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8656636f0d
* update for bcftools merge * Update modules/bcftools/merge/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update modules/bcftools/merge/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * updated test.yml * added the bed file to the main input tuple * merged all output into one output channel * added a test for bcf.gz output * Update modules/bcftools/merge/main.nf Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> * updated the tests Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
72 lines
2.1 KiB
YAML
72 lines
2.1 KiB
YAML
name: bcftools_merge
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description: Merge VCF files
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keywords:
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- variant calling
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- merge
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- VCF
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tools:
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- merge:
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description: |
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Merge VCF files.
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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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- vcfs:
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type: files
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description: |
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List containing 2 or more vcf files
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e.g. [ 'file1.vcf', 'file2.vcf' ]
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- tbis:
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type: files
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description: |
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List containing the tbi index files corresponding to the vcfs input files
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e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
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- bed:
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type: file
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description: "(Optional) The bed regions to merge on"
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pattern: "*.bed"
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- fasta:
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type: file
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description: "(Optional) The fasta reference file (only necessary for the `--gvcf FILE` parameter)"
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pattern: "*.{fasta,fa}"
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- fasta:
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type: file
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description: "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)"
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pattern: "*.fai"
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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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- vcf_gz:
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type: file
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description: VCF merged output file (bgzipped) => when `--output-type z` is used
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pattern: "*.vcf.gz"
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- vcf:
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type: file
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description: VCF merged output file => when `--output-type v` is used
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pattern: "*.vcf"
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- bcf_gz:
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type: file
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description: BCF merged output file (bgzipped) => when `--output-type b` is used
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pattern: "*.bcf.gz"
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- bcf:
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type: file
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description: BCF merged output file => when `--output-type u` is used
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pattern: "*.bcf"
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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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- "@joseespinosa"
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- "@drpatelh"
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- "@nvnieuwk"
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