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04e82ec61a
* First version of the biobambam/bammarkduplicates2 module * Fixed the path of versions.yml * Regenerated the checksums as the previous files were generated with a single core * Added the `when:` block, as per #1261 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
44 lines
1.3 KiB
YAML
44 lines
1.3 KiB
YAML
name: biobambam_bammarkduplicates2
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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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- bam
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- cram
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tools:
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- biobambam:
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description: |
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biobambam is a set of tools for early stage alignment file processing.
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homepage: https://gitlab.com/german.tischler/biobambam2
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documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
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doi: 10.1186/1751-0473-9-13
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licence: ['GPL v3']
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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/CRAM file
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pattern: "*.{bam,cram}"
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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 biobambam
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pattern: "*.{metrics.txt}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@muffato"
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