Use 20.07-RC1, add skip_qc to MD #252
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maxulysse
reviewed
Jul 22, 2020
| include { MERGE_BAM_MAPPED } from './modules/local/merge_mapped_bam' addParams(params) | ||
| include { MARK_DUPLICATES } from './modules/local/mark_duplicates' params(params) | ||
| include { MERGE_BAM_MAPPED } from './modules/local/merge_mapped_bam' | ||
| include { MARK_DUPLICATES } from './modules/local/mark_duplicates' addParams(skip_qc: skip_qc) |
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I see, now I understand better
maxulysse
reviewed
Jul 22, 2020
modules/local/mark_duplicates.nf
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| @@ -11,7 +11,7 @@ process MARK_DUPLICATES { | |||
| output: | |||
| tuple idPatient, idSample, path("${idSample}.md.bam"), path("${idSample}.md.bam.bai"), emit: bam_duplicates_marked | |||
| tuple idPatient, idSample, emit: tsv_bam_duplicates_marked | |||
| path "${idSample}.bam.metrics", emit: duplicates_marked_report //is optional , applies when skip_qc is used(not implemented yet) | |||
| path "${idSample}.bam.metrics", optional : true, emit: duplicates_marked_report //is optional , applies when skip_qc is used(not implemented yet) | |||
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Actually we will need to rename this option.
you can't actually skip markduplicates with skip_qc, but you actually don't keep the report.
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Ah, I see. So maybe skip_markduplicates_report and make it an extra parameter not included in the skip_qc list?
maxulysse
approved these changes
Jul 22, 2020
|
@maxulysse I am done adding things to this PR. Sorry, I wanted to add the new nextflow.enable thing and then had to fix some things after that |
maxulysse
reviewed
Jul 22, 2020
| @@ -12,7 +12,7 @@ jobs: | |||
| strategy: | |||
| matrix: | |||
| # Nextflow versions: check pipeline minimum and current latest | |||
| nxf_ver: ['20.04.1', ''] | |||
| nxf_ver: ['20.07.0-RC1', ''] | |||
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Can you update the README.md too?
maxulysse
approved these changes
Jul 22, 2020
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