Remove explicit reddim_genes.yml requirement

[azedinez]

Since this is an optional file, this should not be required by the pipeline?

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[pinin4fjords]

The logic is intended to check for file existence only where the file is specified. Are you seeing it run this check even without the file being provided?

[pinin4fjords]

This is probably the issue in fact:

scflow/nextflow.config

Line 34 in c49202f

reddim_genes_yml = './conf/reddim_genes.yml'

(i.e. there's a default value for this 'optional' input). Did you try unsetting the optional things?

[pinin4fjords]

Though I'm not sure how optional this really is, given that the channel is used unconditionally

[azedinez]

Yes I try to not specify anything i.e. remove the value that was previously set, but the pipeline still expects it because of the line above

[pinin4fjords]

What I'm saying is, the if (params.reddim_genes_yml) { should prevent the existence check from happening where the parameter is not supplied, which implies that the problem is the value is getting set inappropriately somewhere, rather than the existence check itself.