mirror of
https://github.com/MillironX/nf-core_modules.git
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70 lines
2.1 KiB
YAML
70 lines
2.1 KiB
YAML
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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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- consensus:
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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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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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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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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: FASTA reference consensus file
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pattern: "*.{fasta,fa}"
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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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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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