Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-05-10T16:22:02.877Z
Answers.LastActivityDate: 2024-05-10T16:22:02.877Z
Answers.UserDisplayName: Niklas
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-12T15:48:37.230Z
Comments.Text: 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.
Comments.UserDisplayName: dthorbur
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-23T05:28:15.180Z
Comments.Text: Do you get any output from `nextflow run pgscatalog/pgs-calc --version`?
Comments.UserDisplayName: jared_mamrot
Tags: <nextflow>
Title: Where do I find which PGS Calculator version I am using?
ThreadText: # 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
  
  
  ---
  
  