mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
801240a971
* create files with nf-core command * update meta.yml files * starting to work on index main.nf * prelim test for index * index test working; not finding all output files * index passing tests * index and align passing tests * prototyping biscuitblaster and pileup * update containers * updates to pileup * pileup passing tests * template creation for more biscuit tools * tests passing on blaster,bsconv,pupsom * epiread passing tests, but need to update SNP bed file path * vcf2bed working; change test file * all biscuit commands passing tests * biscuitblaster rename * try to fix permissions * more permission fixes * trying a couple more permission changes * hopefully last permission fixes * really last permission changes * few more permissions * add when blocks * Remove read group meta Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * remove read group meta Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * changes for first round of review * update meta.yml with more specific links * Update modules/biscuit/biscuitblaster/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Apply new version reporting Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/biscuit/pileup/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update main.nf * Update modules/biscuit/pileupsomatic/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * update test file path * Update modules/biscuit/align/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/biscuit/align/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * tests passing again * Update modules/biscuit/align/main.nf * Update modules/biscuit/bsconv/main.nf * Update modules/biscuit/epiread/main.nf * Update modules/biscuit/index/main.nf * Update test.yml * Update modules/biscuit/pileupsomatic/main.nf * remove module-specific extension/prefix * remove module-specific extension/prefix * add missing args * switch pileup strategy * update test.yml * remove debug * whitespace cleanup * add in newline escapes * requested changes * Update modules/biscuit/pileup/meta.yml Co-authored-by: Spix <nathan.spix@submit.cm.cluster> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Spix <nathan.spix@node107.cm.cluster> Co-authored-by: njspix <nathan.spix@vai.org>
48 lines
1.2 KiB
YAML
48 lines
1.2 KiB
YAML
name: biscuit_vcf2bed
|
|
description: |
|
|
Summarizes methylation or SNV information from a Biscuit VCF in a
|
|
standard-compliant BED file.
|
|
keywords:
|
|
- biscuit
|
|
- DNA methylation
|
|
- WGBS
|
|
- scWGBS
|
|
- bisulfite sequencing
|
|
- aligner
|
|
- 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/methylextraction.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 ]
|
|
- vcf:
|
|
type: file
|
|
description: Biscuit vcf file (output of biscuit pileup)
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bed:
|
|
type: file
|
|
description: Gzipped BED file with methylation or SNV information
|
|
pattern: "*.{bed.gz}"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@njspix"
|