# Best way to check the registry for modules that run a specific data processing command-line program

**URL:** <https://community.seqera.io/t/best-way-to-check-the-registry-for-modules-that-run-a-specific-data-processing-command-line-program/2685>\
**Category:** Ask for help\
**Tags:** nextflow, nf-core, modules\
**Created:** [May 22, 2026, 5:08pm UTC](https://community.seqera.io/t/best-way-to-check-the-registry-for-modules-that-run-a-specific-data-processing-command-line-program/2685 "2026-05-22T17:08:22Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![aloraine](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/aloraine/32/2127_2.png) [@aloraine](https://community.seqera.io/u/aloraine)\
**Post date:** [May 22, 2026, 5:08pm UTC](https://community.seqera.io/t/best-way-to-check-the-registry-for-modules-that-run-a-specific-data-processing-command-line-program/2685/1 "2026-05-22T17:08:23Z")

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Hi!

Thanks for the great training materials!

What’s the best way to check the registry for modules that run a specific data processing command-line program?

For reference, I am interested in this one:

> **[bamCoverage — deepTools 3.5.6 documentation](https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html)**

Here also is a slurm script that uses genomeCoverage to make scaled RNA-Seq coverage graphs: [Bitbucket](https://bitbucket.org/lorainelab/tardigrade/src/main/src/bamCoverage.sh)

I’ve been using it to visualize and sanity-check differential expression results, for example the direction of the change in a comparison.

Thanks a lot!

Ann

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**Author:** ![ewels](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/ewels/32/1_2.png) [@ewels](https://community.seqera.io/u/ewels)\
**Post date:** [May 22, 2026, 9:43pm UTC](https://community.seqera.io/t/best-way-to-check-the-registry-for-modules-that-run-a-specific-data-processing-command-line-program/2685/2 "2026-05-22T21:43:03Z")

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Hi Ann,

Glad that the training materials were useful! You should be able to simply search for the module that you’d like, eg. for “[deeptools bamcoverage](https://registry.nextflow.io/modules?query=deeptools+bamcoverage)”. The top hit is the following module:

> **[Nextflow Registry | nf-core/deeptools/bamcoverage@0.0.0-6c4ed3a](https://registry.nextflow.io/modules/nf-core/deeptools/bamcoverage@0.0.0-6c4ed3a)**

Also as for now most modules come from nf-core, you can also just search the nf-core website ([https://nf-co.re/modules/](https://nf-co.re/modules/)) or even the [nf-core/modules](https://github.com/nf-core/modules) GitHub repository [directly](https://github.com/search?q=repo%3Anf-core%2Fmodules%20deeptools%20bamcoverage&type=code)… You’ll see the same module available in those results:

> **[nf-core](https://nf-co.re/modules/deeptools_bamcoverage/)**
>
> This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.

You’ll see in the module `main.nf` that the script executed is very similar to the slurm script you linked to:

> <https://github.com/nf-core/modules/blob/69017e77fd733fb1d8db5add7ca34570223151b5/modules/nf-core/deeptools/bamcoverage/main.nf#L28-L59>

Hope that helps!

Phil

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**Author:** ![system](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/system/32/2402_2.png) [@system](https://community.seqera.io/u/system)\
**Post date:** [May 29, 2026, 9:44pm UTC](https://community.seqera.io/t/best-way-to-check-the-registry-for-modules-that-run-a-specific-data-processing-command-line-program/2685/3 "2026-05-29T21:44:01Z")

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Closed on May 29, 2026, 9:44pm UTC

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