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BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
GNU General Public License v3.0
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Output nice errors when settings files are not defined #50

Closed frenkiboy closed 10 months ago

frenkiboy commented 5 years ago

Wen settings files are not defined the pipeline crashes with uninformative error

borauyar commented 5 years ago

@frenkiboy do you mean the locations section in the settings? There is a check for all locations in the validate_input.py script. See here: https://github.com/BIMSBbioinfo/pigx_rnaseq/blob/cc9d6719b1561b8d3d5c7caa1b40840020b58d73/scripts/validate_input.py#L23

borauyar commented 10 months ago

I can't reproduce this error. When settings.yaml is not provided, the pipeline fails with a message:

usage: pigx-rnaseq [-h] [-v] (--init [{settings,sample-sheet,both}] | -s SETTINGS) [-c CONFIGFILE] [--target TARGET] [-n] [--graph GRAPH] [--force] [--reason] [--unlock] [--verbose] [--printshellcmds] [--snakemake SNAKEMAKE] [sample_sheet]
pigx-rnaseq: error: one of the arguments --init -s/--settings is required