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https://github.com/MillironX/nf-core_modules.git
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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
1.7 KiB
YAML
61 lines
1.7 KiB
YAML
name: bcftools_query
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description: Extracts fields from VCF or BCF files and outputs them in user-defined format.
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keywords:
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- query
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- variant calling
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- bcftools
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- VCF
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tools:
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- query:
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description: |
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Extracts fields from VCF or BCF files and outputs them in user-defined format.
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homepage: http://samtools.github.io/bcftools/bcftools.html
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documentation: http://www.htslib.org/doc/bcftools.html
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doi: 10.1093/bioinformatics/btp352
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licence: ["MIT"]
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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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- vcf:
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type: file
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description: |
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The vcf file to be qeuried.
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pattern: "*.{vcf.gz, vcf}"
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- tbi:
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type: file
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description: |
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The tab index for the VCF file to be inspected.
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pattern: "*.tbi"
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- regions:
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type: file
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description: |
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Optionally, restrict the operation to regions listed in this file.
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- targets:
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type: file
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description: |
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Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
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- samples:
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type: file
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description: |
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Optional, file of sample names to be included or excluded.
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e.g. 'file.tsv'
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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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- txt:
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type: file
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description: BCFTools query output file
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pattern: "*.txt"
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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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authors:
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- "@abhi18av"
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- "@drpatelh"
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