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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
44 lines
1.2 KiB
YAML
44 lines
1.2 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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