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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,

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    $\begingroup$ 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. $\endgroup$
    – dthorbur
    Commented Apr 12 at 15:48
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    $\begingroup$ Do you get any output from nextflow run pgscatalog/pgs-calc --version? $\endgroup$ Commented Apr 23 at 5:28

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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

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