2021-02-12 12:24:10 +00:00
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name: bwamem2_index
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2021-02-12 12:00:02 +00:00
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description: Create BWA-mem2 index for reference genome
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keywords:
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- index
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- fasta
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- genome
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- reference
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tools:
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- bwa:
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description: |
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BWA-mem2 is a software package for mapping DNA sequences against
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a large reference genome, such as the human genome.
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homepage: https://github.com/bwa-mem2/bwa-mem2
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documentation: https://github.com/bwa-mem2/bwa-mem2#usage
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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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- fasta:
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type: file
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description: Input genome fasta file
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output:
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- index:
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type: file
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description: BWA genome index files
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pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}"
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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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- "@maxulysse"
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