nf-core_modules/modules/bwamem2/mem/meta.yml
Matthias Hörtenhuber e745e167c1
Fix formatting in yaml files, add yamllint config (#1279)
* fix yml formatting

* allow fastq.gz and fq.gz as file input, add meta.yml and test

* fix yaml files

* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"

This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.

* prettier magic!

* fix comments for yamllint

* remove node version number

* fix linting errors

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00

49 lines
1.3 KiB
YAML

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.
- 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:
- 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"