Merge branch 'dev' into fix_fusionreport_download

nf-core · Aug 30, 2023 · eb81ba0 · eb81ba0
2 parents bc10b08 + 49fd35a
commit eb81ba0
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Showing 5 changed files with 15 additions and 25 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - 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)
 
 ### Fixed
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -187,24 +187,15 @@ process {
 
     withName: SAMTOOLS_INDEX_FOR_ARRIBA {
         publishDir = [
-            path: { "${params.outdir}/samtools_index_for_arriba" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: SAMTOOLS_INDEX_FOR_QC {
-        ext.when         = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all)}
-        publishDir = [
-            path: { "${params.outdir}/samtools_index_for_qc" },
+            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: { "${params.outdir}/samtools_index_for_starfusion" },
+            path: { "${params.outdir}/star_for_starfusion" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]

diff --git a/subworkflows/local/qc_workflow.nf b/subworkflows/local/qc_workflow.nf
@@ -3,13 +3,13 @@
 //
 
 include { QUALIMAP_RNASEQ }                            from '../../modules/nf-core/qualimap/rnaseq/main'
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_FOR_QC }    from '../../modules/nf-core/samtools/index/main'
 include { PICARD_COLLECTRNASEQMETRICS }                from '../../modules/local/picard/collectrnaseqmetrics/main'
 include { PICARD_MARKDUPLICATES }                      from '../../modules/nf-core/picard/markduplicates/main'
 
 workflow QC_WORKFLOW {
     take:
-        bam_sorted
+        ch_bam_sorted
+        ch_bam_sorted_indexed
         ch_chrgtf
         ch_refflat
         ch_fasta
@@ -19,20 +19,15 @@ workflow QC_WORKFLOW {
     main:
         ch_versions = Channel.empty()
 
-        QUALIMAP_RNASEQ(bam_sorted, ch_chrgtf)
+        QUALIMAP_RNASEQ(ch_bam_sorted, ch_chrgtf)
         ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions)
         ch_qualimap_qc = Channel.empty().mix(QUALIMAP_RNASEQ.out.results)
 
-        SAMTOOLS_INDEX_FOR_QC(bam_sorted)
-        ch_versions = ch_versions.mix(SAMTOOLS_INDEX_FOR_QC.out.versions)
-
-        bam_indexed = bam_sorted.join(SAMTOOLS_INDEX_FOR_QC.out.bai)
-
-        PICARD_COLLECTRNASEQMETRICS(bam_indexed, ch_refflat, ch_rrna_interval)
+        PICARD_COLLECTRNASEQMETRICS(ch_bam_sorted_indexed, ch_refflat, ch_rrna_interval)
         ch_versions = ch_versions.mix(PICARD_COLLECTRNASEQMETRICS.out.versions)
         ch_rnaseq_metrics = Channel.empty().mix(PICARD_COLLECTRNASEQMETRICS.out.metrics)
 
-        PICARD_MARKDUPLICATES(bam_sorted, ch_fasta, ch_fai)
+        PICARD_MARKDUPLICATES(ch_bam_sorted, ch_fasta, ch_fai)
         ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions)
         ch_duplicate_metrics = Channel.empty().mix(PICARD_MARKDUPLICATES.out.metrics)
 

diff --git a/subworkflows/local/starfusion_workflow.nf b/subworkflows/local/starfusion_workflow.nf
@@ -51,8 +51,9 @@ workflow STARFUSION_WORKFLOW {
     emit:
         fusions               = ch_starfusion_fusions
         star_stats            = ch_star_stats
-        bam_sorted            = ch_align
+        ch_bam_sorted         = ch_align.ifEmpty([[],[]])
+        ch_bam_sorted_indexed = bam_sorted_indexed.ifEmpty([[],[],[]])
         versions              = ch_versions.ifEmpty(null)
-        ch_bam_sorted_indexed = bam_sorted_indexed.ifEmpty(null)
+
     }
 
diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf
@@ -220,7 +220,7 @@ workflow RNAFUSION {
 
 //Run stringtie
     STRINGTIE_WORKFLOW (
-        STARFUSION_WORKFLOW.out.bam_sorted,
+        STARFUSION_WORKFLOW.out.ch_bam_sorted,
         ch_chrgtf
     )
     ch_versions = ch_versions.mix(STRINGTIE_WORKFLOW.out.versions.first().ifEmpty(null))
@@ -255,7 +255,8 @@ workflow RNAFUSION {
 
     //QC
     QC_WORKFLOW (
-        STARFUSION_WORKFLOW.out.bam_sorted,
+        STARFUSION_WORKFLOW.out.ch_bam_sorted,
+        STARFUSION_WORKFLOW.out.ch_bam_sorted_indexed,
         ch_chrgtf,
         ch_refflat,
         ch_fasta,