nf-core_modules/modules/bismark/methylationextractor/meta.yml

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}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@phue"