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add BaseRecalibrator plot to MultiQC report #87

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Merged
maxulysse merged 1 commit into from
Jan 27, 2020
Merged

add BaseRecalibrator plot to MultiQC report #87

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
### `Added`

- [#76](https://github.com/nf-core/sarek/pull/76) - Add `GATK Spark` possibilities to Sarek
- [#87](https://github.com/nf-core/sarek/pull/87) - Add `GATK BaseRecalibrator` plot to `MultiQC` report

### `Changed`

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1 change: 1 addition & 0 deletions assets/multiqc_config.yaml
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Expand Up @@ -15,6 +15,7 @@ export_plots: true
top_modules:
- 'fastqc'
- 'picard'
- 'gatk'
- 'samtools'
- 'qualimap'
- 'bcftools'
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2 changes: 2 additions & 0 deletions main.nf
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Expand Up @@ -1103,6 +1103,7 @@ process GatherBQSRReports {

output:
set idPatient, idSample, file("${idSample}.recal.table") into recalTable
file("${idSample}.recal.table") into baseRecalibratorReport
set idPatient, idSample into recalTableTSV

when: !(params.no_intervals)
Expand Down Expand Up @@ -2985,6 +2986,7 @@ process MultiQC {
file ('BCFToolsStats/*') from bcftoolsReport.collect().ifEmpty([])
file ('FastQC/*') from fastQCReport.collect().ifEmpty([])
file ('MarkDuplicates/*') from markDuplicatesReport.collect().ifEmpty([])
file ('DuplicateMarked/*.recal.table') from baseRecalibratorReport.collect().ifEmpty([])
file ('SamToolsStats/*') from samtoolsStatsReport.collect().ifEmpty([])
file ('snpEff/*') from snpeffReport.collect().ifEmpty([])
file ('VCFTools/*') from vcftoolsReport.collect().ifEmpty([])
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