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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>
61 lines
1.5 KiB
YAML
61 lines
1.5 KiB
YAML
name: cmseq_polymut
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description: Calculates polymorphic site rates over protein coding genes
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keywords:
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- polymut
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- polymorphic
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- mags
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- assembly
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- polymorphic sites
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- estimation
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- protein coding genes
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- cmseq
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- bam
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- coverage
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tools:
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- cmseq:
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description: Set of utilities on sequences and BAM files
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homepage: https://github.com/SegataLab/cmseq
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documentation: https://github.com/SegataLab/cmseq
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tool_dev_url: https://github.com/SegataLab/cmseq
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licence: ["MIT License"]
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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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- bai:
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type: file
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description: BAM index file
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pattern: "*.bai"
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- gff:
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type: file
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description: GFF file used to extract protein-coding genes
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pattern: "*.gff"
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- fasta:
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type: file
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description: Optional fasta file to run on a subset of references in the BAM file.
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pattern: .{fa,fasta,fas,fna}
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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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- polymut:
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type: file
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description: Polymut report in `.txt` format.
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pattern: "*.txt"
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authors:
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- "@maxibor"
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