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Subworkflow installation bug #2928

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IreneRobles opened this issue Apr 22, 2024 · 0 comments
Open

Subworkflow installation bug #2928

IreneRobles opened this issue Apr 22, 2024 · 0 comments
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@IreneRobles
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IreneRobles commented Apr 22, 2024

Description of the bug

If you have paths as:

include { MY_SMALL_SUBWORKFLOW }  from '../../../subworkflows/org/my_small_subworkflow/main.nf'

When you do nf-core module install of nf-core module update it looks for a module named modules/org/my/small/subworkflow, which does not exist, and therefore it errors out. What does exist is the subworkflow my_small_subworkflow.

To load a subworkflow inside a subworkflow during installation, the path must be:

include { MY_SMALL_SUBWORKFLOW  }  from '../my_small_subworkflow/main.nf'

I think both path strings should be allowed

Command used and terminal output

$nf-core subworkflows install my_big_subworkflow

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.13.1 - https://nf-co.re


INFO     Reinstalling 'my_big_subworkflow'                                                                                                                                                                                                                    
ERROR    Module 'my/small/subworkflow' not found in list of available modules.

System information

nf-core/tools version 2.13.1

@IreneRobles IreneRobles added the bug Something isn't working label Apr 22, 2024
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