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Remove explicit reddim_genes.yml requirement #25

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Remove explicit reddim_genes.yml requirement #25

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2 changes: 1 addition & 1 deletion workflows/scflow.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ if (params.celltype_mappings) { ch_celltype_mappings = file(params.celltype_mapp
if (params.ensembl_mappings) { ch_ensembl_mappings = file(params.ensembl_mappings, checkIfExists: false) }
if (params.ensembl_mappings) { ch_ensembl_mappings2 = file(params.ensembl_mappings, checkIfExists: false) }
if (params.ensembl_mappings) { ch_ensembl_mappings3 = file(params.ensembl_mappings, checkIfExists: false) }
if (params.reddim_genes_yml) { ch_reddim_genes_yml = file(params.reddim_genes_yml, checkIfExists: true) }
if (params.reddim_genes_yml) { ch_reddim_genes_yml = file(params.reddim_genes_yml, checkIfExists: false) }
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@pinin4fjords pinin4fjords Mar 20, 2023

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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?

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@pinin4fjords pinin4fjords Mar 20, 2023 •
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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?

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@pinin4fjords pinin4fjords Mar 20, 2023

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

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@azedinez azedinez Mar 20, 2023

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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

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@pinin4fjords pinin4fjords Mar 21, 2023

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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.


/*
========================================================================================
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