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nf-core/coverm/genome @ 0.0.0-6c4ed3a

Calculate read coverage per-genome

mapping genomics metagenomics coverage
Latest version: 0.0.0-6c4ed3a
Total downloads: 7
Source: nf-core/modules
Authors: @vinisalazar
Maintainers: @vinisalazar

Summary

Calculate read coverage per-genome

Get started

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

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

License

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 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:11:39 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fcoverm%2Fgenome/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/coverm/genome/blobs/sha256:556d4780ca4f3559a4125e731cba891d468620bbfbc1c33f2e078458eb3b6dea
Size 4.0 KB
Checksum sha256:556d4780ca4f3559a4125e731cba891d468620bbfbc1c33f2e078458eb3b6dea
Downloads 4
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:11:39 (UTC) 4 4.0 KB
0.0.0-0c7146d 08 Apr 2026 18:54:30 (UTC) 3 4.0 KB