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Parameter passing from workflow happens after nextflow.config is resolved. #2

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mahesh-panchal opened this issue Feb 22, 2022 · 0 comments

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@mahesh-panchal
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addParams does not update the parameters before they're used in the nextflow.config.

include { NFCORE_FETCHNGS } from "$projectDir/subworkflows/fetchngs/main" addParams(
        outdir: params.fetchngs_outdir, 
        nf_core_pipeline: 'rnaseq'
    )

This means that the execution reports which also use params.outdir use the default value, or the value from the -params-file/CLI. So this may not be a problem since it's for the entire workflow, but need to be careful with other params.

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