nf-core_modules/modules/bwa/sampe/meta.yml
Gregor Sturm 906577873b
Bulk update modules to use versions.yml (#739)
* New functions.nf

* Convert code to create versions.yml

* Update meta.yml

* update output channel

* Fix more meta.yml

* Manually update remaining modules

* remove superflous echo

* Fix misformatted meta.yml files

* Fix yaml, was list instead of dict

* fix version for bcftools

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 09:41:24 +01:00

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 v3']
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 ]
- version:
type: file
description: File containing software version
pattern: "versions.yml"
- bam:
type: file
description: BAM file
pattern: "*.bam"
authors:
- "@jfy133"