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meta.yml
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meta.yml
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name: "bam_markduplicates_picard"
description: Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats
keywords:
- markduplicates
- bam
- sam
- cram
modules:
- picard/markduplicates
- samtools/index
- samtools/stats
- samtools/idxstats
- samtools/flagstat
input:
- ch_bam:
description: |
BAM/CRAM/SAM file
Structure: [ val(meta), path(bam) ]
- ch_fasta:
description: |
Reference genome fasta file
Structure: [ path(fasta) ]
- ch_fasta:
description: |
Index of the reference genome fasta file
Structure: [ path(fai) ]
output:
- bam:
description: |
processed BAM/CRAM/SAM file
Structure: [ val(meta), path(bam) ]
- bai:
description: |
BAM/CRAM/SAM samtools index
Structure: [ val(meta), path(bai) ]
- csi:
description: |
CSI samtools index
Structure: [ val(meta), path(csi) ]
- stats:
description: |
File containing samtools stats output
Structure: [ val(meta), path(stats) ]
- flagstat:
description: |
File containing samtools flagstat output
Structure: [ val(meta), path(flagstat) ]
- idxstats:
description: |
File containing samtools idxstats output
Structure: [ val(meta), path(idxstats) ]
- versions:
description: |
Files containing software versions
Structure: [ path(versions.yml) ]
authors:
- "@dmarron"
- "@drpatelh"