mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 08:12:03 +00:00
3aacd46da2
* backfilled modules with meta.yml that had no license identifier * harmonized BSD license names * whitespace linting at modules/unzip/meta.yml:12 * harmonized software from US NIH-NCBI/NIST to 'US-Government-Work' * Update modules/bcftools/index/meta.yml `bcftools` is dual-licensed, use associative array to allow for multiple licenses Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Michael L Heuer <heuermh@acm.org>
59 lines
1.7 KiB
YAML
59 lines
1.7 KiB
YAML
name: bismark_align
|
|
description: Performs alignment of BS-Seq reads using bismark
|
|
keywords:
|
|
- bismark
|
|
- 3-letter genome
|
|
- map
|
|
- methylation
|
|
- 5mC
|
|
- methylseq
|
|
- bisulphite
|
|
- bam
|
|
tools:
|
|
- bismark:
|
|
description: |
|
|
Bismark is a tool to map bisulfite treated sequencing reads
|
|
and perform methylation calling in a quick and easy-to-use fashion.
|
|
homepage: https://github.com/FelixKrueger/Bismark
|
|
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
|
doi: 10.1093/bioinformatics/btr167
|
|
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: |
|
|
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
|
respectively.
|
|
- index:
|
|
type: dir
|
|
description: Bismark genome index directory
|
|
pattern: "BismarkIndex"
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: Output BAM file containing read alignments
|
|
pattern: "*.{bam}"
|
|
- unmapped:
|
|
type: file
|
|
description: Output FastQ file(s) containing unmapped reads
|
|
pattern: "*.{fq.gz}"
|
|
- report:
|
|
type: file
|
|
description: Bismark alignment reports
|
|
pattern: "*{report.txt}"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
authors:
|
|
- "@phue"
|