2020-08-07 15:30:28 +00:00
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name: picard_markduplicates
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description: Locate and tag duplicate reads in a BAM file
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keywords:
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- markduplicates
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- pcr
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- duplicates
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- bam
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- sam
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- cram
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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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2020-10-15 10:13:54 +00:00
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- enable_conda:
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2020-08-07 15:30:28 +00:00
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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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2020-12-14 00:34:24 +00:00
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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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2020-08-07 15:30:28 +00:00
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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: BAM file
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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: BAM file with duplicate reads marked/removed
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pattern: "*.{bam}"
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- metrics:
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type: file
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description: Duplicate metrics file generated by picard
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pattern: "*.{metrics.txt}"
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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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