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https://github.com/MillironX/nf-core_modules.git
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bb90e4fb78
* Remove customisation from bcftools modules * Add save_mpileup option to bcftools/mpileup * Remove params.save_mpileup from ivar/consensus * Update meta.ymls
57 lines
1.5 KiB
YAML
57 lines
1.5 KiB
YAML
name: bcftools_mpileup
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description: Compresses VCF files
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keywords:
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- variant calling
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- mpileup
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- VCF
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tools:
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- mpileup:
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description: |
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Generates genotype likelihoods at each genomic position with coverage.
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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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- bam:
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type: file
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description: Input BAM file
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pattern: "*.{bam}"
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- fasta:
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type: file
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description: FASTA reference file
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pattern: "*.{fasta,fa}"
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- save_mpileup:
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type: boolean
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description: Save mpileup file generated by bcftools mpileup
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patter: "*.mpileup"
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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:
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type: file
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description: VCF gzipped output file
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pattern: "*.{vcf.gz}"
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- tbi:
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type: file
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description: tabix index file
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pattern: "*.{tbi}"
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- stats:
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type: file
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description: Text output file containing stats
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pattern: "*{stats.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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- "@joseespinosa"
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- "@drpatelh"
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