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nf-core/gatk4/collectreadcounts @ 0.0.0-0c7146d

Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval.

collectreadcounts bam cram gatk4
Latest version: 0.0.0-0c7146d
Total downloads: 1
Source: nf-core/modules
Authors: @nvnieuwk
Maintainers: @nvnieuwk

Summary

Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval.

Get started

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

include { GATK4_COLLECTREADCOUNTS } from 'nf-core/gatk4/collectreadcounts'

License

MIT License

Process
Name GATK4_COLLECTREADCOUNTS
Input 4 channels
#1 tuple
meta map

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

BAM/CRAM/SAM file

 *.{bam,cram,sam}
input_index file

BAM/CRAM/SAM index file

 *.{bai,crai,sai}
intervals file

A file containing the specified intervals

 *.{bed,intervals}
#2 tuple
meta2 map

Groovy Map containing reference information e.g. [ id:'test' ]
fasta file

Optional - Reference FASTA

 *.{fasta,fa}
#3 tuple
meta3 map

Groovy Map containing reference information e.g. [ id:'test' ]
fai file

Optional - Index of the reference FASTA file

 *.fai
#4 tuple
meta4 map

Groovy Map containing reference information e.g. [ id:'test' ]
dict file

Optional - Sequence dictionary of the reference FASTA file

 *.dict
Output 3 channels
#1 tsv tuple
meta map

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

The read counts in TSV format

 *.tsv
#2 hdf5 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.hdf5 file

The read counts in hdf5 format

 *.hdf5
#3 versions_gatk4 tuple
${task.process} string

The name of the process
gatk4 string

The name of the tool
gatk --version | sed -n '/GATK.*v/s/.*v//p' eval

The expression to obtain the version of the tool
Tool Description Homepage
gatk4 Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. https://gatk.broadinstitute.org/hc/en-us
Version 0.0.0-0c7146d
Commit ID 135d883a43b1a2324b4112cd270cf22e20835533
Release Date 08 Apr 2026 18:41:15 (UTC)
Download URL https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fcollectreadcounts/0.0.0-0c7146d/download
OCI Store URL https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/collectreadcounts/blobs/sha256:97582f9ba907ec071554a1e2fd91fcabe800234233706cc1005cc2a83cb14c0c
Size 3.5 KB
Checksum sha256:97582f9ba907ec071554a1e2fd91fcabe800234233706cc1005cc2a83cb14c0c
Downloads 1
Version Date Status Downloads Size Diff
0.0.0-0c7146d