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Implemented lineage only mode #54

Merged
merged 10 commits into from
Oct 10, 2023
Merged

Implemented lineage only mode #54

merged 10 commits into from
Oct 10, 2023

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johausmann
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@johausmann
Implemented lineage only mode
9d75700 
Implemented generate reference only mode
priesgo
priesgo requested changes Sep 28, 2023
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Would you please add tests to the CI that test for reference_generate and lineage_mode?

Through automated tests you make sure that it works now and that if it's broken later on we know it before it's merged.

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johausmann and others added 9 commits October 5, 2023 16:37
@johausmann
Updated pangolin task to accept vcf with caller == input
27386e7 
Updated main.nf to respect parameter params.skip_normalization
Added integration tests for lineage mode and reference generate mode
@johausmann
Update Makefile
3fa96e2 
Added tests for lineage and reference only modes
@johausmann
Replace whitespace with tab in Makefile
7b0482e
@johausmann
Updated path in test_14.sh
5e90601
@johausmann
Update test_15.sh
ea09b0b 
Make CodeFactor happy
@johausmann
Update test_16.sh
d41a5f0 
Make CodeFactor happy
@johausmann
Update test_14.sh
07b3c52 
Updated test for GATK dict file
@johausmann
Updated lineage test files and added new VCF file as lofreq VCF gives…
ce941c1 
… bcftools errors
@johausmann
Last push did not include updated test scripts
16011f7
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Okay, I've addressed the issues. Let me know if anything else is missing

priesgo
priesgo approved these changes Oct 10, 2023
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Perfect!

@priesgo priesgo merged commit 6a52c63 into master Oct 10, 2023
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@priesgo priesgo priesgo approved these changes

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Pangolin only mode
2 participants
@johausmann @priesgo