Nextflow Registry | nf-core/deeptools/bamcoverage@0.0.0-0c7146d

nf-core/deeptools/bamcoverage @ 0.0.0-0c7146d

This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.

coverage depth track

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @FriederikeHanssen @SusiJo @JoseEspinosa

Maintainers: @FriederikeHanssen @SusiJo @JoseEspinosa

This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.

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

include { DEEPTOOLS_BAMCOVERAGE } from 'nf-core/deeptools/bamcoverage'

MIT License

Process

`Name`	`DEEPTOOLS_BAMCOVERAGE`

Input 4 channels

#1 tuple

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

`fasta` file	Reference file the CRAM file was created with (required with CRAM input) `*.{fasta,fa}`

`fasta_fai` file	Index of the reference file (optional, but recommended) `*.{fai}`

#4 tuple

`meta2` map	Groovy Map containing blacklist metadata e.g. [ id:'blacklist' ]
`blacklist` file	BED/GTF file containing regions to exclude from analysis `*.{bed,gtf}`

Output 4 channels

#1 bigwig tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bigWig` file	BigWig file `*.bigWig`

#2 bedgraph tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bedgraph` file	Bedgraph file `*.bedgraph`

#3 versions_samtools tuple

`${task.process}` string	The name of the process
`samtools` string	The name of the tool
`samtools version \| sed '1!d;s/.* //'` eval	The expression to obtain the version of the tool

#4 versions_deeptools tuple

`${task.process}` string	The name of the process
`deeptools` string	The name of the tool
`bamCoverage --version \| sed "s/bamCoverage //g"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
deeptools	A set of user-friendly tools for normalization and visualization of deep-sequencing data	https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:35:24 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fdeeptools%2Fbamcoverage/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/deeptools/bamcoverage/blobs/sha256:347d359d8af55d886d8a9876fc3d1861192ced936b7eb255d3439fa97cef7d85
Size	3.3 KB
Checksum	sha256:347d359d8af55d886d8a9876fc3d1861192ced936b7eb255d3439fa97cef7d85
Downloads	1

Version	Date	Status	Downloads	Size	Diff