nf-core_modules/software/picard/collectmultiplemetrics/meta.yml

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name: picard_collectmultiplemetrics
description: Collect multiple metrics from a BAM file
keywords:
- alignment
- metrics
- statistics
- insert
- 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/
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
2020-10-15 10:13:54 +00:00
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
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}"
- fasta:
type: file
description: Genome fasta file
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- metrics:
type: file
description: Alignment metrics files generated by picard
pattern: "*_{metrics}"
- pdf:
type: file
description: PDF plots of metrics
pattern: "*.{pdf}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@drpatelh"