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CDCgov / mycosnp-nf

CDCgov/mycosnp-nf
Apache License 2.0
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Downrate Default Behavior Update #94

Closed jwarnn closed 1 year ago

jwarnn commented 1 year ago

PR to address issues #83 and #84. The behavior of the local module DOWNSAMPLE_RATE which also sends variables to SEQTK_SAMPLE to subsample the fastq files was causing issues with resource management and a source excessive/confusing parameter. This PR changes the nextflow.config to eliminate the parameter rate and changes the behavior if coverage is set to 0 so seqtk sample will be skipped. This eliminates seqtk sample running for all the reads; which was the original default behavior that was causing issues. Maybe #90 could be worked into this PR because it would need an edit to modules/local/downsample_rate.nf.

hseabolt commented 1 year ago

Changes look good to me, approving this PR to merge into dev for validation testing.