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TheJacksonLaboratory / cs-nf-pipelines

The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines
MIT License
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initial changes for elion deployment #3

Closed gabyrech closed 6 months ago

gabyrech commented 8 months ago

Added changes for Elion deployment. Modified config/profiles/elion.config, config/rnaseq.config and modules/rsem/rsem_alignment_expression.nf. Created a new variable called REFERENCE_CACHE to redirect to different local instances depending on profile. This work only for rnaseq pipeline. Tested on elion using bowtie2 and star.

MikeWLloyd commented 8 months ago

The proposed change makes sense and I do see the value making the root input directory flexible. The code looks OK but we will need to go through our internal testing to make sure as a final sanity check on our end. Prior to testing, the Sumner profile needs the REFERENCE_CACHE modification.

Prior to merge, the configs files of all major workflows will need to be updated. I would like to avoid having a handful of configs on a different system. @gabyrech would you be able to take a first pass at that?

MikeWLloyd commented 8 months ago

I took care of adding ENV to sumner config. I will do RNA-seq pipeline testing on Sumner with the proposed change.

gabyrech commented 8 months ago

The proposed change makes sense and I do see the value making the root input directory flexible. The code looks OK but we will need to go through our internal testing to make sure as a final sanity check on our end. Prior to testing, the Sumner profile needs the REFERENCE_CACHE modification.

Prior to merge, the configs files of all major workflows will need to be updated. I would like to avoid having a handful of configs on a different system. @gabyrech would you be able to take a first pass at that?

Sure! I can take that.

MikeWLloyd commented 6 months ago

Closed in favor of different approach