mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
8a2f01c416
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add bwa/aln module * Also output reads as required with SAI * Add bwa samse * Fix container paths * remove TODO comment * Updated based on code from from @grst on bwa/sampe * Clarify output docs
59 lines
1.4 KiB
YAML
59 lines
1.4 KiB
YAML
name: bwa_samse
|
|
description: Convert bwa SA coordinate file 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: "*.{version.txt}"
|
|
- bam:
|
|
type: file
|
|
description: BAM file
|
|
pattern: "*.bam"
|
|
|
|
authors:
|
|
- "@jfy133"
|