2.splice.bed",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.pep",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.prot_info.dbm",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.mm2",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.ndb",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nhr",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nin",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.njs",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.not",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nsq",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.ntf",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nto",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Genome",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Log.out",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SA",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SAindex",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/build.ok",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrLength.txt",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrName.txt",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrNameLength.txt",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrStart.txt",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonGeTrInfo.tab",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonInfo.tab",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/geneInfo.tab",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/genomeParameters.txt",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbInfo.txt",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.fromGTF.out.tab",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.out.tab",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/transcriptInfo.tab",
+                "starfusion/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dat",
+                "starfusion/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm",
+                "starfusion/ctat_genome_lib_build_dir/trans.blast.dat.gz",
+                "starfusion/test.starfusion.abridged.coding_effect.tsv",
+                "starfusion/test.starfusion.abridged.tsv",
+                "starfusion/test.starfusion.fusion_predictions.tsv",
+                "stringtie",
+                "stringtie/[:]",
+                "stringtie/[:]/stringtie.merged.gtf",
+                "stringtie/test.ballgown",
+                "stringtie/test.coverage.gtf",
+                "stringtie/test.gene.abundance.txt",
+                "stringtie/test.transcripts.gtf"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-03T19:27:00.717876194"
+        "timestamp": "2024-12-20T14:00:19.311265"
     },
     "stub test with fastp trim": {
         "content": [
-            6,
+            33,
             {
+                "ARRIBA_ARRIBA": {
+                    "arriba": "2.4.0"
+                },
+                "ARRIBA_DOWNLOAD": {
+                    "arriba_download": "2.4.0"
+                },
+                "CTATSPLICING_STARTOCANCERINTRONS": {
+                    "ctat-splicing": "0.0.2"
+                },
                 "FASTP": {
                     "fastp": "0.23.4"
                 },
@@ -56,14 +381,121 @@
                 "FASTQC_FOR_FASTP": {
                     "fastqc": "0.12.1"
                 },
+                "FUSIONCATCHER": {
+                    "fusioncatcher": 1.35
+                },
+                "FUSIONCATCHER_BUILD": {
+                    "fusioncatcher": "fusioncatcher.py 1.35"
+                },
                 "FUSIONREPORT": {
                     "fusion_report": "2.1.5"
                 },
+                "FUSIONREPORT_DOWNLOAD": {
+                    "fusion_report": "2.1.5"
+                },
+                "GATK4_BEDTOINTERVALLIST": {
+                    "gatk4": "4.6.1.0"
+                },
+                "GATK4_CREATESEQUENCEDICTIONARY": {
+                    "gatk4": "4.6.1.0"
+                },
+                "GATK4_MARKDUPLICATES": {
+                    "gatk4": "4.5.0.0",
+                    "samtools": "1.19.2"
+                },
+                "GENCODE_DOWNLOAD": {
+                    "wget": null
+                },
+                "GET_RRNA_TRANSCRIPTS": {
+                    "get_rrna_transcripts": "v1.0"
+                },
+                "GFFREAD": {
+                    "gffread": "0.12.7"
+                },
+                "GTF_TO_REFFLAT": {
+                    "gtfToGenePred": 377
+                },
+                "HGNC_DOWNLOAD": {
+                    "wget": null
+                },
+                "PICARD_COLLECTINSERTSIZEMETRICS": {
+                    "picard": "3.3.0"
+                },
+                "PICARD_COLLECTRNASEQMETRICS": {
+                    "picard": "3.3.0"
+                },
+                "SALMON_INDEX": {
+                    "salmon": "1.10.3"
+                },
+                "SALMON_QUANT": {
+                    "salmon": "1.10.3"
+                },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_INDEX_FOR_STARFUSION": {
+                    "samtools": 1.21
+                },
+                "STARFUSION": {
+                    "STAR-Fusion": "1.14.0"
+                },
+                "STARFUSION_BUILD": {
+                    "STAR-Fusion": "1.14.0"
+                },
+                "STAR_FOR_ARRIBA": {
+                    "star": "2.7.11b",
+                    "samtools": 1.2,
+                    "gawk": "5.1.0"
+                },
+                "STAR_FOR_STARFUSION": {
+                    "star": "2.7.11b",
+                    "samtools": 1.2,
+                    "gawk": "5.1.0"
+                },
+                "STAR_GENOMEGENERATE": {
+                    "star": "2.7.11b",
+                    "samtools": 1.2,
+                    "gawk": "5.1.0"
+                },
+                "STRINGTIE_MERGE": {
+                    "stringtie": "2.2.1"
+                },
+                "STRINGTIE_STRINGTIE": {
+                    "stringtie": "2.2.3"
+                },
                 "Workflow": {
                     "nf-core/rnafusion": "v4.0.0dev"
                 }
             },
             [
+                "arriba",
+                "arriba/test.arriba.fusions.discarded.tsv",
+                "arriba/test.arriba.fusions.tsv",
+                "ctatsplicing",
+                "ctatsplicing/arriba",
+                "ctatsplicing/arriba/test.cancer.introns",
+                "ctatsplicing/arriba/test.cancer.introns.prelim",
+                "ctatsplicing/arriba/test.cancer_intron_reads.sorted.bam",
+                "ctatsplicing/arriba/test.cancer_intron_reads.sorted.bam.bai",
+                "ctatsplicing/arriba/test.chckpts",
+                "ctatsplicing/arriba/test.ctat-splicing.igv.html",
+                "ctatsplicing/arriba/test.gene_reads.sorted.sifted.bam",
+                "ctatsplicing/arriba/test.gene_reads.sorted.sifted.bam.bai",
+                "ctatsplicing/arriba/test.igv.tracks",
+                "ctatsplicing/arriba/test.introns",
+                "ctatsplicing/arriba/test.introns.for_IGV.bed",
+                "ctatsplicing/starfusion",
+                "ctatsplicing/starfusion/test.cancer.introns",
+                "ctatsplicing/starfusion/test.cancer.introns.prelim",
+                "ctatsplicing/starfusion/test.cancer_intron_reads.sorted.bam",
+                "ctatsplicing/starfusion/test.cancer_intron_reads.sorted.bam.bai",
+                "ctatsplicing/starfusion/test.chckpts",
+                "ctatsplicing/starfusion/test.ctat-splicing.igv.html",
+                "ctatsplicing/starfusion/test.gene_reads.sorted.sifted.bam",
+                "ctatsplicing/starfusion/test.gene_reads.sorted.sifted.bam.bai",
+                "ctatsplicing/starfusion/test.igv.tracks",
+                "ctatsplicing/starfusion/test.introns",
+                "ctatsplicing/starfusion/test.introns.for_IGV.bed",
                 "fastp",
                 "fastp/test.fastp.html",
                 "fastp/test.fastp.json",
@@ -76,6 +508,12 @@
                 "fastqc_for_fastp",
                 "fastqc_for_fastp/test_trimmed.html",
                 "fastqc_for_fastp/test_trimmed.zip",
+                "fusioncatcher",
+                "fusioncatcher/human_v46",
+                "fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
+                "fusioncatcher/test.fusioncatcher.fusion-genes.txt",
+                "fusioncatcher/test.fusioncatcher.log",
+                "fusioncatcher/test.fusioncatcher.summary.txt",
                 "fusionreport",
                 "fusionreport/test",
                 "fusionreport/test/AAA_BBB.html",
@@ -84,22 +522,216 @@
                 "fusionreport/test/test.fusions.csv",
                 "fusionreport/test/test.fusions.json",
                 "fusionreport/test/test_fusionreport_index.html",
+                "gatk4",
+                "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict",
+                "get",
+                "get/rrna.bed",
+                "get/rrna.gtf",
                 "multiqc",
                 "multiqc/multiqc_data",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_report.html",
+                "picard",
+                "picard/test.bai",
+                "picard/test.bam",
+                "picard/test.bam.metrics",
+                "picard/test.cram",
+                "picard/test.cram.crai",
+                "picard/test.rna_metrics",
+                "picard/test_collectinsertsize.pdf",
+                "picard/test_collectinsertsize.txt",
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "references",
+                "references/arriba",
+                "references/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz",
+                "references/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv",
+                "references/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz",
+                "references/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3",
+                "references/fusion_report_db",
+                "references/fusion_report_db/DB-timestamp.txt",
+                "references/fusion_report_db/cosmic.db",
+                "references/fusion_report_db/fusion_report.log",
+                "references/fusion_report_db/fusiongdb2.db",
+                "references/fusion_report_db/mitelman.db",
+                "references/gencode",
+                "references/gencode/Homo_sapiens.GRCh38.46.gtf",
+                "references/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list",
+                "references/gencode/Homo_sapiens.GRCh38.46.gtf.refflat",
+                "references/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa",
+                "references/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai",
+                "references/gffread",
+                "references/gffread/Homo_sapiens.GRCh38.46.gtf.fasta",
+                "references/hgnc",
+                "references/hgnc/HGNC-DB-timestamp.txt",
+                "references/hgnc/hgnc_complete_set.txt",
+                "references/salmon",
+                "references/salmon/salmon",
+                "references/salmon/salmon/complete_ref_lens.bin",
+                "references/salmon/salmon/ctable.bin",
+                "references/salmon/salmon/ctg_offsets.bin",
+                "references/salmon/salmon/duplicate_clusters.tsv",
+                "references/salmon/salmon/info.json",
+                "references/salmon/salmon/mphf.bin",
+                "references/salmon/salmon/pos.bin",
+                "references/salmon/salmon/pre_indexing.log",
+                "references/salmon/salmon/rank.bin",
+                "references/salmon/salmon/refAccumLengths.bin",
+                "references/salmon/salmon/ref_indexing.log",
+                "references/salmon/salmon/reflengths.bin",
+                "references/salmon/salmon/refseq.bin",
+                "references/salmon/salmon/seq.bin",
+                "references/salmon/salmon/versionInfo.json",
+                "references/star",
+                "references/star/Genome",
+                "references/star/Log.out",
+                "references/star/SA",
+                "references/star/SAindex",
+                "references/star/chrLength.txt",
+                "references/star/chrName.txt",
+                "references/star/chrNameLength.txt",
+                "references/star/chrStart.txt",
+                "references/star/exonGeTrInfo.tab",
+                "references/star/exonInfo.tab",
+                "references/star/geneInfo.tab",
+                "references/star/genomeParameters.txt",
+                "references/star/sjdbInfo.txt",
+                "references/star/sjdbList.fromGTF.out.tab",
+                "references/star/sjdbList.out.tab",
+                "references/star/transcriptInfo.tab",
                 "salmon",
                 "salmon/test",
                 "salmon/test_lib_format_counts.json",
-                "salmon/test_meta_info.json"
+                "salmon/test_meta_info.json",
+                "star_for_arriba",
+                "star_for_arriba/test.Aligned.sortedByCoord.out.bam",
+                "star_for_arriba/test.Aligned.unsort.out.bam",
+                "star_for_arriba/test.Chimeric.out.junction",
+                "star_for_arriba/test.Log.final.out",
+                "star_for_arriba/test.Log.out",
+                "star_for_arriba/test.Log.progress.out",
+                "star_for_arriba/test.ReadsPerGene.out.tab",
+                "star_for_arriba/test.SJ.out.tab",
+                "star_for_arriba/test.Signal.UniqueMultiple.str1.out.bg",
+                "star_for_arriba/test.Signal.UniqueMultiple.str1.out.wig",
+                "star_for_arriba/test.out.sam",
+                "star_for_arriba/test.sortedByCoord.out.bam",
+                "star_for_arriba/test.tab",
+                "star_for_arriba/test.toTranscriptome.out.bam",
+                "star_for_arriba/test.unmapped_1.fastq.gz",
+                "star_for_arriba/test.unmapped_2.fastq.gz",
+                "star_for_arriba/testXd.out.bam",
+                "star_for_starfusion",
+                "star_for_starfusion/test.Aligned.sortedByCoord.out.bam",
+                "star_for_starfusion/test.Aligned.unsort.out.bam",
+                "star_for_starfusion/test.Chimeric.out.junction",
+                "star_for_starfusion/test.Log.final.out",
+                "star_for_starfusion/test.Log.out",
+                "star_for_starfusion/test.Log.progress.out",
+                "star_for_starfusion/test.ReadsPerGene.out.tab",
+                "star_for_starfusion/test.SJ.out.tab",
+                "star_for_starfusion/test.Signal.UniqueMultiple.str1.out.bg",
+                "star_for_starfusion/test.Signal.UniqueMultiple.str1.out.wig",
+                "star_for_starfusion/test.out.sam",
+                "star_for_starfusion/test.sortedByCoord.out.bam",
+                "star_for_starfusion/test.sortedByCoord.out.bam.bai",
+                "star_for_starfusion/test.tab",
+                "star_for_starfusion/test.toTranscriptome.out.bam",
+                "star_for_starfusion/test.unmapped_1.fastq.gz",
+                "star_for_starfusion/test.unmapped_2.fastq.gz",
+                "star_for_starfusion/testXd.out.bam",
+                "starfusion",
+                "starfusion/ctat_genome_lib_build_dir",
+                "starfusion/ctat_genome_lib_build_dir/AnnotFilterRule.pm",
+                "starfusion/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/_fusion_annot_lib.idx.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/_prot_info_db.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/annotfiltrule_cp.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/blast_pairs.idx.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/cp_gene_blast_pairs.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/cp_pfam_dat.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/cp_ref_annot_cdna.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/fusion_annot_lib.cp.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/index_pfam_hits.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/index_ref_annot_cdna.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/makeblastdb.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/mm2.splice_bed.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/mm2_genome_idx.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.cp.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.idx.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.gene_spans.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.mini.sortu.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_genome.fa.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/ref_genome_fai.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/trans.blast.dat.cp.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/trans.blast.dat.index.ok",
+                "starfusion/ctat_genome_lib_build_dir/__chkpts/validate_ctat_genome_lib.ok",
+                "starfusion/ctat_genome_lib_build_dir/blast_pairs.dat.gz",
+                "starfusion/ctat_genome_lib_build_dir/blast_pairs.idx",
+                "starfusion/ctat_genome_lib_build_dir/fusion_annot_lib.gz",
+                "starfusion/ctat_genome_lib_build_dir/fusion_annot_lib.idx",
+                "starfusion/ctat_genome_lib_build_dir/pfam_domains.dbm",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.cdna.fa",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.cdna.fa.idx",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.cds",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa.idx",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.gtf",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.gtf.mm2.splice.bed",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.pep",
+                "starfusion/ctat_genome_lib_build_dir/ref_annot.prot_info.dbm",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.mm2",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.ndb",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nhr",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nin",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.njs",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.not",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nsq",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.ntf",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nto",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Genome",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Log.out",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SA",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SAindex",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/build.ok",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrLength.txt",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrName.txt",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrNameLength.txt",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrStart.txt",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonGeTrInfo.tab",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonInfo.tab",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/geneInfo.tab",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/genomeParameters.txt",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbInfo.txt",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.fromGTF.out.tab",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.out.tab",
+                "starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/transcriptInfo.tab",
+                "starfusion/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dat",
+                "starfusion/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm",
+                "starfusion/ctat_genome_lib_build_dir/trans.blast.dat.gz",
+                "starfusion/test.starfusion.abridged.coding_effect.tsv",
+                "starfusion/test.starfusion.abridged.tsv",
+                "starfusion/test.starfusion.fusion_predictions.tsv",
+                "stringtie",
+                "stringtie/[:]",
+                "stringtie/[:]/stringtie.merged.gtf",
+                "stringtie/test.ballgown",
+                "stringtie/test.coverage.gtf",
+                "stringtie/test.gene.abundance.txt",
+                "stringtie/test.transcripts.gtf"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-03T19:26:43.375635514"
+        "timestamp": "2024-12-20T13:57:10.179877"
     }
-}
\ No newline at end of file
+}
diff --git a/workflows/build_references.nf b/workflows/build_references.nf
deleted file mode 100644
index a75dfb30..00000000
--- a/workflows/build_references.nf
+++ /dev/null
@@ -1,94 +0,0 @@
-/*
-========================================================================================
-    IMPORT LOCAL MODULES/SUBWORKFLOWS
-========================================================================================
-*/
-
-include { ENSEMBL_DOWNLOAD }                from '../modules/local/ensembl/main'
-include { FUSIONCATCHER_DOWNLOAD }          from '../modules/local/fusioncatcher/download/main'
-include { FUSIONREPORT_DOWNLOAD }           from '../modules/local/fusionreport/download/main'
-include { HGNC_DOWNLOAD }                   from '../modules/local/hgnc/main'
-include { STARFUSION_BUILD }                from '../modules/local/starfusion/build/main'
-include { STARFUSION_DOWNLOAD }             from '../modules/local/starfusion/download/main'
-
-/*
-========================================================================================
-    IMPORT NF-CORE MODULES/SUBWORKFLOWS
-========================================================================================
-*/
-
-include { ARRIBA_DOWNLOAD }                 from '../modules/nf-core/arriba/download/main'
-include { BEDOPS_CONVERT2BED }              from '../modules/nf-core/bedops/convert2bed/main'
-include { GATK4_BEDTOINTERVALLIST }         from '../modules/nf-core/gatk4/bedtointervallist/main'
-include { GATK4_CREATESEQUENCEDICTIONARY }  from '../modules/nf-core/gatk4/createsequencedictionary/main'
-include { RRNATRANSCRIPTS }                 from '../modules/nf-core/rrnatranscripts/main'
-include { SAMTOOLS_FAIDX }                  from '../modules/nf-core/samtools/faidx/main'
-include { STAR_GENOMEGENERATE }             from '../modules/nf-core/star/genomegenerate/main'
-include { UCSC_GTFTOGENEPRED }              from '../modules/nf-core/ucsc/gtftogenepred/main'
-include { SALMON_INDEX }                    from '../modules/nf-core/salmon/index/main'
-include { GFFREAD }                         from '../modules/nf-core/gffread/main'
-
-/*
-========================================================================================
-    RUN MAIN WORKFLOW
-========================================================================================
-*/
-
-workflow BUILD_REFERENCES {
-
-    def fake_meta = [:]
-    fake_meta.id = "Homo_sapiens.${params.genome}.${params.ensembl_version}"
-    ENSEMBL_DOWNLOAD( params.ensembl_version, params.genome, fake_meta )
-    HGNC_DOWNLOAD()
-    SAMTOOLS_FAIDX(ENSEMBL_DOWNLOAD.out.primary_assembly, [[],[]])
-    GATK4_CREATESEQUENCEDICTIONARY(ENSEMBL_DOWNLOAD.out.primary_assembly)
-
-
-    RRNATRANSCRIPTS(ENSEMBL_DOWNLOAD.out.gtf.map{ it -> [ it[1] ] })
-    BEDOPS_CONVERT2BED(RRNATRANSCRIPTS.out.rrna_gtf.map{ it -> [[id:it.Name], it] })
-    GATK4_BEDTOINTERVALLIST(BEDOPS_CONVERT2BED.out.bed, GATK4_CREATESEQUENCEDICTIONARY.out.dict)
-
-    GFFREAD(ENSEMBL_DOWNLOAD.out.gtf, ENSEMBL_DOWNLOAD.out.primary_assembly.map { it -> [ it[1] ] })
-
-    if (!params.skip_salmon_index){
-        SALMON_INDEX(ENSEMBL_DOWNLOAD.out.primary_assembly.map{ it -> [ it[1] ] }, GFFREAD.out.gffread_fasta.map{ it -> [ it[1] ] })
-    }
-
-    if (params.starindex || params.all || params.starfusion || params.arriba) {
-        STAR_GENOMEGENERATE( ENSEMBL_DOWNLOAD.out.primary_assembly, ENSEMBL_DOWNLOAD.out.gtf )
-    }
-
-    if (params.arriba || params.all) {
-        ARRIBA_DOWNLOAD()
-    }
-
-    if (params.fusioncatcher || params.all) {
-        FUSIONCATCHER_DOWNLOAD()
-    }
-
-    if (params.starfusion || params.all) {
-        if (params.starfusion_build){
-            val_species = Channel.value("human")
-            ch_fusion_annot_lib = params.fusion_annot_lib
-            STARFUSION_BUILD( ENSEMBL_DOWNLOAD.out.primary_assembly, ENSEMBL_DOWNLOAD.out.gtf, ch_fusion_annot_lib, val_species)
-        } else {
-            STARFUSION_DOWNLOAD()
-        }
-    }
-
-    if (params.starfusion_build){
-        UCSC_GTFTOGENEPRED(ENSEMBL_DOWNLOAD.out.chrgtf)
-    } else {
-        UCSC_GTFTOGENEPRED(STARFUSION_DOWNLOAD.out.chrgtf)
-    }
-    if (params.fusionreport || params.all) {
-        FUSIONREPORT_DOWNLOAD()
-    }
-
-}
-
-/*
-========================================================================================
-    THE END
-========================================================================================
-*/
diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf
index 74315e84..857827aa 100644
--- a/workflows/rnafusion.nf
+++ b/workflows/rnafusion.nf
@@ -3,7 +3,10 @@
     IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-include { TRIM_WORKFLOW                 }   from '../subworkflows/local/trim_workflow'
+
+include { BUILD_REFERENCES              }   from '../subworkflows/local/build_references'
+include { CAT_FASTQ                     }   from '../modules/nf-core/cat/fastq/main'
+include { TRIM_WORKFLOW                 }   from '../subworkflows/local/trim_workflow/main'
 include { ARRIBA_WORKFLOW               }   from '../subworkflows/local/arriba_workflow'
 include { QC_WORKFLOW                   }   from '../subworkflows/local/qc_workflow'
 include { STARFUSION_WORKFLOW           }   from '../subworkflows/local/starfusion_workflow'
@@ -11,15 +14,14 @@ include { STRINGTIE_WORKFLOW            }   from '../subworkflows/local/stringti
 include { FUSIONCATCHER_WORKFLOW        }   from '../subworkflows/local/fusioncatcher_workflow'
 include { FUSIONINSPECTOR_WORKFLOW      }   from '../subworkflows/local/fusioninspector_workflow'
 include { FUSIONREPORT_WORKFLOW         }   from '../subworkflows/local/fusionreport_workflow'
+include { FASTQC                        }   from '../modules/nf-core/fastqc/main'
+include { MULTIQC                       }   from '../modules/nf-core/multiqc/main'
+include { SALMON_QUANT                  }   from '../modules/nf-core/salmon/quant/main'
+include { paramsSummaryMap              }   from 'plugin/nf-schema'
+include { paramsSummaryMultiqc          }   from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML        }   from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText        }   from '../subworkflows/local/utils_nfcore_rnafusion_pipeline'
 include { validateInputSamplesheet      }   from '../subworkflows/local/utils_nfcore_rnafusion_pipeline'
-include { CAT_FASTQ              } from '../modules/nf-core/cat/fastq/main'
-include { FASTQC                 } from '../modules/nf-core/fastqc/main'
-include { MULTIQC                } from '../modules/nf-core/multiqc/main'
-include { SALMON_QUANT           } from '../modules/nf-core/salmon/quant/main'
-include { paramsSummaryMap       } from 'plugin/nf-schema'
-include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_rnafusion_pipeline'
 
 
 /*
@@ -30,6 +32,7 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_rnaf
 
 workflow RNAFUSION {
 
+
     take:
     ch_samplesheet // channel: samplesheet read in from --input
 
@@ -38,48 +41,38 @@ workflow RNAFUSION {
     def ch_versions = Channel.empty()
     def ch_multiqc_files = Channel.empty()
 
-    def ch_chrgtf                     = params.starfusion_build ? Channel.fromPath(params.chrgtf).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_annot.gtf").map { it -> [[id:it.Name], it] }.collect()
-    def ch_starindex_ref              = params.starfusion_build ? Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_genome.fa.star.idx").map { it -> [[id:it.Name], it] }.collect()
-    def ch_starindex_ensembl_ref      = Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect()
-    def ch_refflat                    = params.starfusion_build ? Channel.fromPath(params.refflat).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.gtf.refflat").map { it -> [[id:it.Name], it] }.collect()
-    def ch_rrna_interval              = params.starfusion_build ?  Channel.fromPath(params.rrna_intervals).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.interval_list").map { it -> [[id:it.Name], it] }.collect()
-    def ch_adapter_fastp              = params.adapter_fasta ? Channel.fromPath(params.adapter_fasta, checkIfExists: true) : Channel.empty()
-    def ch_fusionreport_ref           = Channel.fromPath(params.fusionreport_ref).map { it -> [[id:it.Name], it] }.collect()
-    def ch_arriba_ref_blacklist       = Channel.fromPath(params.arriba_ref_blacklist).map { it -> [[id:it.Name], it] }.collect()
-    def ch_arriba_ref_known_fusions   = Channel.fromPath(params.arriba_ref_known_fusions).map { it -> [[id:it.Name], it] }.collect()
-    def ch_arriba_ref_protein_domains = Channel.fromPath(params.arriba_ref_protein_domains).map { it -> [[id:it.Name], it] }.collect()
-    def ch_arriba_ref_cytobands       = Channel.fromPath(params.arriba_ref_cytobands).map { it -> [[id:it.Name], it] }.collect()
-    def ch_hgnc_ref                   = Channel.fromPath(params.hgnc_ref).map { it -> [[id:it.Name], it] }.collect()
-    def ch_hgnc_date                  = Channel.fromPath(params.hgnc_date).map { it -> [[id:it.Name], it] }.collect()
-    def ch_fasta                      = Channel.fromPath(params.fasta).map { it -> [[id:it.Name], it] }.collect()
-    def ch_gtf                        = Channel.fromPath(params.gtf).map { it -> [[id:it.Name], it] }.collect()
-    def ch_salmon_index               = Channel.fromPath(params.salmon_index).map { it -> [[id:it.Name], it] }.collect()
-    def ch_transcript                 = Channel.fromPath(params.transcript).map { it -> [[id:it.Name], it] }.collect()
-    def ch_fai                        = Channel.fromPath(params.fai).map { it -> [[id:it.Name], it] }.collect()
-    def ch_starfusion_ref             = Channel.fromPath(params.starfusion_ref).map { it -> [[id:it.name], it]}.collect()
+    //
+    // Create references if necessary
+    //
+
+    BUILD_REFERENCES()
+    ch_versions = ch_versions.mix(BUILD_REFERENCES.out.versions)
+
 
     //
-    // MODULE: Run FastQC
+    // QC from FASTQ files
     //
     FASTQC (
         ch_samplesheet
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
-    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
-
+    ch_versions = ch_versions.mix(FASTQC.out.versions)
 
 
+    //
+    // Trimming
+    //
     TRIM_WORKFLOW (
         ch_samplesheet,
-        ch_adapter_fastp,
+        Channel.value(params.adapter_fasta),
         params.fastp_trim
     )
-    ch_reads_fusioncatcher = TRIM_WORKFLOW.out.ch_reads_fusioncatcher
-    ch_reads_all           = TRIM_WORKFLOW.out.ch_reads_all
-    ch_versions            = ch_versions.mix(TRIM_WORKFLOW.out.versions)
+    ch_reads = TRIM_WORKFLOW.out.ch_reads_all
+    ch_versions = ch_versions.mix(TRIM_WORKFLOW.out.versions)
 
-
-    SALMON_QUANT( ch_reads_all, ch_salmon_index.map{ meta, index ->  index  }, ch_gtf.map{ meta, gtf ->  gtf  }, [], false, 'A')
+    SALMON_QUANT( ch_reads, BUILD_REFERENCES.out.ch_salmon_index.map{ it -> it[1] }, BUILD_REFERENCES.out.ch_gtf.map{ it -> it[1] }, [], false, 'A')
+    ch_multiqc_files = ch_multiqc_files.mix(SALMON_QUANT.out.json_info.collect{it[1]})
+    ch_versions = ch_versions.mix(SALMON_QUANT.out.versions)
 
 
     //
@@ -87,19 +80,19 @@ workflow RNAFUSION {
     //
 
     // TODO: add params.seq_platform and pass it as argument to arriba_workflow
-    // TODO: improve how params.arriba_fusions would avoid running arriba module. Maybe inputed from samplesheet?
+    // TODO: improve how params.arriba_fusions would avoid running arriba module. Maybe imputed from samplesheet?
     // TODO: same as above, but with ch_arriba_fusion_fail. It's currently replaces by a dummy file
 
     ARRIBA_WORKFLOW (
-        ch_reads_all,
-        ch_gtf,
-        ch_fasta,
-        ch_starindex_ensembl_ref,
-        ch_arriba_ref_blacklist,
-        ch_arriba_ref_known_fusions,
-        ch_arriba_ref_cytobands,
-        ch_arriba_ref_protein_domains,
-        ch_starfusion_ref,
+        ch_reads,
+        BUILD_REFERENCES.out.ch_gtf,
+        BUILD_REFERENCES.out.ch_fasta,
+        BUILD_REFERENCES.out.ch_starindex_ref,
+        BUILD_REFERENCES.out.ch_arriba_ref_blacklist,
+        BUILD_REFERENCES.out.ch_arriba_ref_cytobands,
+        BUILD_REFERENCES.out.ch_arriba_ref_known_fusions,
+        BUILD_REFERENCES.out.ch_arriba_ref_protein_domains,
+        BUILD_REFERENCES.out.ch_starfusion_ref,
         params.arriba,                   // boolean
         params.all,                      // boolean
         params.fusioninspector_only,     // boolean
@@ -114,18 +107,18 @@ workflow RNAFUSION {
 
     //Run STAR fusion
     STARFUSION_WORKFLOW (
-        ch_reads_all,
-        ch_chrgtf,
-        ch_starindex_ref,
-        ch_fasta,
-        ch_starfusion_ref
+        ch_reads,
+        BUILD_REFERENCES.out.ch_gtf,
+        BUILD_REFERENCES.out.ch_starindex_ref,
+        BUILD_REFERENCES.out.ch_fasta,
+        BUILD_REFERENCES.out.ch_starfusion_ref
     )
     ch_versions = ch_versions.mix(STARFUSION_WORKFLOW.out.versions)
 
 
     //Run fusioncatcher
     FUSIONCATCHER_WORKFLOW (
-        ch_reads_fusioncatcher
+        ch_reads
     )
     ch_versions = ch_versions.mix(FUSIONCATCHER_WORKFLOW.out.versions)
 
@@ -133,15 +126,15 @@ workflow RNAFUSION {
     //Run stringtie
     STRINGTIE_WORKFLOW (
         STARFUSION_WORKFLOW.out.ch_bam_sorted,
-        ch_chrgtf
+        BUILD_REFERENCES.out.ch_gtf
     )
     ch_versions = ch_versions.mix(STRINGTIE_WORKFLOW.out.versions)
 
 
     //Run fusion-report
     FUSIONREPORT_WORKFLOW (
-        ch_reads_all,
-        ch_fusionreport_ref,
+        ch_reads,
+        BUILD_REFERENCES.out.ch_fusionreport_ref,
         ARRIBA_WORKFLOW.out.fusions,
         STARFUSION_WORKFLOW.out.fusions,
         FUSIONCATCHER_WORKFLOW.out.fusions
@@ -150,17 +143,17 @@ workflow RNAFUSION {
 
     //Run fusionInpector
     FUSIONINSPECTOR_WORKFLOW (
-        ch_reads_all,
+        ch_reads,
         FUSIONREPORT_WORKFLOW.out.fusion_list,
         FUSIONREPORT_WORKFLOW.out.fusion_list_filtered,
         FUSIONREPORT_WORKFLOW.out.report,
         FUSIONREPORT_WORKFLOW.out.csv,
         STARFUSION_WORKFLOW.out.ch_bam_sorted_indexed,
-        ch_chrgtf,
-        ch_arriba_ref_protein_domains,
-        ch_arriba_ref_cytobands,
-        ch_hgnc_ref,
-        ch_hgnc_date
+        BUILD_REFERENCES.out.ch_gtf,
+        BUILD_REFERENCES.out.ch_arriba_ref_protein_domains,
+        BUILD_REFERENCES.out.ch_arriba_ref_cytobands,
+        BUILD_REFERENCES.out.ch_hgnc_ref,
+        BUILD_REFERENCES.out.ch_hgnc_date
     )
     ch_versions = ch_versions.mix(FUSIONINSPECTOR_WORKFLOW.out.versions)
 
@@ -168,26 +161,25 @@ workflow RNAFUSION {
     //QC
     QC_WORKFLOW (
         STARFUSION_WORKFLOW.out.ch_bam_sorted,
-        ch_chrgtf,
-        ch_refflat,
-        ch_fasta,
-        ch_fai,
-        ch_rrna_interval
+        BUILD_REFERENCES.out.ch_refflat,
+        BUILD_REFERENCES.out.ch_fasta,
+        BUILD_REFERENCES.out.ch_fai,
+        BUILD_REFERENCES.out.ch_rrna_interval
     )
     ch_versions = ch_versions.mix(QC_WORKFLOW.out.versions)
 
-
     //
     // Collate and save software versions
     //
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_'  + 'pipeline_software_' +  'mqc_'  + 'versions.yml',
+            name: 'nf_core_pipeline_software_mqc_versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }
 
+
     //
     // MODULE: MultiQC
     //