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replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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Freyja integration #268

Closed DataSpott closed 1 month ago

DataSpott commented 1 month ago

Integration of Freyja for metagenomic screening of reads. Includes also a restructuring of the LCS-tool for metagenomic read-analysis.

hoelzer commented 1 month ago

@DataSpott okay, I pushed my changes to make the update for freyja happen in the work dir to also work with Singularity.

Please have a look, I also hope I set all the params correctly so it really uses the downloaded files in the workdir and does not fallback to the old files installed in the freyja conda env

hoelzer commented 1 month ago

please update stub otherwise okay

Can @DataSpott do that? Would be nice if we can merge this then and then we would also test further

DataSpott commented 1 month ago

Had already a look at it, but could not yet identify the reason why stub fails. Happens in the fast5-test but what I saw so far the stub-profiles are setup correctly. Need to investigate this further.

DataSpott commented 1 month ago

Found the error. Will now conduct a test run to make sure that everything works properly and report than if the merge can be done.

replikation commented 1 month ago

can be merged if everything is also fine on your end @hoelzer

DataSpott commented 1 month ago

Just to follow up: my "test_fast5"-profile run was successful with the latest changes.

hoelzer commented 1 month ago

Also fine for me!

After the merge we should still keep an eye on any results bc as we discussed on BC I am not 100% certain the update parameter works as intended. I am 95% sure :)

We can test this with a very recent patient sample that has a very fresh lineage assignment (a lineage not assigned on March) and then see what the pipeline annotates with frejya in default mode and with update. As a sanity check