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nf-core / mcmicro

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
https://nf-co.re/mcmicro
MIT License
4 stars 12 forks source link

workflow runs when outdir parameter is missing #18

Closed RobJY closed 3 months ago

RobJY commented 3 months ago

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

RobJY commented 3 months ago

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.

RobJY commented 3 months ago

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

RobJY commented 3 months ago

I had a bug in the schema file and also needed to explicitly declare the path to the testing schema file. works now.