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33 lines
1.1 KiB
Plaintext
33 lines
1.1 KiB
Plaintext
//
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// Run SAMtools stats, flagstat and idxstats
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//
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include { SAMTOOLS_STATS } from '../../../modules/samtools/stats/main'
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include { SAMTOOLS_IDXSTATS } from '../../../modules/samtools/idxstats/main'
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include { SAMTOOLS_FLAGSTAT } from '../../../modules/samtools/flagstat/main'
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workflow BAM_STATS_SAMTOOLS {
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take:
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bam_bai // channel: [ val(meta), [ bam/cram ], [bai/csi] ]
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fasta // channel: [ fasta ]
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main:
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ch_versions = Channel.empty()
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SAMTOOLS_STATS ( bam_bai, fasta )
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ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
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SAMTOOLS_FLAGSTAT ( bam_bai )
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ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions.first())
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SAMTOOLS_IDXSTATS ( bam_bai )
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ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions.first())
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emit:
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stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), [ stats ] ]
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flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), [ flagstat ] ]
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idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), [ idxstats ] ]
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versions = ch_versions // channel: [ versions.yml ]
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}
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