2020-08-07 12:24:24 +00:00
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name: bwa_mem
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description: Performs fastq alignment to a fasta reference using BWA
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2020-08-05 16:27:42 +00:00
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keywords:
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2020-08-07 14:05:25 +00:00
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- mem
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- bwa
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- alignment
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- map
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- fastq
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- bam
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- sam
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2020-08-05 16:27:42 +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 12:24:24 +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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2020-10-15 10:13:54 +00:00
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- enable_conda:
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2020-08-07 14:05:25 +00:00
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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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2020-12-14 00:34:24 +00:00
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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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2020-08-05 16:27:42 +00:00
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input:
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2020-08-07 14:05:25 +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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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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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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- fasta:
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type: file
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description: Input genome fasta file
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2020-08-05 16:27:42 +00:00
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output:
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2020-08-07 14:05:25 +00:00
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- bam:
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type: file
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description: Output BAM file containing read alignments
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pattern: "*.{bam}"
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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 16:27:42 +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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- "@jeremy1805"
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