[FEATURE] Fix bioconda recipe for deepvariant

[maxulysse]

Latest release is 1.1.0.
Latest available on bioconda is: 1.0.0

[abhi18av]

Hi @maxulysse

As some background work for nf-core/sarek#394 I had a look at the deepvariant container available in biocontainers and conda, however they don't bundle the run_deepvariant.py wrapper utility which was released last year.

For the purpose of the module, I'm relying on Google's container for deepvariant and once the module design is finalized, I'll try to accomodate those changes in conda version of deepvariant recipe.

[FriederikeHanssen]

Hey @abhi18av ! What is the status here?

[abhi18av]

Hi @FriederikeHanssen ,

This is a tough nut, I have initiated an issue on the bioconda side bioconda/bioconda-recipes#30310 and taken a stab at the recipe here https://github.com/bioconda/bioconda-recipes/pull/30311/files, however I found the build script to be a bit convoluted and contacted the core authors through the issue.

Haven't heard back from them regarding the inclusion of run_deepvariant script. However, on the nf-core/modules side (#572 ) the docker and singularity builds directly use the official Google containers which are passing the tests.

[FriederikeHanssen]

ok, then let's leave this issue open :) Thank you, I tried to clean up a bit before tomorrow

[FriederikeHanssen]

Should we move this issue to modules? Not exactly a sarek related one

[SPPearce]

Anyone know if this is fixed yet?

[famosab]

I would say no: https://anaconda.org/bioconda/deepvariant (this is 1.5.0)