quiltdata/nf-quilt

Reduce debug logging

Closed this issue · 5 comments

drernie commented

We don't need ALL this debugging information. Mainly just:

  • which Quilt URIs are used for input and output
  • the exact quilt3 commands
  • whether things succeed
drernie commented

Convert non-fatal errors to warnings

theJasonFan commented

Hi! Thanks for the plugin!

FWIW there's also this one here:

nf-quilt/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy

Line 198 in 9eaf13c

log.error("failed to install $packageName")

I think this error gets hit whenever a new package is created. Tracing the path in the source, setup() is called here

nf-quilt/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy

Line 125 in 9eaf13c

this.setup()
and setup() calls install().

drernie commented

Thanks. this is causing issues in both directions. I will try to wrangle it down next week.

  • 👍1
drernie commented

Seems resolved

drernie commented

@theJasonFan If you are still seeing issues, please try to reproduce with 0.8.6 or later

# export NXF_VER=23.04.3
export LOG4J_DEBUG=true  # for verbose logging
export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.8.6/nf-quilt-0.8.6-meta.json
nextflow run main.nf -plugins nf-quilt@0.8.6