Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add a Customizable IQ-TREE option #232

Merged
merged 2 commits into from
Mar 11, 2025
Merged

Add a Customizable IQ-TREE option #232

merged 2 commits into from
Mar 11, 2025

Conversation

Mxrcon
Copy link
Collaborator

@Mxrcon Mxrcon commented Mar 10, 2025

Hey 👋 @abhi18av,

After our last meeting, I'd like to kindly suggest the addition of a new parameter: iqtree_custom_argument, that would allow users to use specific bootstrap number or a specific phylogeny algoritm, as specified in IQ-TREE manual for advanced use of phylogeny inference, that would help to deal with big datasets.

The two basic changes on iqtree module and standard params would be enough to accommodate both of them, It worth to mention that the modifications cited on this PR have been tested with custom parameters using Evandro Chagas Institute infrastructure.

Example of how this parameter should be used:

nextflow run main.nf -profile docker  --iqtree_standard_bootstrap false --iqtree_custom_argument "-bb 5000" --skip_phylogeny_and_clustering false

Produced .command.sh:

 cat .command.sh
#!/bin/bash -ue
iqtree \
    -s joint.variable.ExDR.ExComplex.fa \
    -T AUTO \
    -bb 5000 \
    --prefix joint.ExDR.ExComplex

We could discuss if turning standard bootstrap off is a requirement to run custom params, or not, as this is a Complex feature intended for advanced users, I would like to suggest the strong enforcement of standard. Please, let me know your thoughts on that.

Kindly,
Davi

@Mxrcon Mxrcon added the enhancement New feature or request label Mar 10, 2025
@Mxrcon Mxrcon requested a review from abhi18av March 10, 2025 19:43
@Mxrcon Mxrcon self-assigned this Mar 10, 2025
Copy link
Member

@abhi18av abhi18av left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thank you @Mxrcon for this suggestion, I have requested one minor design change with user-experience in mind and once that is tested we can merge this into the main branch.

Could you please run the checks with the test profile or another small dataset?

@Mxrcon
Copy link
Collaborator Author

Mxrcon commented Mar 11, 2025

👋 New update:

After changes in cfc096d, the current version from this branch was tested with the following command:
nextflow run main.nf -profile docker,test --skip_phylogeny_and_clustering false --iqtree_custom_argument "-bb 5000"

producing the following .command.sh for IQ-TREE process:

#!/bin/bash -ue
iqtree \
    -s joint.variable.ExDR.ExComplex.fa \
    -T AUTO \
    -bb 5000 \
    --prefix joint.ExDR.ExComplex

And the overall run status was:

Completed at: 11-Mar-2025 11:03:25
Duration : 37m 31s
CPU hours : 10.3 (0% cached)
Succeeded : 134
Cached : 1

I would like to hear your thoughs regarding this test,
Kindly,
Davi

Copy link
Member

@abhi18av abhi18av left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks @Mxrcon , it looks great now. I'm merging this :)

@abhi18av abhi18av merged commit 511e27f into master Mar 11, 2025
@abhi18av abhi18av deleted the dev-add-custom-iq-tree branch March 11, 2025 15:02
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants