Merge pull request #395 from nf-core/update_filenames

Update filenames

CHANGELOG.md

@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Use institutional configs by default [#381](https://github.com/nf-core/rnafusion/pull/381)
 - Remove redundant indexing in starfusion and qc workflows [#387](https://github.com/nf-core/rnafusion/pull/387)
 - Output bai files in same directory as bam files [#387](https://github.com/nf-core/rnafusion/pull/387)
+- Update and review documentation [#396](https://github.com/nf-core/rnafusion/pull/396)
+- Update picard container for `PICARD_COLLECTRNASEQMETRICS` to 3.0.0 [#395](https://github.com/nf-core/rnafusion/pull/395)
 
 ### Fixed
 
@@ -23,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed
 
+- `samtools sort` and `samtools index` for `arriba` workflow were dispensable and were removed [#395](https://github.com/nf-core/rnafusion/pull/395)
 - Removed trimmed fastqc report from multiqc [#394](https://github.com/nf-core/rnafusion/pull/394)
 
 ## v2.3.0 = [2022/04/24]
@@ -40,6 +43,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `Arriba` visualisation now runs for FusionInspector (combined tools) results, not only `Arriba` results
 - Updated metro map with trimming options and placed `Arriba` visualisation after `FusionInspector`
 - Exit with error when using squid in combination with any ensembl version different from 102
+- Renamed output files [#395](https://github.com/nf-core/rnafusion/pull/395)
+  - `Arriba` visualisation pdf from meta.id to meta.id_combined_fusions_arriba_visualisation
+  - cram file from output bam of `STAR_FOR_ARRIBA`: meta.id to meta.id_star_for_arriba
+  - cram file from output bam of `STAR_FOR_STARFUSION`: meta.id to meta.id.star_for_starfusion.Aligned.sortedByCoord.out
+  - `fusion-report` index.html file to meta.id_fusionreport_index.html
+  - meta.id.vcf output from `MEGAFUSION` to meta.id_fusion_data.vcf
 
 ### Fixed
 

conf/modules.config

@@ -36,7 +36,8 @@ 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" },
             mode: params.publish_dir_mode,
@@ -142,6 +143,7 @@ process {
     }
     withName: MEGAFUSION {
         ext.when = {!params.fusioninspector_only}
+        ext.prefix = { "${meta.id}_fusion_data" }
     }
 
 
@@ -185,14 +187,6 @@ process {
         ]
     }
 
-    withName: SAMTOOLS_INDEX_FOR_ARRIBA {
-        publishDir = [
-            path: { "${params.outdir}/star_for_arriba" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: SAMTOOLS_INDEX_FOR_STARFUSION {
         publishDir = [
             path: { "${params.outdir}/star_for_starfusion" },
@@ -201,23 +195,14 @@ process {
         ]
     }
 
-        withName: SAMTOOLS_FAIDX {
+    withName: SAMTOOLS_FAIDX {
         publishDir = [
             path: { "${params.genomes_base}/ensembl" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
-    withName: SAMTOOLS_SORT_FOR_ARRIBA {
-        ext.prefix = { "${meta.id}_sorted" }
-        publishDir = [
-            path: { "${params.outdir}/samtools_sort_for_arriba" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: SAMTOOLS_SORT_FOR_SQUID_CHIMERIC {
         ext.prefix = { "${meta.id}_chimeric_sorted" }
         publishDir = [
@@ -229,6 +214,7 @@ process {
 
     withName: SAMTOOLS_VIEW_FOR_ARRIBA {
         ext.args = { "--output-fmt cram" }
+        ext.prefix = { "${meta.id}_star_for_arriba" }
         publishDir = [
             path: { "${params.outdir}/cram_arriba" },
             mode: params.publish_dir_mode,
@@ -267,6 +253,7 @@ process {
 
     withName: SAMTOOLS_VIEW_FOR_STARFUSION {
         ext.args = { "--output-fmt cram" }
+        ext.prefix = { "${meta.id}.star_for_starfusion.Aligned.sortedByCoord.out" }
         publishDir = [
             path: { "${params.outdir}/cram_starfusion" },
             mode: params.publish_dir_mode,

modules.json

@@ -32,7 +32,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117",
+                        "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
                         "installed_by": ["modules"]
                     },
                     "gatk4/bedtointervallist": {
@@ -62,7 +62,7 @@
                     },
                     "picard/markduplicates": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448",
                         "installed_by": ["modules"]
                     },
                     "qualimap/rnaseq": {

modules/local/fusionreport/detect/main.nf

@@ -15,7 +15,7 @@ process FUSIONREPORT {
     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
@@ -37,6 +37,7 @@ process FUSIONREPORT {
 
     mv fusion_list.tsv ${prefix}.fusionreport.tsv
     mv fusion_list_filtered.tsv ${prefix}.fusionreport_filtered.tsv
+    mv index.html ${prefix}_fusionreport_index.html
     [ ! -f fusions.csv ] || mv fusions.csv ${prefix}.fusions.csv
     [ ! -f fusions.json ] || mv fusions.json ${prefix}.fusions.json
 
@@ -52,7 +53,7 @@ process FUSIONREPORT {
     """
     touch ${prefix}.fusionreport_filtered.tsv
     touch ${prefix}.fusionreport.tsv
-    touch index.html
+    touch ${prefix}_fusionreport_index.html
     touch AAA_BBB.html
     touch ${prefix}.fusions.csv
     touch ${prefix}.fusions.json

modules/local/picard/collectrnaseqmetrics/main.nf

@@ -2,10 +2,10 @@ process PICARD_COLLECTRNASEQMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=2.27.4"
+    conda "bioconda::picard=3.0.0 r::r-base"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
+        'biocontainers/picard:3.0.0--hdfd78af_1' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

subworkflows/local/arriba_workflow.nf

@@ -1,6 +1,4 @@
 include { ARRIBA }                                      from '../../modules/nf-core/arriba/main'
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_FOR_ARRIBA}  from '../../modules/nf-core/samtools/index/main'
-include { SAMTOOLS_SORT as SAMTOOLS_SORT_FOR_ARRIBA }   from '../../modules/nf-core/samtools/sort/main'
 include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_FOR_ARRIBA}    from '../../modules/nf-core/samtools/view/main'
 include { STAR_ALIGN as STAR_FOR_ARRIBA }               from '../../modules/nf-core/star/align/main'
 
@@ -23,16 +21,7 @@ workflow ARRIBA_WORKFLOW {
             STAR_FOR_ARRIBA( reads, ch_starindex_ref, ch_gtf, params.star_ignore_sjdbgtf, '', params.seq_center ?: '')
             ch_versions = ch_versions.mix(STAR_FOR_ARRIBA.out.versions)
 
-            SAMTOOLS_SORT_FOR_ARRIBA(STAR_FOR_ARRIBA.out.bam)
-            ch_versions = ch_versions.mix(SAMTOOLS_SORT_FOR_ARRIBA.out.versions)
-
-            SAMTOOLS_INDEX_FOR_ARRIBA(SAMTOOLS_SORT_FOR_ARRIBA.out.bam)
-            ch_versions = ch_versions.mix(SAMTOOLS_INDEX_FOR_ARRIBA.out.versions)
-
-            bam_indexed = SAMTOOLS_SORT_FOR_ARRIBA.out.bam.join(SAMTOOLS_INDEX_FOR_ARRIBA.out.bai)
-
             if (params.arriba_fusions) {
-                // [meta, reads], fusions -> [meta, fusions]
                 ch_arriba_fusions = reads.combine( Channel.value( file( params.arriba_fusions, checkIfExists: true ) ) )
                     .map { meta, reads, fusions -> [ meta, fusions ] }
                 ch_arriba_fusion_fail = ch_dummy_file
@@ -45,9 +34,9 @@ workflow ARRIBA_WORKFLOW {
             }
 
             if (params.cram.contains('arriba') ){
-                SAMTOOLS_VIEW_FOR_ARRIBA(bam_indexed, ch_fasta, [])
-                ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_ARRIBA.out.versions )
 
+                SAMTOOLS_VIEW_FOR_ARRIBA(STAR_FOR_ARRIBA.out.bam.map { meta, bam -> [ meta, bam, [] ] }, ch_fasta, [])
+                ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_ARRIBA.out.versions )
             }