mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
eb9178970f
* add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/summary * remove md5sum check for bismark_summary_report.html it contains a timestamp * fix tests * update meta.yml * remove mysterious index files
53 lines
1.5 KiB
YAML
53 lines
1.5 KiB
YAML
name: bismark_summary
|
|
description: |
|
|
Uses Bismark report files of several samples in a run folder
|
|
to generate a graphical summary HTML report.
|
|
keywords:
|
|
- bismark
|
|
- qc
|
|
- methylation
|
|
- 5mC
|
|
- methylseq
|
|
- bisulphite
|
|
- report
|
|
- summary
|
|
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
|
|
input:
|
|
- bam:
|
|
type: file
|
|
description: Bismark alignment
|
|
pattern: "*.{bam}"
|
|
- align_report:
|
|
type: file
|
|
description: Bismark alignment reports
|
|
pattern: "*{report.txt}"
|
|
- dedup_report:
|
|
type: file
|
|
description: Bismark deduplication reports
|
|
pattern: "*.{deduplication_report.txt}"
|
|
- splitting_report:
|
|
type: file
|
|
description: Bismark splitting reports
|
|
pattern: "*{splitting_report.txt}"
|
|
- mbias:
|
|
type: file
|
|
description: Text file containing methylation bias information
|
|
pattern: "*.{txt}"
|
|
output:
|
|
- summary:
|
|
type: file
|
|
description: Bismark summary
|
|
pattern: "*.{html,txt}"
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
authors:
|
|
- "@phue"
|