Nextflow Registry | nf-core/crumble@0.0.0-0c7146d

nf-core/crumble @ 0.0.0-0c7146d

Controllable lossy compression of BAM/CRAM files

compress bam sam cram

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @priyanka-surana

Maintainers: @priyanka-surana

Controllable lossy compression of BAM/CRAM files

Add the following snippet to your workflow script to include this module.

include { CRUMBLE } from 'nf-core/crumble'

MIT License

Process

`Name`	`CRUMBLE`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM/SAM file `*.{bam,cram,sam}`

`keepbed` file	BED file defining regions to keep quality

`bedout` boolean	set to true to output suspicious regions to a BED file

Output 5 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bam` file	optional filtered/compressed BAM file `*.{bam}`

#2 bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bed` file	optional suspicious regions BED file `*{bed}`

#3 sam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.sam` file	optional filtered/compressed SAM file `*.{sam}`

#4 cram tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cram` file	optional filtered/compressed CRAM file `*.{cram}`

#5 versions_crumble tuple

`${task.process}` string	The name of the process
`crumble` string	The name of the tool
`0.9.1` string	The expression to obtain the version of the tool

Tool	Description	Homepage
crumble	Controllable lossy compression of BAM/CRAM files	https://github.com/jkbonfield/crumble

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:33:26 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcrumble/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/crumble/blobs/sha256:80a2e681ede58d252a9c1cabc90d16c13494a447dbb41c132fefda91694e4b14
Size	2.7 KB
Checksum	sha256:80a2e681ede58d252a9c1cabc90d16c13494a447dbb41c132fefda91694e4b14
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:33:26 (UTC)		1	2.7 KB	-