From 3328c76087df70afbc0edf5eea568286e00ba9ff Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 27 Nov 2023 16:51:58 +0100 Subject: [PATCH 1/6] update version to 4.0.0 --- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 6e00ca8c..5930000d 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnafusion + This report has been generated by the nf-core/rnafusion analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: nf-core-rnafusion-methods-description: diff --git a/nextflow.config b/nextflow.config index 7570a93b..34f47361 100644 --- 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 = '4.0.0dev' doi = '' } From 279daf42c6f84f26e067ff0f466511fbc4a33ecf Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 27 Nov 2023 16:53:03 +0100 Subject: [PATCH 2/6] prepare changelog for 4.0.0 --- CHANGELOG.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 75d0ce76..08b1132f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,16 @@ 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). +## v4.0.0 - [date] + +### Added + +### Changed + +### Fixed + +### Removed + ## v3.0.0 - [2023-11-27] ### Added From bb271bbf508a7b6a4998e978c6a4cd659ccfb64c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 29 Nov 2023 12:03:09 +0100 Subject: [PATCH 3/6] fix versions --- modules/local/fusioncatcher/detect/main.nf | 4 ++-- subworkflows/local/arriba_workflow.nf | 2 +- subworkflows/local/fusioncatcher_workflow.nf | 3 ++- .../local/fusioninspector_workflow.nf | 2 +- subworkflows/local/fusionreport_workflow.nf | 2 +- subworkflows/local/qc_workflow.nf | 2 +- subworkflows/local/starfusion_workflow.nf | 2 +- subworkflows/local/stringtie_workflow.nf | 4 +++- subworkflows/local/trim_workflow.nf | 2 +- workflows/rnafusion.nf | 20 +++++++++---------- 10 files changed, 23 insertions(+), 20 deletions(-) diff --git a/modules/local/fusioncatcher/detect/main.nf b/modules/local/fusioncatcher/detect/main.nf index fa072bf4..2977d668 100644 --- 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/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf index 3aa9c090..f59018dc 100644 --- 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 index a9058dc6..ebb09e60 100644 --- 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 index 48fcc19f..7a31d7cd 100644 --- 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 index 632ba2a3..09ec9965 100644 --- 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 index 576701e5..6b53358a 100644 --- 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 index 38264c01..ec7a832c 100644 --- 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 index 93a50e0c..60bd4f38 100644 --- 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 index 61cce26f..ea21134d 100644 --- 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 index 8319b49e..992f72fc 100644 --- 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 @@ -187,14 +187,14 @@ 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 @@ -202,7 +202,7 @@ workflow RNAFUSION { 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') From d264cead3a30c347fafbeeb2ade9dc339b9aa2c2 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 29 Nov 2023 14:16:36 +0100 Subject: [PATCH 4/6] update changelog --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 08b1132f..e68ff0df 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## v4.0.0 - [date] +## v3.0.1 - [2023-11-29] ### Added @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### 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] From 226b24a3db3eddc33e8a55fd481539a222b034f0 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 29 Nov 2023 14:22:00 +0100 Subject: [PATCH 5/6] update version to 3.0.1 --- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 5930000d..dd83ce70 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnafusion + This report has been generated by the nf-core/rnafusion analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: nf-core-rnafusion-methods-description: diff --git a/nextflow.config b/nextflow.config index 34f47361..3a54be0c 100644 --- 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 = '4.0.0dev' + version = '3.0.1' doi = '' } From 35cb3feb7fbf8afe3511e3c28ef2618b9e96fd58 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 29 Nov 2023 14:28:54 +0100 Subject: [PATCH 6/6] - --- CHANGELOG.md | 2 ++ bin/vcf_collect.py | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 08b1132f..70b6b9eb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed +- python3 explicit in vcf_collect [#452](https://github.com/nf-core/rnafusion/pull/452) + ### Fixed ### Removed diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 2401d2e8..a8ab85f4 100755 --- 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