mirror of
https://github.com/MillironX/nf-core_modules.git
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97 lines
2.9 KiB
YAML
97 lines
2.9 KiB
YAML
name: mosdepth
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description: Calculates genome-wide sequencing coverage.
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keywords:
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- mosdepth
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- bam
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- cram
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- coverage
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tools:
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- mosdepth:
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description: |
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Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
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documentation: https://github.com/brentp/mosdepth
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doi: 10.1093/bioinformatics/btx699
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: Input BAM/CRAM file
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pattern: "*.{bam,cram}"
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- bai:
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type: file
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description: Index for BAM/CRAM file
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pattern: "*.{bai,crai}"
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- bed:
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type: file
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description: BED file with intersected intervals
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pattern: "*.{bed}"
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- window_size:
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type: integer
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description: Window size
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pattern: "[0-9]+"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- global_txt:
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type: file
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description: Text file with global cumulative coverage distribution
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pattern: "*.{global.dist.txt}"
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- regions_txt:
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type: file
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description: Text file with region cumulative coverage distribution
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pattern: "*.{region.dist.txt}"
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- summary_txt:
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type: file
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description: Text file with summary mean depths per chromosome and regions
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pattern: "*.{summary.txt}"
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- per_base_bed:
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type: file
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description: BED file with per-base coverage
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pattern: "*.{per-base.bed.gz}"
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- per_base_csi:
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type: file
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description: Index file for BED file with per-base coverage
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pattern: "*.{per-base.bed.gz.csi}"
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- regions_bed:
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type: file
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description: BED file with per-region coverage
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pattern: "*.{regions.bed.gz}"
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- regions_csi:
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type: file
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description: Index file for BED file with per-region coverage
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pattern: "*.{regions.bed.gz.csi}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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