nf-core_modules/software/bwa/mem/meta.yml

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name: bwa_mem
description: Performs fastq alignment to a fasta reference using BWA
keywords:
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- mem
- bwa
- alignment
- map
tools:
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- bwa:
description: |
BWA is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
input:
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- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: file
description: |
BWA genome index files
pattern: "*.{amb,ann,bwt,pac,sa}"
- fasta:
type: file
description: |
Input genome fasta file
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
output:
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- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.bam"
- version:
type: file
description: File containing software version
pattern: "*.version.txt"
authors:
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- "@drpatelh"
- "@jeremy1805"