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f62e4cf5f0
* Added Somalier extract module * changed somalier_dbg4 to somalier for versions.yml * added and minor changes in meta.yml * Apply suggestions from code review * Update main.nf * Typo in quay.io rl * updated the input * new updates * linting * linting * changed the test.yml * Update modules/somalier/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/extract/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/somalier/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/somalier/extract/test.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * last changes * Update modules/somalier/extract/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/extract/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
65 lines
1.9 KiB
YAML
65 lines
1.9 KiB
YAML
name: "somalier_extract"
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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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- input:
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type: file
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description: BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file
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- input_index:
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type: file
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description: index file of the input data, e.g., bam.bai, cram.crai
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- fasta:
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type: file
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description: The reference fasta file
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pattern: "*.{fasta,fna,fas,fa}"
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- fai:
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type: file
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description: FASTA index file
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pattern: "*.fai"
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- sites:
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type: file
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description: sites file in VCF format which can be taken from https://github.com/brentp/somalier
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pattern: "*.vcf.gz"
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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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- somalierExtract:
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type: file
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description: binary output file based on extracted sites
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pattern: "*.{somalier}"
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authors:
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- "@ashotmarg"
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