Merge pull request #453 from nf-core/dev

Release 3.0.1
nf-core · Nov 29, 2023 · 98f02be · 98f02be
2 parents f5ecf8d + 0d189d2
commit 98f02be
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,20 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v3.0.1 - [2023-11-29]
+
+### Added
+
+### Changed
+
+- python3 explicit in vcf_collect [#452](https://github.com/nf-core/rnafusion/pull/452)
+
+### Fixed
+
+- software-version.yml and in general version track-keeping was incomplete [#451](https://github.com/nf-core/rnafusion/pull/451)
+
+### Removed
+
 ## v3.0.0 - [2023-11-27]
 
 ### Added

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/rnafusion/releases/tag/3.0.0" target="_blank">nf-core/rnafusion</a>
+  This report has been generated by the <a href="https://github.com/nf-core/rnafusion/releases/tag/3.0.1" target="_blank">nf-core/rnafusion</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/rnafusion/3.0.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/rnafusion/3.0.1/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   nf-core-rnafusion-methods-description:

diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import argparse
 import logging

diff --git a/modules/local/fusioncatcher/detect/main.nf b/modules/local/fusioncatcher/detect/main.nf
@@ -39,7 +39,7 @@ process FUSIONCATCHER {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        fusioncatcher: \$(echo \$(fusioncatcher --version 2>&1)| sed 's/fusioncatcher.py //')
+        fusioncatcher: \$(echo \$(fusioncatcher.py --version 2>&1)| sed 's/fusioncatcher.py //')
     END_VERSIONS
     """
 
@@ -52,7 +52,7 @@ process FUSIONCATCHER {
     touch ${prefix}.fusioncatcher.log
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        fusioncatcher: \$(echo \$(fusioncatcher --version 2>&1)| sed 's/fusioncatcher.py //')
+        fusioncatcher: \$(echo \$(fusioncatcher.py --version 2>&1)| sed 's/fusioncatcher.py //')
     END_VERSIONS
     """
 }
diff --git a/nextflow.config b/nextflow.config
@@ -290,7 +290,7 @@ manifest {
     description     = """Nextflow rnafusion analysis pipeline, part of the nf-core community."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version = '3.0.0'
+    version = '3.0.1'
     doi             = ''
 }
 

diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf
@@ -59,6 +59,6 @@ workflow ARRIBA_WORKFLOW {
     emit:
         fusions         = ch_arriba_fusions
         fusions_fail    = ch_arriba_fusion_fail
-        versions        = ch_versions.ifEmpty(null)
+        versions        = ch_versions
     }
 
diff --git a/subworkflows/local/fusioncatcher_workflow.nf b/subworkflows/local/fusioncatcher_workflow.nf
@@ -19,6 +19,7 @@ workflow FUSIONCATCHER_WORKFLOW {
                     params.fusioncatcher_ref
                 )
                 ch_fusioncatcher_fusions = FUSIONCATCHER.out.fusions
+                ch_versions = ch_versions.mix(FUSIONCATCHER.out.versions)
             }
         }
         else {
@@ -28,6 +29,6 @@ workflow FUSIONCATCHER_WORKFLOW {
 
     emit:
         fusions  = ch_fusioncatcher_fusions
-        versions = ch_versions.ifEmpty(null)
+        versions = ch_versions
     }
 
diff --git a/subworkflows/local/fusioninspector_workflow.nf b/subworkflows/local/fusioninspector_workflow.nf
@@ -60,6 +60,6 @@ workflow FUSIONINSPECTOR_WORKFLOW {
 
     emit:
         ch_arriba_visualisation
-        versions             = ch_versions.ifEmpty(null)
+        versions             = ch_versions
 }
 
diff --git a/subworkflows/local/fusionreport_workflow.nf b/subworkflows/local/fusionreport_workflow.nf
@@ -34,7 +34,7 @@ workflow FUSIONREPORT_WORKFLOW {
         }
 
     emit:
-        versions                 = ch_versions.ifEmpty(null)
+        versions                 = ch_versions
         fusion_list              = ch_fusion_list
         fusion_list_filtered     = ch_fusion_list_filtered
         report                   = ch_report.ifEmpty(null)

diff --git a/subworkflows/local/qc_workflow.nf b/subworkflows/local/qc_workflow.nf
@@ -33,7 +33,7 @@ workflow QC_WORKFLOW {
 
 
     emit:
-        versions            = ch_versions.ifEmpty(null)
+        versions            = ch_versions
         rnaseq_metrics      = ch_rnaseq_metrics
         duplicate_metrics   = ch_duplicate_metrics
         insertsize_metrics  = ch_insertsize_metrics

diff --git a/subworkflows/local/starfusion_workflow.nf b/subworkflows/local/starfusion_workflow.nf
@@ -60,7 +60,7 @@ workflow STARFUSION_WORKFLOW {
         star_gene_count       = ch_star_gene_count
         ch_bam_sorted         = ch_align.ifEmpty([[],[]])
         ch_bam_sorted_indexed = bam_sorted_indexed.ifEmpty([[],[],[]])
-        versions              = ch_versions.ifEmpty(null)
+        versions              = ch_versions
 
     }
 
diff --git a/subworkflows/local/stringtie_workflow.nf b/subworkflows/local/stringtie_workflow.nf
@@ -20,6 +20,8 @@ workflow STRINGTIE_WORKFLOW {
                 .transcript_gtf
                 .map { it -> it[1] }
                 .set { stringtie_gtf }
+            ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions)
+
 
             STRINGTIE_MERGE (stringtie_gtf, ch_chrgtf.map { meta, gtf -> [ gtf ]})
             ch_versions = ch_versions.mix(STRINGTIE_MERGE.out.versions)
@@ -28,7 +30,7 @@ workflow STRINGTIE_WORKFLOW {
 
     emit:
         stringtie_gtf = ch_stringtie_gtf.ifEmpty(null)
-        versions      = ch_versions.ifEmpty(null)
+        versions      = ch_versions
 
     }
 
diff --git a/subworkflows/local/trim_workflow.nf b/subworkflows/local/trim_workflow.nf
@@ -37,6 +37,6 @@ workflow TRIM_WORKFLOW {
         ch_fastp_html
         ch_fastp_json
         ch_fastqc_trimmed
-        versions      = ch_versions.ifEmpty(null)
+        versions = ch_versions
     }
 
diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf
@@ -149,7 +149,7 @@ workflow RNAFUSION {
     .reads
     .mix(ch_fastq.single)
     .set { ch_cat_fastq }
-    ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
 
 
     //
@@ -158,14 +158,14 @@ workflow RNAFUSION {
     FASTQC (
         ch_cat_fastq
     )
-    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+    ch_versions = ch_versions.mix(FASTQC.out.versions)
 
     TRIM_WORKFLOW (
         ch_cat_fastq
     )
     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)
 
     // Run STAR alignment and Arriba
     ARRIBA_WORKFLOW (
@@ -177,7 +177,7 @@ workflow RNAFUSION {
         ch_arriba_ref_known_fusions,
         ch_arriba_ref_protein_domains
     )
-    ch_versions = ch_versions.mix(ARRIBA_WORKFLOW.out.versions.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(ARRIBA_WORKFLOW.out.versions)
 
 
 //Run STAR fusion
@@ -187,22 +187,22 @@ workflow RNAFUSION {
         ch_starindex_ref,
         ch_fasta
     )
-    ch_versions = ch_versions.mix(STARFUSION_WORKFLOW.out.versions.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(STARFUSION_WORKFLOW.out.versions)
 
 
 //Run fusioncatcher
     FUSIONCATCHER_WORKFLOW (
         ch_reads_fusioncatcher
     )
-    ch_versions = ch_versions.mix(FUSIONCATCHER_WORKFLOW.out.versions.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(FUSIONCATCHER_WORKFLOW.out.versions)
 
 
 //Run stringtie
     STRINGTIE_WORKFLOW (
         STARFUSION_WORKFLOW.out.ch_bam_sorted,
         ch_chrgtf
     )
-    ch_versions = ch_versions.mix(STRINGTIE_WORKFLOW.out.versions.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(STRINGTIE_WORKFLOW.out.versions)
 
 
     //Run fusion-report
@@ -213,7 +213,7 @@ workflow RNAFUSION {
         STARFUSION_WORKFLOW.out.fusions,
         FUSIONCATCHER_WORKFLOW.out.fusions
     )
-    ch_versions = ch_versions.mix(FUSIONREPORT_WORKFLOW.out.versions.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(FUSIONREPORT_WORKFLOW.out.versions)
 
 
     //Run fusionInpector
@@ -230,7 +230,7 @@ workflow RNAFUSION {
         ch_hgnc_ref,
         ch_hgnc_date
     )
-    ch_versions = ch_versions.mix(FUSIONINSPECTOR_WORKFLOW.out.versions.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(FUSIONINSPECTOR_WORKFLOW.out.versions)
 
 
     //QC
@@ -243,7 +243,7 @@ workflow RNAFUSION {
         ch_fai,
         ch_rrna_interval
     )
-    ch_versions = ch_versions.mix(QC_WORKFLOW.out.versions.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(QC_WORKFLOW.out.versions)
 
     CUSTOM_DUMPSOFTWAREVERSIONS (
         ch_versions.unique().collectFile(name: 'collated_versions.yml')