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61 lines
1.9 KiB
YAML
61 lines
1.9 KiB
YAML
name: picard_mergesamfiles
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description: Merges multiple BAM files into a single file
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keywords:
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- merge
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- alignment
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- bam
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- sam
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tools:
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- picard:
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description: |
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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
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data and formats such as SAM/BAM/CRAM and VCF.
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homepage: https://broadinstitute.github.io/picard/
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documentation: https://broadinstitute.github.io/picard/
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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: List of BAM files
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pattern: "*.{bam}"
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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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- bam:
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type: file
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description: Merged BAM file
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pattern: "*.{bam}"
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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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- "@drpatelh"
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