Comments (3)
I'll test a version >=0.4.3
to ensure full compatibility but assuming all is well I will update the pinned version with the next conda release, however if you wish to try this locally you can do so by installing from source and updating the version in environment.yml
prior to solving the conda environment.
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Version 1.2.3 now pins a version of longshot >= 0.4.5 to fix this and a few other errors.
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I've finally gotten around to trying this for myself locally. Have been trying it with something that reliably fails using longshot 0.4.1 and it works with longshot 0.4.5, and the update doesn't break my usual test dataset either, so I'll go ahead and create a pull request.
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Related Issues (20)
- artic pipeline not installing properly: ModuleNotFoundError: No module named 'importlib.metadata' HOT 1
- vcf_filter.py filtering parameters and align_trim.py for alternative primer scheme
- Error with medaka consensus HOT 1
- Unable to install artic on mac
- artic_vcf_merge Fails HOT 2
- What is the default mindepth ? HOT 4
- pipeline has stopped working...! HOT 5
- Conda recipe for 1.2.3 not working HOT 8
- no version information available (required by samtools) HOT 5
- Overlapping variants in fail.vcf and pass.vcf cause preconsensus to be masked and thus bcftools complains when applying the "pass" variant HOT 2
- Artic v5 mismatched primer names in bedfile causes "dropped" amplicons HOT 1
- Update medaka version HOT 2
- KeyError: 'SupportFraction' when running margin_cons.py
- Clarify what's meant by 'Suppress variant'
- Conda environment set up HOT 3
- Custom bed file with "primer gaps" causes workflow to crash at artic-tools vcf_checker step HOT 1
- Error: bcftools consensus fail with overlapping variants HOT 5
- htslib =1.17 dependency PLEASE UPDATE HOT 1
- PyVCF assigns a QUAL value of '.' instead of zero
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