mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
906577873b
* 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>
58 lines
1.4 KiB
YAML
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"
|