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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>
51 lines
1.2 KiB
YAML
51 lines
1.2 KiB
YAML
name: bcftools_reheader
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description: Reheader a VCF file
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keywords:
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- reheader
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- vcf
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- update header
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tools:
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- reheader:
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description: |
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Modify header of VCF/BCF files, change sample names.
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homepage: http://samtools.github.io/bcftools/bcftools.html
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documentation: http://samtools.github.io/bcftools/bcftools.html#reheader
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doi: 10.1093/gigascience/giab008
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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: VCF/BCF file
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pattern: "*.{vcf.gz,vcf,bcf}"
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- fai:
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type: file
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description: Fasta index to update header sequences with
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pattern: "*.{fai}"
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- header:
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type: file
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description: New header to add to the VCF
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pattern: "*.{header.txt}"
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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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- vcf:
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type: file
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description: VCF with updated header
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pattern: "*.{vcf.gz}"
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authors:
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- "@bjohnnyd"
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