# Skipping processes in an nf-core pipeline

**URL:** https://community.seqera.io/t/skipping-processes-in-an-nf-core-pipeline/406
**Category:** Tips & Tricks
**Tags:** nextflow
**Created:** [January 18, 2024, 4:24pm UTC](https://community.seqera.io/t/skipping-processes-in-an-nf-core-pipeline/406 "2024-01-18T16:24:14Z")
**Posts on this page:** 1
**Page:** 1

<div class="post-metadata">

### Author: ![mribeirodantas](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/mribeirodantas/32/235_2.png) [@mribeirodantas](https://community.seqera.io/u/mribeirodantas)
#### Post date: [January 18, 2024, 4:24pm UTC](https://community.seqera.io/t/skipping-processes-in-an-nf-core-pipeline/406/1 "2024-01-18T16:24:14Z")

</div>

You may want to run an [nf-core pipeline](https://nf-co.re/pipelines), without having to go through all the steps. Some pipelines such as [sarek](https://nf-co.re/sarek/3.4.0/) will already have you covered with pipeline options such as `--skip_tools` (check [here](https://nf-co.re/sarek/3.4.0/docs/usage#how-to-handle-umis)), but what if this specific nf-core pipeline doesn’t provide you with this feature? (It’s still worth checking the pipeline page, as some will have skip options, though not as powerful as sarek’s one).

All nf-core modules check `ext.when`, which is passed to the `when` block in the process body. With that, you can disable any process and go step by step if you like using a custom config such as:

```Groovy
process {
    withName: 'FASTQC' {
        ext.when = false
    }

```

With the configuration above, the `FASTQC` process will be skipped. You can use process selectors and regular expressions to make very powerful decisions. Check the one below:

```Groovy
    withName: '!(FASTQC|MULTIQC)' {
        ext.when = false

```

In the situation above, you are disabling everything but `FASTQC` and `MULTIQC`.

Thanks to @mahesh.binzerpanchal for this powerful insight originally [here](https://nextflow.slack.com/archives/C02T98A23U7/p1705398418129349?thread_ts=1705333454.467599&cid=C02T98A23U7).