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pangolin stub, nf-test, snap #4671

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pangolin stub, nf-test, snap #4671

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sateeshperi
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@sateeshperi sateeshperi requested review from KevinMenden, drpatelh and a team as code owners December 30, 2023 18:46
@sateeshperi sateeshperi added Ready for Review nf-test mismatched hashes Conda/singularity hashes aren't right labels Dec 30, 2023
CarsonJM
CarsonJM approved these changes Jan 4, 2024
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Any idea what's going on with the conda tests?

modules/nf-core/pangolin/tests/main.nf.test Show resolved Hide resolved
@sateeshperi
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not sure whats up with conda...have to check the bioconda recipe

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csv output from docker:

taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note
"MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome",B.1,0.0,,,,,,PANGO-v1.17,4.2,0.3.17,v0.1.10,True,pass,Ambiguous_content:0.02,Assigned from designation hash.

csv output from conda:

taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note
"MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome",B.1,0.0,,,,,,PANGO-v1.28,4.2,0.3.19,v0.1.12,True,pass,Ambiguous_content:0.02,Assigned from designation hash.

This suggests there is a different database being used.
Maybe seqera containers will fix this?

@SPPearce SPPearce added container-issue and removed nf-test mismatched hashes Conda/singularity hashes aren't right labels Jun 26, 2024
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sateeshperi commented Oct 6, 2024 •
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closing in favor of #6740

@sateeshperi sateeshperi closed this Oct 6, 2024
@sateeshperi sateeshperi deleted the feat/pangolin-nf-test branch October 6, 2024 10:11
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@CarsonJM CarsonJM CarsonJM approved these changes

@KevinMenden KevinMenden Awaiting requested review from KevinMenden

@drpatelh drpatelh Awaiting requested review from drpatelh

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@sateeshperi @SPPearce @CarsonJM