nf-core_modules/modules/bismark/methylationextractor/meta.yml
Harshil Patel e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567)
* Update README

* Rename pytest_software.yml to pytest_modules.yml

* Rename main software directory to modules

* Remove deprecated modules

* Rename tests software to modules

* Replace paths for tests in pytest_modules.yml

* Replace software with modules in Github Actions

* Replace software with modules in main.nf tests

* Rename software to modules in test.yml
2021-07-07 10:10:18 +01:00

66 lines
2 KiB
YAML

name: bismark_methylationextractor
description: Extracts methylation information for individual cytosines from alignments.
keywords:
- bismark
- consensus
- map
- methylation
- 5mC
- methylseq
- bisulphite
- bam
- bedGraph
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:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file containing read alignments
pattern: "*.{bam}"
- 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 ]
- bedgraph:
type: file
description: Bismark output file containing coverage and methylation metrics
pattern: "*.{bedGraph.gz}"
- methylation_calls:
type: file
description: Bismark output file containing strand-specific methylation calls
pattern: "*.{txt.gz}"
- coverage:
type: file
description: Bismark output file containing coverage metrics
pattern: "*.{cov.gz}"
- report:
type: file
description: Bismark splitting reports
pattern: "*_{splitting_report.txt}"
- mbias:
type: file
description: Text file containing methylation bias information
pattern: "*.{M-bias.txt}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@phue"