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nf-core/goleft/indexcov @ 0.0.0-0c7146d

Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that's what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome.

coverage cnv genomics depth
Latest version: 0.0.0-0c7146d
Total downloads: 1
Source: nf-core/modules
Authors: @lindenb
Maintainers: @lindenb

Summary

Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that's what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome.

Get started

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

include { GOLEFT_INDEXCOV } from 'nf-core/goleft/indexcov'

License

MIT License

Process
Name GOLEFT_INDEXCOV
Input 2 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false]
bams file

Sorted BAM/CRAM/SAM files

 *.{bam,cram,sam}
indexes file

BAI/CRAI files

 *.{bai,crai}
#2 tuple
meta2 map

Groovy Map containing sample information e.g. [ id:'test', single_end:false]
fai file

FASTA index

 *.{fai}
Output 8 channels
#1 bed tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}/*bed.gz file

bed files

 *bed.gz
#2 ped tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}/*ped file

ped files

 *ped
#3 png tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}/*png file

png files

 *png
#4 roc tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}/*roc file

roc files

 *roc
#5 html tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}/*html file

html files

 *html
#6 output tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}/* file

Files generated by indexcov
#7 versions
versions.yml file

File containing software versions

 versions.yml
#8 bed_index tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}/*bed.gz.tbi file

bed index files

 *bed.gz.tbi
Tool Description Homepage
goleft goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary https://github.com/brentp/goleft
Version 0.0.0-0c7146d
Commit ID 135d883a43b1a2324b4112cd270cf22e20835533
Release Date 08 Apr 2026 18:45:07 (UTC)
Download URL https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgoleft%2Findexcov/0.0.0-0c7146d/download
OCI Store URL https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/goleft/indexcov/blobs/sha256:6df48916063d4ba2ce0d1df87c7fcf4a3ceb4e6e81ebaa4657f9d47f146310e9