2021-01-31 21:23:26 +00:00
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name: bcftools_consensus
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description: Compresses VCF files
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keywords:
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- variant calling
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- consensus
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- VCF
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tools:
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- consensus:
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2021-02-01 08:28:51 +00:00
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description: |
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Create consensus sequence by applying VCF variants to a reference fasta file.
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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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2021-01-31 21:23:26 +00:00
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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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2021-01-31 21:23:26 +00:00
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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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2021-01-31 21:23:26 +00:00
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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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2021-02-01 08:28:51 +00:00
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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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2021-02-01 08:28:51 +00:00
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type: map
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description: |
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2021-02-02 08:57:55 +00:00
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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 file
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pattern: "*.{vcf}"
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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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- 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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output:
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2021-02-01 08:28:51 +00:00
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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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- fasta:
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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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- 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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2021-01-31 21:23:26 +00:00
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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