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Feature request: parameter override in config inclusion #4239

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itamary1 opened this issue Aug 30, 2023 · 1 comment
Open

Feature request: parameter override in config inclusion #4239

itamary1 opened this issue Aug 30, 2023 · 1 comment

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@itamary1
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New feature

when including pipeline modules, there is an option of addParams, and it would be ver convinient if such an option also existed for config inclusion.

Usage scenario

Specific use case: variable representing path is used in script to access directory and in config to mout a path.

When overriding the path, the variable get changed only in script while mounting remains the same and a bug occurs due to writing to a non-mounted path

Suggest implementation

includeConfig './SubP_configs/sra_download.nf.docker.config' addParams(sra_fastq_outdir: "${params.raw_data_dir}/Orig_fq")

@bentsherman
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Related to #2662

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