nf-core_modules/modules/bwa/sampe/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

58 lines
1.4 KiB
YAML

name: bwa_sampe
description: Convert paired-end bwa SA coordinate files to SAM format
keywords:
- bwa
- aln
- short-read
- align
- reference
- fasta
- map
- sam
- bam
tools:
- 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://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324"
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information.
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: FASTQ files specified alongside meta in input channel.
pattern: "*.{fastq,fq}.gz"
- sai:
type: file
description: SAI file specified alongside meta and reads in input channel.
pattern: "*.sai"
- index:
type: directory
description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX
pattern: "bwa/"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: BAM file
pattern: "*.bam"
authors:
- "@jfy133"