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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
46 lines
1.3 KiB
YAML
46 lines
1.3 KiB
YAML
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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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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