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d1794d1934
* added template for tiddit/cov * test finished * quick fix to meta info * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * applying suggestions Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
52 lines
1.4 KiB
YAML
52 lines
1.4 KiB
YAML
name: tiddit_cov
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description: Computes the coverage of different regions from the bam file.
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keywords:
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- coverage
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- bam
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- statistics
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- chromosomal rearrangements
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tools:
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- tiddit:
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description: TIDDIT - structural variant calling.
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homepage: https://github.com/SciLifeLab/TIDDIT
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documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md
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doi: "10.12688/f1000research.11168.1"
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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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- fasta:
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type: file
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description: |
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Reference genome file. Only needed when passing in CRAM instead of BAM.
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If not using CRAM, please pass an empty file instead.
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pattern: "*.fasta"
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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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- cov:
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type: file
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description: The coverage of different regions. Optional.
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pattern: "*.tab"
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- wig:
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type: file
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description: The coverage of different regions in WIG format. Optional.
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pattern: "*.wig"
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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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- "@projectoriented"
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