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Merge pull request #650 from maxulysse/dev_intervals_checks
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fix intervals checks
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FriederikeHanssen authored Jul 18, 2022
2 parents 45aab1c + 6f481bb commit c43ef33
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Showing 3 changed files with 4 additions and 5 deletions.
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -138,6 +138,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#618](https://github.com/nf-core/sarek/pull/618) - Fix channel issue with `targets.bed` in prepare_intervals
- [#634](https://github.com/nf-core/sarek/pull/634) - Fix issue with samtools/mosdepth plots in multiqc_report
- [#641](https://github.com/nf-core/sarek/pull/641) - Fix issue with duplicate substring in tools and skip_tools
- [#650](https://github.com/nf-core/sarek/pull/650) - Fix intervals checks

### Deprecated

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1 change: 1 addition & 0 deletions conf/test.config
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Expand Up @@ -54,6 +54,7 @@ profiles {
params.step = 'annotate'
}
no_intervals {
params.intervals = null
params.no_intervals = true
}
pair {
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7 changes: 2 additions & 5 deletions workflows/sarek.nf
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Expand Up @@ -57,11 +57,8 @@ ch_input_sample = extract_csv(file(params.input, checkIfExists: true))
// Fails when wrongfull extension for intervals file
if (params.wes && !params.step == 'annotate') {
if (params.intervals && !params.intervals.endsWith("bed")) exit 1, "Target file specified with `--intervals` must be in BED format for targeted data"
} else {
log.warn("Interval file was provided without parameter `--wes`: Pipeline will assume this is Whole-genome-sequencing data.")

if (params.intervals && !params.intervals.endsWith("bed") && !params.intervals.endsWith("interval_list")) exit 1, "Interval file must end with .bed or .interval_list"
}
else log.warn("Intervals file was provided without parameter `--wes`: Pipeline will assume this is Whole-Genome-Sequencing data.")
} else if (params.intervals && !params.intervals.endsWith("bed") && !params.intervals.endsWith("interval_list")) exit 1, "Intervals file must end with .bed or .interval_list"

// Fails or warns when missing files or params for ascat
if(params.tools && params.tools.split(',').contains('ascat')){
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