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* Working version of somalier relate * few changes * new changes * corrected test.yml * updated container paths and file paths * changed container and inputFile paths * changed left padding * requested changes * Update modules/somalier/relate/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/relate/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/relate/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/relate/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/relate/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/relate/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/relate/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * requested changes * requested changes Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
62 lines
1.8 KiB
YAML
62 lines
1.8 KiB
YAML
name: "somalier_relate"
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description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
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keywords:
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- relatedness
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- QC
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- bam
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- cram
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- vcf
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- gvcf
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- ancestry
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- identity
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- kinship
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- informative sites
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- family
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tools:
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- "somalier":
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description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs"
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homepage: "https://github.com/brentp/somalier"
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documentation: "https://github.com/brentp/somalier/blob/master/README.md"
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tool_dev_url: "https://github.com/brentp/somalier"
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doi: "https://doi.org/10.1186/s13073-020-00761-2"
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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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- extract:
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type: file
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description: extract file from Somlaier extract
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pattern: "*.somalier"
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- sample_groups:
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type: file
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description: optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line
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pattern: "*.{txt,csv}"
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- ped:
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type: file
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description: optional path to a ped or fam file indicating the expected relationships among samples
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pattern: "*.{ped,fam}"
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output:
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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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- html:
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type: file
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description: html file
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pattern: "*.html"
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- pairs_tsv:
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type: file
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description: tsv file with output stats for pairs of samples
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pattern: "*.pairs.tsv"
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- samples_tsv:
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type: file
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description: tsv file with sample-level information
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pattern: "*.samples.tsv"
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authors:
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- "@ashotmarg"
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