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4619d012e5
* Add CRAM support to allelecounter * Update meta.yml * Rename bam,bai to input,input_index * Apply suggestions from code review * Fix reference to renamed variable Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
55 lines
1.4 KiB
YAML
55 lines
1.4 KiB
YAML
name: allelecounter
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description: Generates a count of coverage of alleles
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keywords:
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- allele
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- count
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tools:
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- allelecounter:
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description: Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele at that location (given any filter settings)
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homepage: https://github.com/cancerit/alleleCount
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documentation: https://github.com/cancerit/alleleCount
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tool_dev_url: https://github.com/cancerit/alleleCount
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doi: ""
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licence: A-GPL 3.0
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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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- input:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- input_index:
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type: file
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description: BAM/CRAM/SAM index file
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pattern: "*.{bai,crai,sai}"
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- loci:
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type: file
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description: loci file <CHR><tab><POS1>
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pattern: "*.{tsv}"
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- fasta:
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type: file
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description: Input genome fasta file. Required when passing CRAM files.
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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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- 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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- alleleCount:
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type: file
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description: Allele count file
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pattern: "*.{alleleCount}"
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authors:
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- "@fullama"
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- "@fbdtemme"
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