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
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.
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.logProblem is in file https://github.com/fmalmeida/MpGAP/blob/master/nf_functions/writeCSV.nf
Instead of
println
should belog.error
and instead ofexit 1
should beSystem.exit(1)
.