nf-core_modules/modules/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
- fastq
- bam
- sam
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
licence: ['GPL-3.0-or-later']
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
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pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
- sort_bam:
type: boolean
description: use samtools sort (true) or samtools view (false)
pattern: "true or false"
output:
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- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- versions:
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type: file
description: File containing software versions
pattern: "versions.yml"
authors:
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- "@drpatelh"
- "@jeremy1805"