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bacterial-genomics / wf-paired-end-illumina-assembly

pathogen agnostic general workflow for genome assembly of Illumina paired-end sequence data
Apache License 2.0
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Silence warns when miniburk skesa test run performed #59

Closed chrisgulvik closed 8 months ago

chrisgulvik commented 9 months ago

Description of feature

https://github.com/bacterial-genomics/wf-paired-end-illumina-assembly/actions/runs/7848816398/job/21420781580?pr=50 GH Actions using skesa shows several WARN messages such as:

WARN: Kraken could not be performed - database not specified using --kraken1_db!
WARN: Kraken2 could not be performed - database not specified using --kraken2_db!
WARN: There's no process matching config selector: ASSEMBLY:ASSEMBLE_CONTIGS:ASSEMBLE_CONTIGS_SPADES -- Did you mean: ASSEMBLY:ASSEMBLE_CONTIGS:ASSEMBLE_CONTIGS_SKESA?
WARN: There's no process matching config selector: ASSEMBLY:READ_CLASSIFY_KRAKEN_ONE
WARN: Undocumented setting `docker.userEmulation` is not supported any more - please remove it from your config