fmalmeida / MpGAP

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
https://mpgap.readthedocs.io/en/latest/
GNU General Public License v3.0
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When not giving `--genome_size` for long reads, message goes to log and not console #68

Closed fmalmeida closed 4 months ago

fmalmeida commented 4 months ago

When running a samplesheet that has longreads assemblies, if one forget to give the --genome_size parameter, the pipeline exits without showing the error message in the console. The message appears only in the .nextflow.log

Problem is in file https://github.com/fmalmeida/MpGAP/blob/master/nf_functions/writeCSV.nf

Instead of println should be log.error and instead of exit 1 should be System.exit(1).

fmalmeida commented 4 months ago

This was a problem in master but in the dev branch, the log.error function is already being used and thus, it is working properly and this is irrelevant.