Add a Customizable IQ-TREE option

[Mxrcon]

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

[abhi18av]

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]

👋 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

[abhi18av]

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