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seqeralabs / showcase-automation

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Params outdir should *not* end with a trailing slash #27

Open pditommaso opened 2 months ago

pditommaso commented 2 months ago

https://github.com/seqeralabs/showcase-automation/blob/9be94368f0e5145657a719b70c4828cdd29ff84c/launch_pipelines.py#L111-L112

The outdir parameter should not end with a training slashed because this value is expected to be used as a prefix for other directory paths using the pattern ${params.outdir}/foo/bar and therefore, the trailing slash with result in double slashes

See for example

https://github.com/nf-core/rnaseq/blob/b89fac32650aacc86fcda9ee77e00612a1d77066/conf/modules.config#L54

https://github.com/nf-core/rnaseq/blob/b89fac32650aacc86fcda9ee77e00612a1d77066/conf/modules.config#L63

https://github.com/nf-core/rnaseq/blob/b89fac32650aacc86fcda9ee77e00612a1d77066/conf/modules.config#L71

adamrtalbot commented 1 month ago

It's true but it fails validation with nf-validation before it can reach those string formatting steps. PR is open here but we're struggling to test properly right now. Once it's done we can remove this.

adamrtalbot commented 1 week ago

https://github.com/nextflow-io/nf-validation/pull/171 is merged and released. Once tested we can remove this line.