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

nf-core/bamcmp @ 0.0.0-0c7146d

Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX).

filter xenograft host graft contamination mouse

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @kmurat1 @sppearce

Maintainers: @sppearce

Summary

Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX).

Get started

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

include { BAMCMP } from 'nf-core/bamcmp'

License

MIT License

Process

`Name`	`BAMCMP`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`primary_aligned_bam` file	BAM/CRAM/SAM file with the reads aligned to the primary genome (the one you want to keep) `*.{bam,cram,sam}`
`contaminant_aligned_bam` file	BAM/CRAM/SAM file with the reads aligned to the contaminant genome (the one you want to filter out) `*.{bam,cram,sam}`

Output 4 channels

#1 versions_bamcmp tuple

`${task.process}` string	The process the versions were collected from
`bamcmp` string	The tool name
`echo 2.2` string	The version used (constant)

#2 contamination_bam tuple

`meta` map	Groovy Map containing sample information
`${prefix2}.bam` file	Bam file containing the reads which align better to the contaminant genome. `*.{bam,cram,sam}`

#3 versions_samtools tuple

`${task.process}` string	The process the versions were collected from
`samtools` string	The tool name
`samtools version \| sed '1!d;s/.* //'` string	The command used to generate the version of the tool

#4 primary_filtered_bam tuple

`meta` map	Groovy Map containing sample information
`${prefix}.bam` file	Bam file containing the reads which align better to the primary genome. `*.{bam,cram,sam}`

Tool	Description	Homepage
bamcmp	Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped, sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else reads which multimap to the contamination genome will be spuriously kept.	https://github.com/CRUKMI-ComputationalBiology/bamcmp

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:23:41 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbamcmp/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bamcmp/blobs/sha256:50457d4432547401ba353a3e9988be02001c73f0bdebe994b9baa403efc5246a
Size	3.5 KB
Checksum	sha256:50457d4432547401ba353a3e9988be02001c73f0bdebe994b9baa403efc5246a
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:23:41 (UTC)		1	3.5 KB	-