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Merge branch 'dev' into python3
2 parents 35cb3fe + 754d7c6 commit 1c86d07

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‎CHANGELOG.md

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@@ -3,7 +3,7 @@
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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6-
## v4.0.0 - [date]
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## v3.0.1 - [2023-11-29]
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### Added
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@@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### Fixed
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- software-version.yml and in general version track-keeping was incomplete [#451](https://github.com/nf-core/rnafusion/pull/451)
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### Removed
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## v3.0.0 - [2023-11-27]

‎assets/multiqc_config.yml

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@@ -1,7 +1,7 @@
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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/rnafusion/releases/tag/dev" target="_blank">nf-core/rnafusion</a>
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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>
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analysis pipeline. For information about how to interpret these results, please see the
4-
<a href="https://nf-co.re/rnafusion/dev/docs/output" target="_blank">documentation</a>.
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<a href="https://nf-co.re/rnafusion/3.0.1/docs/output" target="_blank">documentation</a>.
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report_section_order:
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nf-core-rnafusion-methods-description:

‎modules/local/fusioncatcher/detect/main.nf

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@@ -39,7 +39,7 @@ process FUSIONCATCHER {
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fusioncatcher: \$(echo \$(fusioncatcher --version 2>&1)| sed 's/fusioncatcher.py //')
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fusioncatcher: \$(echo \$(fusioncatcher.py --version 2>&1)| sed 's/fusioncatcher.py //')
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END_VERSIONS
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"""
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@@ -52,7 +52,7 @@ process FUSIONCATCHER {
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touch ${prefix}.fusioncatcher.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fusioncatcher: \$(echo \$(fusioncatcher --version 2>&1)| sed 's/fusioncatcher.py //')
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fusioncatcher: \$(echo \$(fusioncatcher.py --version 2>&1)| sed 's/fusioncatcher.py //')
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END_VERSIONS
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"""
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}

‎nextflow.config

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@@ -290,7 +290,7 @@ manifest {
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description = """Nextflow rnafusion analysis pipeline, part of the nf-core community."""
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mainScript = 'main.nf'
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nextflowVersion = '!>=23.04.0'
293-
version = '4.0.0dev'
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version = '3.0.1'
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doi = ''
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}
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‎subworkflows/local/arriba_workflow.nf

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@@ -59,6 +59,6 @@ workflow ARRIBA_WORKFLOW {
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emit:
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fusions = ch_arriba_fusions
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fusions_fail = ch_arriba_fusion_fail
62-
versions = ch_versions.ifEmpty(null)
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versions = ch_versions
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}
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‎subworkflows/local/fusioncatcher_workflow.nf

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@@ -19,6 +19,7 @@ workflow FUSIONCATCHER_WORKFLOW {
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params.fusioncatcher_ref
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)
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ch_fusioncatcher_fusions = FUSIONCATCHER.out.fusions
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ch_versions = ch_versions.mix(FUSIONCATCHER.out.versions)
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}
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}
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else {
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emit:
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fusions = ch_fusioncatcher_fusions
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versions = ch_versions.ifEmpty(null)
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versions = ch_versions
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}
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‎subworkflows/local/fusioninspector_workflow.nf

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@@ -60,6 +60,6 @@ workflow FUSIONINSPECTOR_WORKFLOW {
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emit:
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ch_arriba_visualisation
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versions = ch_versions.ifEmpty(null)
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versions = ch_versions
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}
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‎subworkflows/local/fusionreport_workflow.nf

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@@ -34,7 +34,7 @@ workflow FUSIONREPORT_WORKFLOW {
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}
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emit:
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versions = ch_versions.ifEmpty(null)
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versions = ch_versions
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fusion_list = ch_fusion_list
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fusion_list_filtered = ch_fusion_list_filtered
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report = ch_report.ifEmpty(null)

‎subworkflows/local/qc_workflow.nf

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@@ -33,7 +33,7 @@ workflow QC_WORKFLOW {
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emit:
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versions = ch_versions.ifEmpty(null)
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versions = ch_versions
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rnaseq_metrics = ch_rnaseq_metrics
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duplicate_metrics = ch_duplicate_metrics
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insertsize_metrics = ch_insertsize_metrics

‎subworkflows/local/starfusion_workflow.nf

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@@ -60,7 +60,7 @@ workflow STARFUSION_WORKFLOW {
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star_gene_count = ch_star_gene_count
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ch_bam_sorted = ch_align.ifEmpty([[],[]])
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ch_bam_sorted_indexed = bam_sorted_indexed.ifEmpty([[],[],[]])
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versions = ch_versions.ifEmpty(null)
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versions = ch_versions
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}
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‎subworkflows/local/stringtie_workflow.nf

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@@ -20,6 +20,8 @@ workflow STRINGTIE_WORKFLOW {
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.transcript_gtf
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.map { it -> it[1] }
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.set { stringtie_gtf }
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ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions)
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STRINGTIE_MERGE (stringtie_gtf, ch_chrgtf.map { meta, gtf -> [ gtf ]})
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ch_versions = ch_versions.mix(STRINGTIE_MERGE.out.versions)
@@ -28,7 +30,7 @@ workflow STRINGTIE_WORKFLOW {
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emit:
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stringtie_gtf = ch_stringtie_gtf.ifEmpty(null)
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versions = ch_versions.ifEmpty(null)
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versions = ch_versions
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}
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‎subworkflows/local/trim_workflow.nf

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@@ -37,6 +37,6 @@ workflow TRIM_WORKFLOW {
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ch_fastp_html
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ch_fastp_json
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ch_fastqc_trimmed
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versions = ch_versions.ifEmpty(null)
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versions = ch_versions
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}
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‎workflows/rnafusion.nf

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@@ -149,7 +149,7 @@ workflow RNAFUSION {
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.reads
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.mix(ch_fastq.single)
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.set { ch_cat_fastq }
152-
ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null))
152+
ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
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//
@@ -158,14 +158,14 @@ workflow RNAFUSION {
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FASTQC (
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ch_cat_fastq
160160
)
161-
ch_versions = ch_versions.mix(FASTQC.out.versions.first())
161+
ch_versions = ch_versions.mix(FASTQC.out.versions)
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163163
TRIM_WORKFLOW (
164164
ch_cat_fastq
165165
)
166166
ch_reads_fusioncatcher = TRIM_WORKFLOW.out.ch_reads_fusioncatcher
167167
ch_reads_all = TRIM_WORKFLOW.out.ch_reads_all
168-
168+
ch_versions = ch_versions.mix(TRIM_WORKFLOW.out.versions)
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// Run STAR alignment and Arriba
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ARRIBA_WORKFLOW (
@@ -177,7 +177,7 @@ workflow RNAFUSION {
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ch_arriba_ref_known_fusions,
178178
ch_arriba_ref_protein_domains
179179
)
180-
ch_versions = ch_versions.mix(ARRIBA_WORKFLOW.out.versions.first().ifEmpty(null))
180+
ch_versions = ch_versions.mix(ARRIBA_WORKFLOW.out.versions)
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//Run STAR fusion
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187187
ch_starindex_ref,
188188
ch_fasta
189189
)
190-
ch_versions = ch_versions.mix(STARFUSION_WORKFLOW.out.versions.first().ifEmpty(null))
190+
ch_versions = ch_versions.mix(STARFUSION_WORKFLOW.out.versions)
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//Run fusioncatcher
194194
FUSIONCATCHER_WORKFLOW (
195195
ch_reads_fusioncatcher
196196
)
197-
ch_versions = ch_versions.mix(FUSIONCATCHER_WORKFLOW.out.versions.first().ifEmpty(null))
197+
ch_versions = ch_versions.mix(FUSIONCATCHER_WORKFLOW.out.versions)
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//Run stringtie
201201
STRINGTIE_WORKFLOW (
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STARFUSION_WORKFLOW.out.ch_bam_sorted,
203203
ch_chrgtf
204204
)
205-
ch_versions = ch_versions.mix(STRINGTIE_WORKFLOW.out.versions.first().ifEmpty(null))
205+
ch_versions = ch_versions.mix(STRINGTIE_WORKFLOW.out.versions)
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//Run fusion-report
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STARFUSION_WORKFLOW.out.fusions,
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FUSIONCATCHER_WORKFLOW.out.fusions
215215
)
216-
ch_versions = ch_versions.mix(FUSIONREPORT_WORKFLOW.out.versions.first().ifEmpty(null))
216+
ch_versions = ch_versions.mix(FUSIONREPORT_WORKFLOW.out.versions)
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//Run fusionInpector
@@ -230,7 +230,7 @@ workflow RNAFUSION {
230230
ch_hgnc_ref,
231231
ch_hgnc_date
232232
)
233-
ch_versions = ch_versions.mix(FUSIONINSPECTOR_WORKFLOW.out.versions.first().ifEmpty(null))
233+
ch_versions = ch_versions.mix(FUSIONINSPECTOR_WORKFLOW.out.versions)
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236236
//QC
@@ -243,7 +243,7 @@ workflow RNAFUSION {
243243
ch_fai,
244244
ch_rrna_interval
245245
)
246-
ch_versions = ch_versions.mix(QC_WORKFLOW.out.versions.first().ifEmpty(null))
246+
ch_versions = ch_versions.mix(QC_WORKFLOW.out.versions)
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248248
CUSTOM_DUMPSOFTWAREVERSIONS (
249249
ch_versions.unique().collectFile(name: 'collated_versions.yml')

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