[Augur] Expose Augur versions

[Michal-Babins]

This PR closes #685

🗑️ This dev branch should be deleted after merging to main.

🧠 Summary

This PR captures versions for iqtree, fasttree, raxml, and version of iqtree model being used with Augur.

⚡ Impacted Workflows/Tasks

wf_augur
task_augur_tree

This PR may lead to different results in pre-existing outputs: No

This PR uses an element that could cause duplicate runs to have different results: No

🛠️ Changes

Outputs have been added to capture the following version outputs for augur:

String iqtree_version = read_string("IQTREE_VERSION")
String fasttree_version = read_string("FASTTREE_VERSION")
String raxml_version = read_string("RAXML_VERSION")
String iqtree_model_used = read_string("FINAL_MODEL.txt")

Where iqtree_model_used is for the actual iqtree model and not iqtree software version which is captured in iqtree_version.

⚙️ Algorithm

In task_augur_tree, now depending on what method is chosen (iqtree,fasttree,raxml) that sofware version will be captured in the output.

➡️ Inputs

⬅️ Outputs

The following output has been added to task_augur_tree:

String iqtree_version = read_string("IQTREE_VERSION")
String fasttree_version = read_string("FASTTREE_VERSION")
String raxml_version = read_string("RAXML_VERSION")
String iqtree_model_used = read_string("FINAL_MODEL.txt")

The following outputs have been added top level to wf_augur:

String augur_iqtree_model_used = augur_tree.iqtree_model_used
String augur_iqtree_version = augur_tree.iqtree_version
String augur_fasttree_version = augur_tree.fasttree_version
String augur_raxml_version = augur_tree.raxml_version

🧪 Testing

Suggested Scenarios for Reviewer to Test

🔬 Final Developer Checklist

• The workflow/task has been tested and results, including file contents, are as anticipated
• The CI/CD has been adjusted and tests are passing (Theiagen developers)
• Code changes follow the style guide
• Documentation and/or workflow diagrams have been updated if applicable (Theiagen developers only)

🎯 Reviewer Checklist

• All changed results have been confirmed
• You have tested the PR appropriately (see the testing guide for more information)
• All code adheres to the style guide
• MD5 sums have been updated
• The PR author has addressed all comments
• The documentation has been updated

[kapsakcj]

For clarity - iqtree_model_used output String was implemented/added in a separate PR: #674

This PR adds the ability to capture the model used in the rare scenario that the user provides a BED file to augur_tree task for masking. This was not working previously.

Want to also note that this PR adds augur_mafft_version to the wf_augur top level workflow.

And lastly, we added set -euo pipefail to the augur_tree and augur_align tasks.

Here are links to my tests in Terra:

• ✅ testing new String outputs augur_raxml_version & augur_mafft_version output.
  • augur_fasttree_version, augur_iqtree_version, and augur_iqtree_model_used are blank as expected.
  • https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/CDPH_Support_Sandbox/job_history/f1c8ce59-d7dc-4a01-9b81-0be7f9a98bf4
• ✅ testing new String outputs augur_fasttree_version & augur_mafft_version.
  • augur_raxml_version, augur_iqtree_version, and augur_iqtree_model_used are blank as expected.
  • https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/CDPH_Support_Sandbox/job_history/802227b1-cefb-44df-9670-500111ecca71
• ✅ testing new String output augur_iqtree_version. Ensuring (somewhat new) String output augur_iqtree_model_used is output
  • augur_fasttree_version and augur_raxml_version are blank as expected.
  • https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/CDPH_Support_Sandbox/job_history/5f1f3aa0-e904-4e03-a6b9-a58eea460de4

I'm going to launch one more test with a BED file used as input for the augur_tree task, just to ensure iqtree version and model output strings are still present

[kapsakcj]

last test. Ran successfully ✅ and produced the augur_iqtree_model_used even when using a BED file as input to the exclude_sites variable for the augur_tree task for masking. https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/CDPH_Support_Sandbox/job_history/5e89f9f8-221e-454b-965a-5be714810a10

Don't forget about updating the Augur docs for these new output strings

[Michal-Babins]

I tested the following above to confirm:

augur_raxml_version & augur_mafft_version:
https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/CDPH_Bioinformatics_Development/job_history/608547cd-9f11-46a9-8da8-50ac175e8255

augur_fasttree_version & augur_mafft_version:
https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/CDPH_Bioinformatics_Development/job_history/f4b194ae-1496-47b0-b0f7-8b89c9babb7d

augur_iqtree_version & augur_iqtree_model_used:
https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/CDPH_Bioinformatics_Development/job_history/91bc7dc0-68b4-404c-a95e-3c43720ff350

augur_iqtree_model_used & bed file with exclude sites.
https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/CDPH_Bioinformatics_Development/job_history/a352ea1b-f61d-458d-880e-c7148fbaacd7

Documentation also updated.

[kapsakcj]

Thanks for running those tests and updating the docs, much appreciated! Nice work on this PR 👍

CC @sage-wright I believe it's ready for merging

[sage-wright]

you've got an extra echo here

[sage-wright]

ah i see you're using them as line breaks in the output log

[sage-wright]

⭐