mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
f080015754
* style: Add prettier config files * build: Add prettier vscode extension * ci: Replace markdownlint and yamllint with prettier * style: Run prettier * style: Use indent of 2 for markdown as well https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358 * style: Fix indent * style: Let editorconfig take over tab widths * style: yaml => yml * ci: Run prettier once Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se> Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
70 lines
2.3 KiB
YAML
70 lines
2.3 KiB
YAML
name: biscuit_pileup
|
|
description: Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants
|
|
keywords:
|
|
- bisulfite
|
|
- DNA methylation
|
|
- pileup
|
|
- variant calling
|
|
- WGBS
|
|
- scWGBS
|
|
- bam
|
|
- vcf
|
|
tools:
|
|
- biscuit:
|
|
description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
|
|
homepage: https://huishenlab.github.io/biscuit/
|
|
documentation: https://huishenlab.github.io/biscuit/docs/pileup.html
|
|
tool_dev_url: https://github.com/huishenlab/biscuit
|
|
doi: ""
|
|
licence: ["MIT"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- normal_bams:
|
|
type: file(s)
|
|
description: |
|
|
BAM files to be analyzed. If no tumor_bam file is provided, any number of "normal" BAMs may be provided
|
|
("normal" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a
|
|
tumor BAM file is provided, exactly one normal (germline) BAM must be provided.
|
|
pattern: "*.{bam}"
|
|
- normal_bais:
|
|
type: file(s)
|
|
description: BAM index file or files corresponding to the provided normal_bams
|
|
pattern: "*.{bai}"
|
|
- tumor_bam:
|
|
type: file(s)
|
|
description: |
|
|
Optional. If a tumor BAM file is provided, pileup will run in "somatic" mode and will annotate variants with
|
|
their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a
|
|
tumor BAM file is provided, exactly one normal BAM must be provided.
|
|
pattern: "*.{bam}"
|
|
- tumor_bai:
|
|
type: file(s)
|
|
description: Optional. BAM index file corresponding to provided tumor_bam
|
|
pattern: "*.{bai}"
|
|
- index:
|
|
type: dir
|
|
description: Biscuit genome index directory (generated with 'biscuit index')
|
|
pattern: "BiscuitIndex"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- vcf:
|
|
type: file
|
|
description: vcf file with methylation information
|
|
pattern: "*.{vcf.gz}"
|
|
|
|
authors:
|
|
- "@njspix"
|