mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
e745e167c1
* 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>
60 lines
1.6 KiB
YAML
60 lines
1.6 KiB
YAML
name: bismark_report
|
|
description: Collects bismark alignment reports
|
|
keywords:
|
|
- bismark
|
|
- qc
|
|
- methylation
|
|
- 5mC
|
|
- methylseq
|
|
- bisulphite
|
|
- report
|
|
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 ]
|
|
- align_report:
|
|
type: file
|
|
description: Bismark alignment reports
|
|
pattern: "*{report.txt}"
|
|
- splitting_report:
|
|
type: file
|
|
description: Bismark splitting reports
|
|
pattern: "*{splitting_report.txt}"
|
|
- dedup_report:
|
|
type: file
|
|
description: Bismark deduplication reports
|
|
pattern: "*.{deduplication_report.txt}"
|
|
- mbias:
|
|
type: file
|
|
description: Text file containing methylation bias information
|
|
pattern: "*.{txt}"
|
|
- fasta:
|
|
type: file
|
|
description: Input genome fasta file
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- report:
|
|
type: file
|
|
description: Bismark reports
|
|
pattern: "*.{html,txt}"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
authors:
|
|
- "@phue"
|