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DRAFT: Allow any step but annotation to start from bam-files #654

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merged 4 commits into from
Jul 18, 2022
Merged

DRAFT: Allow any step but annotation to start from bam-files #654

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2b034da
Allow any step but annotation to start from bam-files
asp8200 Jul 18, 2022
93be3b0
Merge branch 'dev' into adjust_checks_step_plus_csv
asp8200 Jul 18, 2022
783b4d2
Updating changelog
asp8200 Jul 18, 2022
9be3c5c
Removing redundant blank line
asp8200 Jul 18, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -142,6 +142,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#641](https://github.com/nf-core/sarek/pull/641) - Fix issue with duplicate substring in tools and skip_tools
- [#642](https://github.com/nf-core/sarek/pull/642) - Only unzip ref files if tool is run, only publish ref files if `--save_reference` and simplify CNKit logic
- [#650](https://github.com/nf-core/sarek/pull/650) - Fix intervals checks
- [#654](https://github.com/nf-core/sarek/pull/654) - Allow any step but annotation to start from BAM files

### Deprecated

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4 changes: 2 additions & 2 deletions workflows/sarek.nf
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Expand Up @@ -1154,9 +1154,9 @@ def extract_csv(csv_file) {

meta.size = 1 // default number of splitted fastq

if (params.step == 'mapping') return [meta, bam, bai]
if (params.step != 'annotate') return [meta, bam, bai]
else {
log.error "Samplesheet contains ubam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations"
log.error "Samplesheet contains bam files but step is `annotate`. The pipeline is expecting vcf files for the annotation. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations"
System.exit(1)
}

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