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gm_thresholds cannot be set to "1" #32

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sgsutcliffe opened this issue Jan 6, 2025 · 0 comments
Open

gm_thresholds cannot be set to "1" #32

sgsutcliffe opened this issue Jan 6, 2025 · 0 comments
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@sgsutcliffe
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sgsutcliffe commented Jan 6, 2025

Description of the bug

It seems that from the CLI if you try and set the parameter --gm_thresholds to "1" it believes it is an integer and fails expecting a string for the parameter.

Works from within the nextflow.config just not from CLI

Command used and terminal output

gasnomenclature$ nextflow run main.nf -profile docker --input tests/data/samplesheets/samplesheet1.csv --outdir results-pipeline-1 --gm_thresholds "1"
Nextflow 24.10.3 is available - Please consider updating your version to it
N E X T F L O W   ~  version 24.04.4
Launching `main.nf` [drunk_lamarck] DSL2 - revision: c64c757f52ERROR ~ ERROR: Validation of pipeline parameters failed!
-- Check '.nextflow.log' file for details
The following invalid input values have been detected:
* --gm_thresholds: expected type: String, found: Integer (1)

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@sgsutcliffe sgsutcliffe added the bug Something isn't working label Jan 6, 2025
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