<p>If the output is File, you can add this step <a href="https://github.com/Barski-lab/workflows/blob/master/tools/rename.cwl" rel="nofollow noreferrer">https://github.com/Barski-lab/workflows/blob/master/tools/rename.cwl</a> to rename the output file.</p>

CC BY-SA 4.0
2019-08-04T22:23:33.943Z
2019-08-04T22:23:33.943Z
Michael Kotliar
<p>I would like to run the CNVkit workflow on <a href="https://www.cancergenomicscloud.org" rel="nofollow noreferrer">Cancer Genomics Cloud</a>.</p>

<p>However, the two workflows that I'd like to use:</p>

<ul>
<li><a href="https://cgc.sbgenomics.com/raw/admin/sbg-public-data/cnvkit-reference/7" rel="nofollow noreferrer">CNVkit Reference</a>, for building a reference from normal samples</li>
<li><a href="https://cgc.sbgenomics.com/raw/admin/sbg-public-data/cnvkit-pipeline-from-baseline-093/10" rel="nofollow noreferrer">CNVkit CNV Calling</a>, for calling CNVs by comparing tumors to the reference</li>
</ul>

<p>don't have parameters that can be set to define in which folder to save the results or which prefix to add to the results. This means that if you're generating multiple references or calling CNV for multiple tumor samples you will end up with results having the same name for each run (tumor).</p>

<p>I tried to modify the CWL workflow, online and through Rabix composer, but I was unable to make it work. I would like to use the published workflow to not code everything from the ground up.</p>

<p>Do you know how to update/use the current CWL workflow in order to avoid having the same filename/folder for all the results?</p>

CC BY-SA 4.0
2019-02-06T15:50:28.227Z
@llrs updated question with links to the workflows' code
gc5
<cnv>
Save output to a specific folder and/or with a specific prefix in Cancer Genomics Cloud
# Save output to a specific folder and/or with a specific prefix in Cancer Genomics Cloud

(Asked by: username_0 on 2019-02-05)

I would like to run the CNVkit workflow on [Cancer Genomics Cloud](https://www.cancergenomicscloud.org).

However, the two workflows that I'd like to use:

* [CNVkit Reference](https://cgc.sbgenomics.com/raw/admin/sbg-public-data/cnvkit-reference/7), for building a reference from normal samples
* [CNVkit CNV Calling](https://cgc.sbgenomics.com/raw/admin/sbg-public-data/cnvkit-pipeline-from-baseline-093/10), for calling CNVs by comparing tumors to the reference

don't have parameters that can be set to define in which folder to save the results or which prefix to add to the results. This means that if you're generating multiple references or calling CNV for multiple tumor samples you will end up with results having the same name for each run (tumor).

I tried to modify the CWL workflow, online and through Rabix composer, but I was unable to make it work. I would like to use the published workflow to not code everything from the ground up.

Do you know how to update/use the current CWL workflow in order to avoid having the same filename/folder for all the results?

**Tags:** cnv
> **Comments:**
> **username_0**: @llrs updated question with links to the workflows' code  

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## 1 answers

### Answer by username_1 on 2019-08-04. Score: 1

If the output is File, you can add this step <https://github.com/Barski-lab/workflows/blob/master/tools/rename.cwl> to rename the output file.


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