Nextflow Registry | nf-core/coverm/genome@0.0.0-0c7146d

nf-core/coverm/genome @ 0.0.0-0c7146d

Calculate read coverage per-genome

mapping genomics metagenomics coverage

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @vinisalazar

Maintainers: @vinisalazar

Calculate read coverage per-genome

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

include { COVERM_GENOME } from 'nf-core/coverm/genome'

MIT License

Process

`Name`	`COVERM_GENOME`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`input` file	FASTA/FASTQ containing reads (can be gzipped), or sorted BAM files of reads mapped to a reference. If supplying PE fasta for multiple samples, should be in the order "sample1_1, sample1_2, sample2_1, sample2_2...". `*.{fa,fq,fa.gz,fq.gz,bam}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. `[ id:'sample1', single_end:false ]`
`reference` file	Genome FASTA file(s) to map reads to, or a directory containing genome FASTA files. `*.{fasta,fasta.gz,mmi,sti,fna,fna.gz,fa,fa.gz}`

`bam_input` boolean	True if input is bam files

`interleaved` boolean	True if input is interleaved fastq file

`ref_mode` string	How to interpret the `reference` input: `"dir"`: Treat as a directory containing one or more FASTA files. `"file"`: Treat as a single FASTA file. `"auto"`: Automatically detect based on whether the `reference` path is a directory or file. Defaults to `"auto"` if not provided. `^(dir\|file\|auto)$`

`enable_bam_output` boolean	True to enable BAM output of aligned reads

Output 3 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.bam` file	BAM file containing aligned reads. `*.bam`

#2 coverage tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.depth.tsv` map	Tab-delimited file containing coverage information for each contig and sample. `*.depth.tsv`

#3 versions_coverm tuple

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

Tool	Description	Homepage
coverm	CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications	https://github.com/wwood/CoverM

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:33:10 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcoverm%2Fgenome/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/coverm/genome/blobs/sha256:856f5d34d69d1874cc5a40f9adb72544b7377c60be090edacbdec1b9d07d1cc4
Size	4.0 KB
Checksum	sha256:856f5d34d69d1874cc5a40f9adb72544b7377c60be090edacbdec1b9d07d1cc4
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:33:10 (UTC)		1	4.0 KB	-