nf-core_modules/modules/biscuit/epiread/meta.yml
Nathan Spix 801240a971
Add core Biscuit tools (#1354)
* 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>
2022-03-14 09:34:22 -04:00

58 lines
1.5 KiB
YAML

name: biscuit_epiread
description: |
Summarizes read-level methylation (and optionally SNV) information from a
Biscuit BAM file in a standard-compliant BED format.
keywords:
- biscuit
- DNA methylation
- WGBS
- scWGBS
- bisulfite sequencing
- aligner
- bam
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/epiread_format/
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 ]
- bam:
type: file
description: Biscuit BAM file
- bai:
type: file
description: BAM index
- snp_bed:
type: file
description: BED file containing SNP information (optional)
- 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 ]
- epiread_bed:
type: file
description: Gzipped BED file with methylation (and optionally SNV) information
pattern: "*.{epiread.bed.gz}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@njspix"