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Kurt-Hetrick / CIDR_WES

CIDR's production pipeline for WES and other targeted DNA sequencing projects.
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switch to doing concordance on grch38 arrays #134

Closed Kurt-Hetrick closed 4 months ago

Kurt-Hetrick commented 6 months ago

not sure about the best strategy at the moment. options to consider.

  1. new pipelines for every pipeline. not my favorite, but doable. mostly the submitters have to be new with a couple new scripts added to either build specific or common scripts.
  2. new branch, change the current one to a new branch and make the grch38 branch the main branch. probably less favorable than number 1 b/c of having to push/pull changes from branches to keep both of the current...probalby have to another branch specific dev branch as well. yeah, not doing this one after typing it down.
  3. add a new default switch/argument. one that specifies array build and then build an if/then statement calling specific functions for concordance workflow. can either make it optional and default it to a specific build or mandatory and validate that it is both present and specified in a specific way. this is probably the best option, but of course it would take the most amount of work/expertise. would have to start on it soon.
Kurt-Hetrick commented 4 months ago

went with option 3. done for the grch37 pipeline.

Kurt-Hetrick commented 4 months ago

done for all wes/targeted seq qc pipelines