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1.4.0 pre-release version#135

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Merged

BioWilko merged 64 commits intoartic-network:1.4.0-devartic-network/fieldbioinformatics:1.4.0-devfrom BioWilko:1.4.0-devBioWilko/fieldbioinformatics:1.4.0-devCopy head branch name to clipboardAug 19, 2024

+3,166-2,035

Commits

Commits on Jun 20, 2024

• Deprecate old tools and black format

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• Support fragmented data

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• use new trim primer arg in minion

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• reverse the (revolting) primer position logic

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• Fix find primer logic

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• Improve the cursed report writer logic

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• explicitly named function args, what a novel idea

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• add temp debugging prints to find_primer

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• Add logic to handle segments outside of primer scheme

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• fix typo

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Commits on Jun 21, 2024

• General bugfixes, test fix for overlapping variant issue

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Commits on Jun 25, 2024

• add min mapq argument

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• properly provide min_mapq to handle_segment

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• Fix unmatched read group issue

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Commits on Jun 26, 2024

• Fix 8 bit int error

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Commits on Aug 9, 2024

• First attempt to integrate clair3 as optional

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• Slightly change env yaml format

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• Specify env name in mamba gh action

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• Checkout repo before installing env

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• python 3.6.15

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• Run on ubuntu 20.04

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• unpin python

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• Unpin python entirely

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• Separate out tests

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• correct unit test path

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• remove retvar hints for compatibility

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• Fix silly relative imports

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• Switch to cyvcf and fix unit tests

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• Fix pipeline parse unit test

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• Fix fstring

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Commits on Aug 12, 2024

• Large changes to make clair3 work, various unit test updates

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• Fix fuzzy primer site match logic

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• Fix minion_validator path

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• Fix vcf merge bug with empty VCF files

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• Increase fuzzy match default threshold to 20

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• Fix CHROM bug in vcf merge properly

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• Report failed workflow when variants are missed

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• Fix vcf merge again

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• Separate out tests

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• No counter anymore

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• Add C241T to SP1 variants

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Commits on Aug 13, 2024

• Add limit on ref pileup

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• Single copy of CVR1 12733 var

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• re-enable other consensus tests

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• First attempt to make minion validator less fragile

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• Unify testvariants, improve test logic

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• medaka has to be different smh

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Commits on Aug 14, 2024

• Index ref fasta when using the clair3 workflow

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Commits on Aug 15, 2024

• Add mean amplicon depth TSV output

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Commits on Aug 17, 2024

• Update CLI and scheme fetcher

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• Update align trim unit test

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• Use proper version of V3 bedfile

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• Fix pipeline unit test

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• Fix align trim amp depth bug

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• Call variants on non primertrimmed bam

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• Don't test MT vs clair

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• properly disable test

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• Add docker build push action on release

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• Grab wget in dockerfile

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Commits on Aug 18, 2024

• Update docs and readme

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• docker push on release only

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• Remove debugging print statement

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• Make fuzzy primer match logic clearer

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• Install procps for nxf compatibility

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