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meta.yml
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meta.yml
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name: bwamem2_mem
description: Performs fastq alignment to a fasta reference using BWA
keywords:
- mem
- bwa
- alignment
- map
- fastq
- bam
- sam
tools:
- bwa:
description: |
BWA-mem2 is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: https://github.com/bwa-mem2/bwa-mem2
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ["MIT"]
input:
- 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.
- meta2:
type: map
description: |
Groovy Map containing reference/index information
e.g. [ id:'test' ]
- index:
type: file
description: BWA genome index files
pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}"
- sort_bam:
type: boolean
description: use samtools sort (true) or samtools view (false)
pattern: "true or false"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@maxulysse"
maintainers:
- "@maxulysse"