From 96cc533c5fc95baea653499f56f2ce6290eb512c Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 6 Sep 2023 13:42:17 +0200
Subject: [PATCH 01/14] remove sorting and indexing of star_for_arriba bam,
 changing filenames

---
 conf/modules.config                   |  5 ++++-
 subworkflows/local/arriba_workflow.nf | 18 ++++++++----------
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 4bee29b3..a13d8b10 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -210,7 +210,7 @@ process {
     }
 
     withName: SAMTOOLS_SORT_FOR_ARRIBA {
-        ext.prefix = { "${meta.id}_sorted" }
+        ext.prefix = { "${meta.id}_star_for_arriba_sorted" }
         publishDir = [
             path: { "${params.outdir}/samtools_sort_for_arriba" },
             mode: params.publish_dir_mode,
@@ -229,6 +229,7 @@ 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,
@@ -248,6 +249,7 @@ process {
 
     withName: SAMTOOLS_VIEW_FOR_SQUID_CRAM {
         ext.args = { "--output-fmt cram" }
+        ext.prefix = { "${meta.id}_star_for_squid_sorted" }
         publishDir = [
             path: { "${params.outdir}/cram_squid" },
             mode: params.publish_dir_mode,
@@ -267,6 +269,7 @@ process {
 
     withName: SAMTOOLS_VIEW_FOR_STARFUSION {
         ext.args = { "--output-fmt cram" }
+        ext.prefix = { "${meta.id}_star_for_starfusion_sorted" }
         publishDir = [
             path: { "${params.outdir}/cram_starfusion" },
             mode: params.publish_dir_mode,
diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf
index 9f770190..114e64ba 100644
--- a/subworkflows/local/arriba_workflow.nf
+++ b/subworkflows/local/arriba_workflow.nf
@@ -23,16 +23,7 @@ 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 +36,16 @@ workflow ARRIBA_WORKFLOW {
             }
 
             if (params.cram.contains('arriba') ){
+                // 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.map { meta, bam -> [ meta, bam, [] ] }
+
                 SAMTOOLS_VIEW_FOR_ARRIBA(bam_indexed, ch_fasta, [])
                 ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_ARRIBA.out.versions )
-
             }
 
 

From 2bf946a05344a2e7f1ede4eba374d74cb9bfb945 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 6 Sep 2023 15:46:11 +0200
Subject: [PATCH 02/14] add filename changes

---
 conf/modules.config                       | 5 +++--
 modules/local/fusionreport/detect/main.nf | 1 +
 subworkflows/local/arriba_workflow.nf     | 9 +--------
 3 files changed, 5 insertions(+), 10 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index a13d8b10..6ff57e26 100644
--- a/conf/modules.config
+++ b/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,
@@ -269,7 +270,7 @@ process {
 
     withName: SAMTOOLS_VIEW_FOR_STARFUSION {
         ext.args = { "--output-fmt cram" }
-        ext.prefix = { "${meta.id}_star_for_starfusion_sorted" }
+        ext.prefix = { "${meta.id}.star_for_starfusion.Aligned.sortedByCoord.out" }
         publishDir = [
             path: { "${params.outdir}/cram_starfusion" },
             mode: params.publish_dir_mode,
diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf
index 0b18c34a..3d5853a7 100644
--- a/modules/local/fusionreport/detect/main.nf
+++ b/modules/local/fusionreport/detect/main.nf
@@ -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
 
diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf
index 114e64ba..3255d6d9 100644
--- a/subworkflows/local/arriba_workflow.nf
+++ b/subworkflows/local/arriba_workflow.nf
@@ -36,15 +36,8 @@ workflow ARRIBA_WORKFLOW {
             }
 
             if (params.cram.contains('arriba') ){
-                // 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.map { meta, bam -> [ meta, bam, [] ] }
-
-                SAMTOOLS_VIEW_FOR_ARRIBA(bam_indexed, ch_fasta, [])
+                SAMTOOLS_VIEW_FOR_ARRIBA(SAMTOOLS_SORT_FOR_ARRIBA.out.bam.map { meta, bam -> [ meta, bam, [] ] }, ch_fasta, [])
                 ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_ARRIBA.out.versions )
             }
 

From 7cc05672c4489d4ec2c8d09f395d6d380dacbdfb Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 6 Sep 2023 16:51:27 +0200
Subject: [PATCH 03/14] fix arriba cram from bam used in arriba

---
 subworkflows/local/arriba_workflow.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf
index 3255d6d9..5bbd7ea2 100644
--- a/subworkflows/local/arriba_workflow.nf
+++ b/subworkflows/local/arriba_workflow.nf
@@ -37,7 +37,7 @@ workflow ARRIBA_WORKFLOW {
 
             if (params.cram.contains('arriba') ){
 
-                SAMTOOLS_VIEW_FOR_ARRIBA(SAMTOOLS_SORT_FOR_ARRIBA.out.bam.map { meta, bam -> [ meta, bam, [] ] }, ch_fasta, [])
+                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 )
             }
 

From 4ff060eb227e10de39e67f495337138b10f1d4d8 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 6 Sep 2023 16:57:50 +0200
Subject: [PATCH 04/14] remove specification for unused modules

---
 conf/modules.config                   | 19 +------------------
 subworkflows/local/arriba_workflow.nf |  2 --
 2 files changed, 1 insertion(+), 20 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 6ff57e26..29d28a9f 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -186,14 +186,6 @@ 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" },
@@ -202,7 +194,7 @@ process {
         ]
     }
 
-        withName: SAMTOOLS_FAIDX {
+    withName: SAMTOOLS_FAIDX {
         publishDir = [
             path: { "${params.genomes_base}/ensembl" },
             mode: params.publish_dir_mode,
@@ -210,15 +202,6 @@ process {
         ]
     }
 
-    withName: SAMTOOLS_SORT_FOR_ARRIBA {
-        ext.prefix = { "${meta.id}_star_for_arriba_sorted" }
-        publishDir = [
-            path: { "${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 = [
diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf
index 5bbd7ea2..36c3924f 100644
--- a/subworkflows/local/arriba_workflow.nf
+++ b/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'
 

From d61601a53f00b58fad920e8b4c826883601d732d Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 6 Sep 2023 16:58:59 +0200
Subject: [PATCH 05/14] change regex to emit fusionreport index

---
 modules/local/fusionreport/detect/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf
index 3d5853a7..e3ea5149 100644
--- a/modules/local/fusionreport/detect/main.nf
+++ b/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

From cae8374a9c5754d21a1fdb542cffded3d728cd12 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Fri, 8 Sep 2023 10:21:10 +0200
Subject: [PATCH 06/14] update changelog

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e57f2ea6..854e8bba 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed
 
+- Removed trimmed fastqc report from multiqc [#394](https://github.com/nf-core/rnafusion/pull/394)
+
 ## v2.3.0 = [2022/04/24]
 
 ### Added

From 9ce149c305c3742029fb2c3f9c265682c36e1461 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Fri, 8 Sep 2023 10:44:54 +0200
Subject: [PATCH 07/14] reverse squid change

---
 conf/modules.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 29d28a9f..911fe292 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -233,7 +233,6 @@ process {
 
     withName: SAMTOOLS_VIEW_FOR_SQUID_CRAM {
         ext.args = { "--output-fmt cram" }
-        ext.prefix = { "${meta.id}_star_for_squid_sorted" }
         publishDir = [
             path: { "${params.outdir}/cram_squid" },
             mode: params.publish_dir_mode,

From 57337c237b28f49622e269c8fcf27cb4529d90a4 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Fri, 8 Sep 2023 10:48:42 +0200
Subject: [PATCH 08/14] update changelog

---
 CHANGELOG.md | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 854e8bba..056aa71e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,7 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed
 
-- Removed trimmed fastqc report from multiqc [#394](https://github.com/nf-core/rnafusion/pull/394)
+- `samtools sort` and `samtools index` for `arriba` workflow were dispensable and were removed [#395](https://github.com/nf-core/rnafusion/pull/395)
 
 ## v2.3.0 = [2022/04/24]
 
@@ -39,6 +39,11 @@ 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
+- Renaming [#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
 
 ### Fixed
 

From e639142012ce4fda6f29c3107d84f1cbe78dc960 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 13 Sep 2023 14:47:33 +0200
Subject: [PATCH 09/14] Update CHANGELOG.md

Co-authored-by: Eva C <29628428+fevac@users.noreply.github.com>
---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5b48c16e..21d68689 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -41,7 +41,7 @@ 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
-- Renaming [#395](https://github.com/nf-core/rnafusion/pull/395)
+- 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

From 061589ba23d622538dc2f7d2c82461982ee1168f Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 13 Sep 2023 16:12:22 +0200
Subject: [PATCH 10/14] add missing fusionreport stub and changelog update for
 previous PR

---
 CHANGELOG.md                              | 1 +
 modules/local/fusionreport/detect/main.nf | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 21d68689..fa68a69e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ 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)
 
 ### Fixed
 
diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf
index e3ea5149..20db8c2f 100644
--- a/modules/local/fusionreport/detect/main.nf
+++ b/modules/local/fusionreport/detect/main.nf
@@ -53,7 +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

From b4e2461f843674d15e696cea54d534aa5b5a5825 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 13 Sep 2023 16:21:50 +0200
Subject: [PATCH 11/14] update megafusion output to _fusion_data.vcf

---
 CHANGELOG.md        | 1 +
 conf/modules.config | 1 +
 2 files changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fa68a69e..f26e61d6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -47,6 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - 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
 
diff --git a/conf/modules.config b/conf/modules.config
index 911fe292..b4dc96d6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -143,6 +143,7 @@ process {
     }
     withName: MEGAFUSION {
         ext.when = {!params.fusioninspector_only}
+        ext.prefix = { "${meta.id}_fusion_data" }
     }
 
 

From 91f65d0c8a5f8f3a068052ccf59a81c923f4d2e1 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 13 Sep 2023 16:25:16 +0200
Subject: [PATCH 12/14] prettify

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f26e61d6..f94b2031 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -47,7 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - 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
+  - meta.id.vcf output from `MEGAFUSION` to meta.id_fusion_data.vcf
 
 ### Fixed
 

From c715953599fa43f4beaea3b7e5bc5518df44010f Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 13 Sep 2023 16:28:19 +0200
Subject: [PATCH 13/14] update modules from nf-core, update picard
 collectrnametrics container

---
 modules.json                                  |  4 +--
 .../local/picard/collectrnaseqmetrics/main.nf |  6 ++--
 modules/nf-core/fastqc/tests/main.nf.test     | 32 +++++++++++++++++++
 modules/nf-core/picard/markduplicates/main.nf |  4 +++
 4 files changed, 41 insertions(+), 5 deletions(-)
 create mode 100644 modules/nf-core/fastqc/tests/main.nf.test

diff --git a/modules.json b/modules.json
index 38ba9c33..162a71b5 100644
--- a/modules.json
+++ b/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": {
diff --git a/modules/local/picard/collectrnaseqmetrics/main.nf b/modules/local/picard/collectrnaseqmetrics/main.nf
index 5651c6c1..af0b8958 100644
--- a/modules/local/picard/collectrnaseqmetrics/main.nf
+++ b/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)
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
new file mode 100644
index 00000000..3961de60
--- /dev/null
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test Process FASTQC"
+    script "modules/nf-core/fastqc/main.nf"
+    process "FASTQC"
+    tag "fastqc"
+
+    test("Single-Read") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', single_end:true ],
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html"
+            assert path(process.out.html.get(0).get(1)).getText().contains("<tr><td>File type</td><td>Conventional base calls</td></tr>")
+            assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip"
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf
index facd7efb..ebfa0864 100644
--- a/modules/nf-core/picard/markduplicates/main.nf
+++ b/modules/nf-core/picard/markduplicates/main.nf
@@ -30,6 +30,9 @@ process PICARD_MARKDUPLICATES {
     } else {
         avail_mem = (task.memory.mega*0.8).intValue()
     }
+
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+
     """
     picard \\
         -Xmx${avail_mem}M \\
@@ -48,6 +51,7 @@ process PICARD_MARKDUPLICATES {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     touch ${prefix}.bam
     touch ${prefix}.bam.bai

From 5ee433c70a93ca98034ea5d72c118eabb65c7909 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 13 Sep 2023 16:34:33 +0200
Subject: [PATCH 14/14] update changelog with picard update

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f94b2031..b61486da 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 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