nf-core_modules/modules/picard/collecthsmetrics/meta.yml

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name: picard_collecthsmetrics
description: Collects hybrid-selection (HS) metrics for a SAM or BAM file.
keywords:
- alignment
- metrics
- statistics
- insert
- hybrid-selection
- quality
- bam
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/
tool_dev_url: https://github.com/broadinstitute/picard/
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: An aligned BAM/SAM file
pattern: "*.{bam,sam}"
- fasta:
type: file
description: |
A reference file to calculate dropout metrics measuring reduced representation of reads.
Optional input.
pattern: "*.fasta"
- fai:
type: file
description: Index of FASTA file. Only needed when fasta is supplied.
pattern: "*.fai"
- bait_intervals:
type: file
description: An interval list file that contains the locations of the baits used.
pattern: "baits.interval_list"
- target_intervals:
type: file
description: An interval list file that contains the locations of the targets.
pattern: "targets.interval_list"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- hs_metrics:
type: file
description: The metrics file.
pattern: "*_collecthsmetrics.txt"
authors:
- "@projectoriented"