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Nf composition#14

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aw-watson merged 32 commits intomainLANL-Bioinformatics/EDGEv3:mainfrom nf_compositionLANL-Bioinformatics/EDGEv3:nf_compositionCopy head branch name to clipboardDec 23, 2024

+665,107-1,328

Commits

Commits on Sep 3, 2024

• initial commit

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Commits on Sep 4, 2024

• Prokka and RATT running

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Commits on Sep 5, 2024

• generating plots and KEGG pathway views

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Commits on Sep 6, 2024

• Full workflow, with explicit outputs and TODOs resolved.

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Commits on Sep 9, 2024

• Containerized

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Commits on Sep 12, 2024

• comments

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Commits on Sep 23, 2024

• Nf phage finder (#9)

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• proof of concept: linked runAnnotation and phageFinder, with phageFinder able to be turned on or off

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Commits on Sep 24, 2024

• Merge branch 'main' into nf_composition

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Commits on Oct 22, 2024

• restructured early pipeline. added nf-test infrastructure

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Commits on Oct 23, 2024

• testing added for sra2fastq

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Commits on Oct 29, 2024

• Testing for the first few modules

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Commits on Oct 30, 2024

• merged main into nf_composition to resolve conflicts

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Commits on Nov 5, 2024

• integrated hostRemoval

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Commits on Nov 6, 2024

• runAssembly in pipeline

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Commits on Nov 21, 2024

• host removal testing + cleanup

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Commits on Nov 26, 2024

• tests for runAssembly

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Commits on Dec 9, 2024

• reads to contig restructured as subworkflow. adding nf-test CI

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• fixing JDK version for CI

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• testing Apptainer for CI

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• cleanup

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Commits on Dec 10, 2024

• updated snapshots for JDK 17

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• adding debugging output

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• more testing output for GH actions

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• added Git LFS to testing yml

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• adding sharding to tests - checking to see if this resolves space issues with the runner

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• removing files from LFS

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Commits on Dec 17, 2024

• basic testing for runReadsToContig

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• adding nf-test file

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• attempting optimized testing requirements

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• reverting testing strategy

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Commits on Dec 23, 2024

• host removal testing accounts for inconsistent file naming

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