mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
d8ba32c6b5
* 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"
|
|
description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
|
|
keywords:
|
|
- relatedness
|
|
- QC
|
|
- bam
|
|
- cram
|
|
- vcf
|
|
- gvcf
|
|
- ancestry
|
|
- identity
|
|
- kinship
|
|
- informative sites
|
|
- family
|
|
tools:
|
|
- "somalier":
|
|
description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs"
|
|
homepage: "https://github.com/brentp/somalier"
|
|
documentation: "https://github.com/brentp/somalier/blob/master/README.md"
|
|
tool_dev_url: "https://github.com/brentp/somalier"
|
|
doi: "https://doi.org/10.1186/s13073-020-00761-2"
|
|
licence: "MIT License"
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- extract:
|
|
type: file
|
|
description: extract file from Somlaier extract
|
|
pattern: "*.somalier"
|
|
- sample_groups:
|
|
type: file
|
|
description: optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line
|
|
pattern: "*.{txt,csv}"
|
|
- ped:
|
|
type: file
|
|
description: optional path to a ped or fam file indicating the expected relationships among samples
|
|
pattern: "*.{ped,fam}"
|
|
|
|
output:
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- html:
|
|
type: file
|
|
description: html file
|
|
pattern: "*.html"
|
|
- pairs_tsv:
|
|
type: file
|
|
description: tsv file with output stats for pairs of samples
|
|
pattern: "*.pairs.tsv"
|
|
- samples_tsv:
|
|
type: file
|
|
description: tsv file with sample-level information
|
|
pattern: "*.samples.tsv"
|
|
|
|
authors:
|
|
- "@ashotmarg"
|