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Ash O'Farrell edited this page Mar 20, 2025 · 2 revisions

To summarize:

  • If you are trying to reproduce our published results as closely as possible, use the latest version of the pipeline in "2024 mode," which is essentially the same pipeline as what we built the tree with but with some minor bugfixes
  • Ash went through versions with a fine-tooth comb to make sure this is the case
  • You don't need to read anything else on this page

To maximize reproducibility, we created a "2024 mode" for the pipeline. Originally this was its own branch of the pipeline, but we quickly realized it made more sense to simply include the very minor updates in the reproducible version of the pipeline, since a lot of changes are helpful to the user.

This page is current as of x.x.x of TB-D. We do not intend on updating it for every small version update. This started as an internal checklist.

SRANWRP pull and processing's direct calls

Exact same across versions

VCF-to-Diff (0.0.3)

Exact same across versions

Decontamination and Cleaning (v2.13.0 vs v2.16.5)

  • Preliminary Q30 and QC_min_q30 are ints instead of floats
  • Can no longer fastp after decontamination (intentional simplification)
  • More fallback files for error handling
  • Supports more than just .fq and .fastq file extensions
  • Does not apt-get install pigz at runtime
  • More precise and informative exits
  • More precise decontam counts parser Additionally, the Docker image is ashedpotaotes/clockwork-plus:0.11.3.12-CRYPTIC instead of ashedpotaotes/clockwork-plus:0.11.3.9-full. Differences:

ashedpotatoes/clockwork-plus:0.11.3.9-full

  • cb15ed82a682c36175ae4c604a727d08 Ref.remove_contam/ref.fa
  • b834ab51337890ba71149a82ded87857 Ref.remove_contam/ref.fa.fai
  • fed44036a9c44347779fc44038b7a65e Ref.remove_contam/ref.fa.minimap2_idx
  • 4b44b3ee898de36e5998b98741d30817 Ref.remove_contam/remove_contam_metadata.tsv

ashedpotatoes/clockwork-plus:0.11.3.12-CRYPTIC

  • cb15ed82a682c36175ae4c604a727d08 Ref.remove_contam/ref.fa
  • b834ab51337890ba71149a82ded87857 Ref.remove_contam/ref.fa.fai
  • d37cfa30728984338fffdea4cca695af Ref.remove_contam/ref.fa.minimap2_idx
  • 4b44b3ee898de36e5998b98741d30817 Ref.remove_contam/remove_contam_meta

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