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nf-core/crumble @ 0.0.0-0c7146d

Controllable lossy compression of BAM/CRAM files

compress bam sam cram
Latest version: 0.0.0-6c4ed3a
Total downloads: 11
Source: nf-core/modules
Authors: @priyanka-surana
Maintainers: @priyanka-surana

Summary

Controllable lossy compression of BAM/CRAM files

Get started

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

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

License

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 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 08 Apr 2026 18:54:47 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fcrumble/0.0.0-0c7146d/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/crumble/blobs/sha256:7a652d9a2fd91bc522c62c63ef15ab03a07827190901a44294541394a991db6e
Size 2.7 KB
Checksum sha256:7a652d9a2fd91bc522c62c63ef15ab03a07827190901a44294541394a991db6e
Downloads 4
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:11:51 (UTC) 3 2.8 KB
0.0.0-3fc6d40 22 Apr 2026 15:08:13 (UTC) 4 2.8 KB
0.0.0-0c7146d 08 Apr 2026 18:54:47 (UTC) 4 2.7 KB