Parallelism Using Pypeliner

[um-pdavila]

Thank you for ReMixT team for your work. Thank you community for your comments.

I think we are missing critical information in the Parallelism Using Pypeliner section of the documentation. A couple examples of following the documentation that do not work are listed below.

I've been modifying the ReMixT code in efforts to get parallelization working, defaulting to using all available cores on the local machine. I will fork the project and update once I get it working.

Setup ReMixT

Reference genome
Following the documentation, I tried running:

remixt create_ref_data $ref_data_dir --maxjobs 32

The commands fails when we add --maxjobs. The remixt create_ref_data $ref_data_dir command completes, but only uses one core.

Mappability file
I had to add --submit local to get the remixt mappability_bwa $ref_data_dir command to run. Unfortunately, it only used 1 core. I ran:

remixt mappability_bwa $ref_data_dir --submit local --maxjobs 32