workflow runs when outdir parameter is missing
RobJY opened this issue · comments
Description of the bug
Even though the outdir parameter is defined as required in the schema file the workflow runs when it is missing.
Command used and terminal output
'''
nextflow run ~/github/mcmicro-nf-core/main.nf --input_cycle ~/github/mcmicro-nf-core/assets/samplesheet_1_row_sample_cycle_multi_2.csv --marker_sheet ~/github/mcmicro-nf-core/assets/markers_multi_8.csv -profile test_work -params-file ~/github/mcmicro-nf-core/conf/workflow.json
'''
It runs to completion, but output is stored in a directory named 'null'.Relevant files
No response
System information
No response
I just pushed an update that explicitly checks for the outdir parameter and stops execution with an error message if it's missing.
I still need to figure out why it isn't being caught by the schema check, but this will fix the issue for now.
Interestingly, if I fail to provide a markersheet I get an error that looks like it's from schema validation as we expect
nextflow.validation.SchemaValidationException:
Still looking into why we don't get the same for a missing outdir parameter
I had a bug in the schema file and also needed to explicitly declare the path to the testing schema file.
works now.