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AndersenLab / alignment-nf

A nextflow pipeline for genome sequences alignment
MIT License
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test run is ok; suggestions for conda #5

Closed danrlu closed 4 years ago

danrlu commented 4 years ago

Results can be found here: /projects/b1059/projects/Dan/alignment-nf

The only thing I noticed is that conda "bwa=0.7.17 sambamba=0.7.0" will create the environment on the fly and (1) is slow (2) will create a new environment every time the script runs (3) add all these unnamed environment to conda env list.

So it's probably better to take environment creation out of the pipeline. Can export the .yml from conda as a record for the environment.

Otherwise all is good.

danielecook commented 4 years ago

I believe we are all set on this.