nf-core_modules/software/mosdepth/meta.yml

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2021-02-15 13:33:44 +00:00
name: mosdepth
description: Calculates genome-wide sequencing coverage.
keywords:
- mosdepth
- bam
- cram
- coverage
tools:
- mosdepth:
description: |
Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
documentation: https://github.com/brentp/mosdepth
doi: 10.1093/bioinformatics/btx699
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.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Input BAM/CRAM file
pattern: "*.{bam,cram}"
- bai:
type: file
description: Index for BAM/CRAM file
pattern: "*.{bai,crai}"
- bed:
type: file
description: BED file with intersected intervals
pattern: "*.{bed}"
- window_size:
type: integer
description: Window size
pattern: "[0-9]+"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- global_txt:
type: file
description: Text file with global cumulative coverage distribution
pattern: "*.{global.dist.txt}"
- regions_txt:
type: file
description: Text file with region cumulative coverage distribution
pattern: "*.{region.dist.txt}"
- summary_txt:
type: file
description: Text file with summary mean depths per chromosome and regions
pattern: "*.{summary.txt}"
- per_base_bed:
type: file
description: BED file with per-base coverage
pattern: "*.{per-base.bed.gz}"
- per_base_csi:
type: file
description: Index file for BED file with per-base coverage
pattern: "*.{per-base.bed.gz.csi}"
- regions_bed:
type: file
description: BED file with per-region coverage
pattern: "*.{regions.bed.gz}"
- regions_csi:
type: file
description: Index file for BED file with per-region coverage
pattern: "*.{regions.bed.gz.csi}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@joseespinosa"
- "@drpatelh"