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fix logical gate: when stringtie and not starfusion, only alignment i… #482

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merged 4 commits into from
Apr 3, 2024
Merged

fix logical gate: when stringtie and not starfusion, only alignment i… #482

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3ab9344
fix logical gate: when stringtie and not starfusion, only alignment i…
rannick Apr 3, 2024
6a36c3e
fix conda package requirements
rannick Apr 3, 2024
d506c69
update changelog
rannick Apr 3, 2024
88a3540
Merge branch 'dev' into fix_stringtie_log_gate
rannick Apr 3, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -18,6 +18,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- fix VCF_COLLECT handling when a tool is absent from FUSIONREPORT report [#458](https://github.com/nf-core/rnafusion/pull/458)
- fix VCF_COLLECT when fusioninspector output is empty but fusionreport is not [#465](https://github.com/nf-core/rnafusion/pull/465)
- fix VCF_COLLECT bug [#481](https://github.com/nf-core/rnafusion/pull/481)
- fix conda package for starfusion/detect[#482](https://github.com/nf-core/rnafusion/pull/482)
- fix logical gate so when stringtie should run but not starfusion, starfusion will not run[#482](https://github.com/nf-core/rnafusion/pull/482)

### Removed

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2 changes: 1 addition & 1 deletion modules/local/starfusion/detect/main.nf
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Expand Up @@ -2,7 +2,7 @@ process STARFUSION {
tag "$meta.id"
label 'process_high'

conda "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.12.0 bioconda::=2.13.2 bioconda::samtools=1.9 bioconda::star=2.7.8a"
conda "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.12.0 bioconda::trinity=2.13.2 bioconda::samtools=1.9 bioconda::star=2.7.8a"
container 'docker.io/trinityctat/starfusion:1.12.0'

input:
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11 changes: 6 additions & 5 deletions subworkflows/local/starfusion_workflow.nf
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Expand Up @@ -30,6 +30,7 @@ workflow STARFUSION_WORKFLOW {
SAMTOOLS_INDEX_FOR_STARFUSION(STAR_FOR_STARFUSION.out.bam_sorted)
ch_versions = ch_versions.mix(SAMTOOLS_INDEX_FOR_STARFUSION.out.versions)
bam_sorted_indexed = STAR_FOR_STARFUSION.out.bam_sorted.join(SAMTOOLS_INDEX_FOR_STARFUSION.out.bai)
reads_junction = reads.join(STAR_FOR_STARFUSION.out.junction )

if (params.cram.contains('starfusion')){
SAMTOOLS_VIEW_FOR_STARFUSION (bam_sorted_indexed, ch_fasta, [] )
Expand All @@ -38,12 +39,12 @@ workflow STARFUSION_WORKFLOW {
SAMTOOLS_INDEX_FOR_STARFUSION_CRAM (SAMTOOLS_VIEW_FOR_STARFUSION.out.cram)
ch_versions = ch_versions.mix(SAMTOOLS_INDEX_FOR_STARFUSION_CRAM.out.versions)
}
reads_junction = reads.join(STAR_FOR_STARFUSION.out.junction )

STARFUSION( reads_junction, params.starfusion_ref)
ch_versions = ch_versions.mix(STARFUSION.out.versions)
if (params.starfusion || params.all){
STARFUSION( reads_junction, params.starfusion_ref)
ch_versions = ch_versions.mix(STARFUSION.out.versions)
ch_starfusion_fusions = STARFUSION.out.fusions
}

ch_starfusion_fusions = STARFUSION.out.fusions
ch_star_stats = STAR_FOR_STARFUSION.out.log_final
ch_star_gene_count = STAR_FOR_STARFUSION.out.read_per_gene_tab
}
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