2020-08-07 11:38:01 +00:00
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name: bwa_index
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description: Create BWA index for reference genome
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2020-08-05 16:27:28 +00:00
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keywords:
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2020-08-07 14:05:25 +00:00
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- index
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- fasta
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- genome
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- reference
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2020-08-05 16:27:28 +00:00
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tools:
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2020-08-07 14:05:25 +00:00
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- bwa:
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description: |
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BWA 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: http://bio-bwa.sourceforge.net/
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documentation: http://www.htslib.org/doc/samtools.html
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arxiv: arXiv:1303.3997
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2020-08-07 11:38:01 +00:00
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params:
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2020-08-07 14:05:25 +00:00
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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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- 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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2020-08-05 16:27:28 +00:00
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input:
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2020-08-07 14:05:25 +00:00
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- fasta:
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type: file
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description: Input genome fasta file
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- options:
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type: map
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description: |
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Groovy Map containing module options for passing command-line arguments and
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output file paths.
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2020-08-05 16:27:28 +00:00
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output:
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2020-08-07 14:05:25 +00:00
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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: "*.{amb,ann,bwt,pac,sa}"
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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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2020-08-05 16:27:28 +00:00
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authors:
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2020-08-07 14:05:25 +00:00
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- "@drpatelh"
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- "@maxulysse"
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