Reduce debug logging

[drernie]

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]

Convert non-fatal errors to warnings

[theJasonFan]

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]

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

[drernie]

Seems resolved

[drernie]

@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 [email protected]

[theJasonFan]

@drernie Thanks for closing the issue. If I run into this issue again I will try to reproduce.