Dsl2 #263
Dsl2 #263
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Still working on it, but managed to fix so far:
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| pon = params.pon ? file(params.pon) : file("${params.outdir}/no_file") | ||
| snpeff_cache = params.snpeff_cache ? file(params.snpeff_cache) : file("${params.outdir}/no_file") | ||
| target_bed = params.target_bed ? file(params.target_bed) : file("${params.outdir}/no_file") | ||
| vep_cache = params.vep_cache ? file(params.vep_cache) : file("${params.outdir}/no_file") | ||
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Does the no_file folder then remain empty?
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I'm actually creating the no_file file a couple of lines before with:
file("${params.outdir}/no_file").text = "no_file\n"
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Ah ok, so actually just an empty file is used then?
| known_indels_tbi = params.known_indels ? params.known_indels_index ?: BUILD_INDICES.out.known_indels_tbi.collect() : Channel.empty() | ||
| pon_tbi = params.pon ? params.pon_index ?: BUILD_INDICES.out.pon_tbi : Channel.empty() | ||
| known_indels_tbi = params.known_indels ? params.known_indels_index ? file(params.known_indels_index) : BUILD_INDICES.out.known_indels_tbi.collect() : Channel.empty() | ||
| pon_tbi = params.pon ? params.pon_index ? file(params.pon_index) : BUILD_INDICES.out.pon_tbi : Channel.empty() | ||
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We should indent this at some point so it looks as nice as the rest :)
| //But if SAMTOOLS_INDEX is not run, markduplicates does not work | ||
| bam_mapped = SAMTOOLS_INDEX_MAPPED(bam_mapped) | ||
| //But if SAMTOOLS_INDEX is not run, markduplicates does not work | ||
| bam_mapped = SAMTOOLS_INDEX_MAPPED(bam_mapped) |
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This comment is obsolet with your fix, right?
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Wasn't sure about it, but probably
| @@ -464,31 +464,55 @@ workflow { | |||
| } | |||
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| GATHERBQSRREPORTS(recaltable) | |||
| // if ('baserecalibrator' in skip_qc) baseRecalibratorReport.close() | |||
| table = GATHERBQSRREPORTS.out.table | |||
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rename to bqsr_table?
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Yes, that's a good idea
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| if (!('bamqc' in skip_qc)) { | ||
| BAMQC(BWAMEM2_MEM.out.mix(recal), target_bed) | ||
| } |
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Maybe for consistency we could always set the output to a variable, so above somewhere bwamem2_out = BWAMEM2_MEM.out ..... Maybe a more descriptive variable name.
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That's a good idea too.
Maybe something like bwamem2_bam or mapped_bam
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