<p>Since you are running via singularity you can find out the version you are using from the container, defined in modules.config for this pipeline (<a href="https://github.com/PGScatalog/pgsc_calc/blob/main/conf%2Fmodules.config#L42" rel="nofollow noreferrer">https://github.com/PGScatalog/pgsc_calc/blob/main/conf%2Fmodules.config#L42</a>), the current version seems to be 0.5.2 for utils and for calc (<a href="https://github.com/PGScatalog/pgsc_calc/blob/main/conf%2Fmodules.config#L56" rel="nofollow noreferrer">https://github.com/PGScatalog/pgsc_calc/blob/main/conf%2Fmodules.config#L56</a>) it is 1.4.8</p>

CC BY-SA 4.0
2024-05-10T16:22:02.877Z
2024-05-10T16:22:02.877Z
Niklas
<p>I have run this command:</p>
<pre><code>nextflow run pgscatalog/pgscalc -profile singularity --input {input.samplesheet} --target_build GRCh38 --scorefile {input.scorefile} --outdir /output/{wildcards.PGS_ID}/
</code></pre>
<p>I am now preparing methods for a paper. I need to cite:</p>
<ul>
<li>PGS Catalog Calculator. PGS Catalog Team. <a href="https://github.com/PGScatalog/pgsc_calc" rel="nofollow noreferrer">https://github.com/PGScatalog/pgsc_calc</a>
Lambert et al. (2021)</li>
<li>The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nature Genetics. 53:420–425 doi:10.1038/s41588-021-00783-5</li>
<li>Ewels, P.A., Peltzer, A., Fillinger, S. et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol 38, 276–278 (2020). <a href="https://doi.org/10.1038/s41587-020-0439-x" rel="nofollow noreferrer">https://doi.org/10.1038/s41587-020-0439-x</a></li>
</ul>
<p>In the output of PGS Calculator, I have found a file named versions.yaml containing the followng information:</p>
<pre><code>pgscatalog_utils: 0.3.1
</code></pre>
<p>but I do not think this is the PGS Calculator version. Where do I find the version of the PGS Calculator I used so that I can mention it in the Methods section of a paper?
Thanks, and best wishes,</p>

CC BY-SA 4.0
2024-04-12T15:48:37.230Z
Did you use git to clone the repo? If so, you can use `git log` to find the hash and date of the commit you worked under and cross reference versions on their github repo. Unless I missed something, they haven't made it easy.
dthorbur
CC BY-SA 4.0
2024-04-23T05:28:15.180Z
Do you get any output from `nextflow run pgscatalog/pgs-calc --version`?
jared_mamrot
<nextflow>
Where do I find which PGS Calculator version I am using?
# Where do I find which PGS Calculator version I am using?

(Asked by: username_0 on 2024-04-11)

I have run this command:
nextflow run pgscatalog/pgscalc -profile singularity --input {input.samplesheet} --target_build GRCh38 --scorefile {input.scorefile} --outdir /output/{wildcards.PGS_ID}/

I am now preparing methods for a paper. I need to cite:

PGS Catalog Calculator. PGS Catalog Team. https://github.com/PGScatalog/pgsc_calc
Lambert et al. (2021)
The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nature Genetics. 53:420–425 doi:10.1038/s41588-021-00783-5
Ewels, P.A., Peltzer, A., Fillinger, S. et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol 38, 276–278 (2020). https://doi.org/10.1038/s41587-020-0439-x

In the output of PGS Calculator, I have found a file named versions.yaml containing the followng information:
pgscatalog_utils: 0.3.1

but I do not think this is the PGS Calculator version. Where do I find the version of the PGS Calculator I used so that I can mention it in the Methods section of a paper?
Thanks, and best wishes,

**Tags:** nextflow
> **Comments:**
> **username_1**: Did you use git to clone the repo? If so, you can use `git log` to find the hash and date of the commit you worked under and cross reference versions on their github repo. Unless I missed something, they haven't made it easy.  
> **username_2**: Do you get any output from `nextflow run pgscatalog/pgs-calc --version`?  

---

## 1 answers

### Answer by username_3 on 2024-05-10. Score: 2

Since you are running via singularity you can find out the version you are using from the container, defined in modules.config for this pipeline (<https://github.com/PGScatalog/pgsc_calc/blob/main/conf%2Fmodules.config#L42>), the current version seems to be 0.5.2 for utils and for calc (<https://github.com/PGScatalog/pgsc_calc/blob/main/conf%2Fmodules.config#L56>) it is 1.4.8


---

