Code

[Augur] Expose Augur versions #686

Code

Merged

sage-wright merged 15 commits intomaintheiagen/public_health_bioinformatics:mainfrom mb-augur-automodel-output-devtheiagen/public_health_bioinformatics:mb-augur-automodel-output-devCopy head branch name to clipboardDec 11, 2024

+44-2

Commits

Commits on Nov 8, 2024

• Add iqtree model extraction to augur_tree task and update workflow output

  Michal-Babins

  committed
  39ece66

• Refactor augur_tree task to correctly derive FASTA basename and directory for iqtree model extraction

  Michal-Babins

  committed
  d181a17

Commits on Nov 12, 2024

• Add iqtree model used field to augur workflow documentation

  Michal-Babins

  committed
  2ac0c0d

• Handle empty substitution model case in augur_tree task

  Michal-Babins

  committed
  a9a4e65

• Ensure iqtree_model_used is a non-nullable String in augur_tree task and workflow

  Michal-Babins

  committed
  064d677

Commits on Nov 14, 2024

• Update augur workflow documentation to include model options for substitution model and rename iqtree model variable for clarity

  Michal-Babins

  committed
  8e8f1f2

• Add augur_iqtree_model_used variable to documentation for clarity

  Michal-Babins

  committed
  548ca26

Commits on Nov 26, 2024

• added wildcard so we can parse the model name out of log file is a BED file is supplied by user for masking. also added DEBUG echo statement to see model string printed to log file. tested successf…

  Show description for a55fbbb
  kapsakcj

  committed
  a55fbbb

Commits on Dec 2, 2024

• added "set --euo pipefail" to augur tree task, also added 2 output strings for mafft version and iqtree version. added these 2 output strings to Augur workflow

  kapsakcj

  committed
  d7737af

Commits on Dec 3, 2024

• added string output mafft_version to augur_align task; also added set -euo pipefail. tested successfully w miniwdl

  kapsakcj

  committed
  86be573

Commits on Dec 4, 2024

• augur_tree task: added version capture for 3 tree building methods and thus 2 new String outputs. tested all 3 w miniwdl. Also updated augur wf to output these strings

  kapsakcj

  committed
  d8ccef5

Commits on Dec 9, 2024

• Merge remote-tracking branch 'origin/main' into mb-augur-automodel-output-dev

  Michal-Babins

  committed
  7c13734

Commits on Dec 10, 2024

• docs: add version variables for fasttree, iqtree, and raxml in augur workflow

  Michal-Babins

  committed
  e476731

• docs: add mafft version variable to augur workflow documentation

  Michal-Babins

  committed
  4606885

• docs: update descriptions for tree method version variables in augur workflow

  Michal-Babins

  committed
  34ead16