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## main #5993 +/- ##
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+ Coverage 83.88% 83.94% +0.05%
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Files 336 336
Lines 21022 21069 +47
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+ Hits 17635 17686 +51
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scout/models/omics_variant.py
Outdated
| elif "cpg_label" in values: | ||
| cpg_label = values.get("cpg_label").split("_") | ||
| values["hgncSymbol"] = [cpg_label[1]] | ||
| values["hgncId"] = [cpg_label[2].split(":")[1]] |
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Seems like it might have been a good thing to do this in the pipeline.
Especially if we would like to be able to filter on clinical/research HGNCs before upload, or run with a GoS background file that might have e.g. CpG:_104 as cpg_label.
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Absolutely! I got the impression from Ine that was as far as you got? It would also be prudent to have the sample ID in the file, not just in the filename.
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Yes, this is indeed the current state. We can add it to the Nallo TODO.
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It would also be prudent to have the sample ID in the file, not just in the filename.
Are you happy to have these files per sample, or would you rather have them per case if we add sample ID as a column?
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Both are ok. We would be very used to joint case VCF files, but many of these "extras" are provided on a per sample basis anyway. I guess conceptually I would like more of a per-sample single analysis "outcome" column. I have a feeling if we want to pass more of the values for full cases, we will be straining the tsv format and perhaps better go to a VCF.
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The DROP files went single sample per line. That is one way to avoid having a "FORMAT" type column.
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Hm, and yes, they are per-case files, as are the other variant files, so it would be convenient.
…oci with no signal
| somalier_ancestry: Optional[str] = None | ||
| somalier_pairs: Optional[str] = None | ||
| somalier_samples: Optional[str] = None | ||
| exe_ver: Optional[str] = None |
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Just duplicated, likely from an older sort. 🤷♂️
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3 participants
This PR adds a functionality or fixes a bug.
For a start, this PR presumes we will have
sample_idas a column in https://github.com/Clinical-Genomics/MTP-NALLO/issues/88. It is intended to be agnostic of https://github.com/Clinical-Genomics/MTP-NALLO/issues/89, at least with regard to HGNC id being present as a separate column, or as part of thecpg_label- which is the current state.Testing on cg-vm1 server (Clinical Genomics Stockholm)
Prepare for testing
scout-stageand the server iscg-vm1.ssh <USER.NAME>@cg-vm1.scilifelab.sesudo -iu hiseq.clinicalssh localhostpodman pssystemctl --user stop scout@<name_of_currently_deployed_branch>systemctl --user start scout@<this_branch>systemctl --user status scout.targetscout-stage) to be used for testing by other users.Testing on hasta server (Clinical Genomics Stockholm)
Prepare for testing
ssh <USER.NAME>@hasta.scilifelab.seus; paxa -u <user> -s hasta -r scout-stage. You can also use the WSGI Pax app available at https://pax.scilifelab.se/.conda activate S_scout; pip freeze | grep scout-browserbash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>us; scout --versionpaxaprocedure, which will release the allocated resource (scout-stage) to be used for testing by other users.How to test:
Expected outcome:
The functionality should be working
Take a screenshot and attach or copy/paste the output.
Review: