Code

Nf composition#14

Code

Merged

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

  aw-watson

  committed
  c4f8afa

Commits on Sep 4, 2024

• Prokka and RATT running

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  committed
  a06a7cb

Commits on Sep 5, 2024

• generating plots and KEGG pathway views

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  committed
  56e79a0

Commits on Sep 6, 2024

• Full workflow, with explicit outputs and TODOs resolved.

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  f4e8762

Commits on Sep 9, 2024

• Containerized

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  a4eb229

Commits on Sep 12, 2024

• comments

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  committed
  ede9fec

Commits on Sep 23, 2024

• Nf phage finder (#9)

  Show description for f9ad25d
  aw-watson

  authored
  f9ad25d

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

  aw-watson

  committed
  e4a124d

Commits on Sep 24, 2024

• Merge branch 'main' into nf_composition

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  committed
  7db78b1

Commits on Oct 22, 2024

• restructured early pipeline. added nf-test infrastructure

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  committed
  323f0f6

Commits on Oct 23, 2024

• testing added for sra2fastq

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  99bae23

Commits on Oct 29, 2024

• Testing for the first few modules

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  committed
  2d50a04

Commits on Oct 30, 2024

• merged main into nf_composition to resolve conflicts

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  committed
  4e66bb4

Commits on Nov 5, 2024

• integrated hostRemoval

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  46f5ede

Commits on Nov 6, 2024

• runAssembly in pipeline

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  committed
  79219ec

Commits on Nov 21, 2024

• host removal testing + cleanup

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  committed
  f4abc8e

Commits on Nov 26, 2024

• tests for runAssembly

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  committed
  6472018

Commits on Dec 9, 2024

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

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  0fcb34a

• fixing JDK version for CI

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  184f453

• testing Apptainer for CI

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  b11e4dc

• cleanup

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  committed
  eddba05

Commits on Dec 10, 2024

• updated snapshots for JDK 17

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  1cd85d7

• adding debugging output

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  committed
  d544168

• more testing output for GH actions

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  committed
  b110dcb

• added Git LFS to testing yml

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  49c618e

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

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  167adfc

• removing files from LFS

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  76c285d

Commits on Dec 17, 2024

• basic testing for runReadsToContig

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  46f4aa2

• adding nf-test file

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  d587915

• attempting optimized testing requirements

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  497acdd

• reverting testing strategy

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  c69b0e0

Commits on Dec 23, 2024

• host removal testing accounts for inconsistent file naming

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  committed
  44f80bf