Code

Refactor with fixes from Champagne QC#32

Code

Merged

kelly-sovacool merged 29 commits intomainCCBR/nf-modules:mainfrom champagne-qc-fixesCCBR/nf-modules:champagne-qc-fixesCopy head branch name to clipboardNov 1, 2023

+302-15

Commits

Commits on Oct 27, 2023

• fix: refactor from QC fixes for CHAMPAGNE

  kelly-sovacool

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• feat: create custom module to count fastq reads

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• docs: metadata for countfastq module

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• docs: update filter_blacklist meta w/ custom/countfastq component

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• fix: path to custom/countfastq module

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• fix: CUSTOM_COUNTFASTQ module name

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Commits on Oct 31, 2023

• fix: get flagstat of filtered bam

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• fix: use biopython to count fastqs

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Commits on Nov 1, 2023

• fix: use standard process label

  kelly-sovacool

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• fix: increase resources for samtools sort

  kelly-sovacool

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• fix: input type integer->value

  kelly-sovacool

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• fix: count fastq records w/ Biopython instead of grep

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  kelly-sovacool

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• refactor: use custom count fastq

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  kelly-sovacool

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• chore: Merge branch 'champagne-qc-fixes' of https://github.com/CCBR/nf-modules into champagne-qc-fixes

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• test: create test infra for custom/countfastq

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• test: create blank gzip file

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• fix: Revert "fix: input type integer->value"

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• fix: add 'when' condition

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• fix: add custom/countfastq to tags

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• test: fix path to custom test data config

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• fix: stub for custom_countfastq

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• docs: add biopython to keywords

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• feat: output versions in countfastq

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• refactor: make write_versions() function

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• fix: touch versions.yml in stub

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• feat: include versions from custom/countfastq

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• test: create test.yml for custom/countfastq

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• docs: add custom/countfastq to changelog

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• fix: linting errors

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