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Commits on Jul 29, 2025

• Merge pull request #345 from biowdl/mqc-add

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• Merge branch 'develop' into mqc-add

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• Merge pull request #346 from biowdl/churra-scylla

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• Merge branch 'develop' into churra-scylla

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• Merge pull request #338 from biowdl/bam2fq

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• Merge branch 'develop' into bam2fq

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• Merge pull request #347 from biowdl/monster-celsius

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Commits on Jul 22, 2025

• Fix duplicate declarations

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• incorrect inputs

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• I don't feel like documenting it if it isn't used

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• I don't feel like documenting it if it isn't used

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• Add modkit tasks

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• Improve whatshap runtime/memory estimates

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• Update clair3 image

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• Merge branch 'develop' into churra-scylla

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Commits on Jul 7, 2025

• Add no name check support, requiring bumping Intersect as well

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• document

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• bump bedtools sort

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Commits on Jun 18, 2025

• ahmust be flatter

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Commits on Jun 17, 2025

• Support supplying additional reports/config to multiqc

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Commits on Jun 11, 2025

• Disable ai in multiqc

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Commits on Jun 10, 2025

• Merge branch 'develop' into bam2fq

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Commits on Jun 6, 2025

• missing trailing slash breaks samtools flagstat

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Commits on May 30, 2025

• Merge branch 'develop' into modkit

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Commits on May 28, 2025

• re-correct it.

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• Update modkit.wdl

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• Update modkit.wdl

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Commits on Apr 23, 2025

• documentation

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• Probably unnecessary

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• require being explicit about locations

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• add biopets validate fastq

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• The caches in containers caused issues

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• do not intermingle singletons

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Commits on Apr 2, 2025

• Add a summary task

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• Add filterThreshold, filterPercent to modkit pileup

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