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meta.yml
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meta.yml
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name: picard_markduplicates
description: Locate and tag duplicate reads in a BAM file
keywords:
- markduplicates
- pcr
- duplicates
- bam
- sam
- cram
tools:
- picard:
description: |
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
data and formats such as SAM/BAM/CRAM and VCF.
homepage: https://broadinstitute.github.io/picard/
documentation: https://broadinstitute.github.io/picard/
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file
pattern: "*.{bam,cram,sam}"
- fasta:
type: file
description: Reference genome fasta file
pattern: "*.{fasta,fa}"
- fai:
type: file
description: Reference genome fasta index
pattern: "*.{fai}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file with duplicate reads marked/removed
pattern: "*.{bam}"
- bai:
type: file
description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag
pattern: "*.{bai}"
- metrics:
type: file
description: Duplicate metrics file generated by picard
pattern: "*.{metrics.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@drpatelh"
- "@projectoriented"