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Missing pipeline parameters #391

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chasemc opened this issue Jun 20, 2023 · 2 comments
Open

Missing pipeline parameters #391

chasemc opened this issue Jun 20, 2023 · 2 comments

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@chasemc
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chasemc commented Jun 20, 2023

Not sure if this a me issue or tower issue.

When launching a pipeline of mine (https://github.com/socialgene/sgnf) a large number of parameters are missing, even when expanding "hidden". nf-core schema lint . says there aren't any issue, and nf-core launch Web based shows all of the parameters

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

    nf-core/tools version 2.8 - https://nf-co.re


INFO     [✓] Default parameters match schema validation                                                                                                
INFO     [✓] Pipeline schema looks valid (found 88 params) 

I've attached a picture showing tower and nf-core's web-based launcher for the version 0.0.5 of the pipeline


Tower

image

nf-core

image

@chasemc
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chasemc commented Jun 20, 2023

This was due to the definition within the schema.json. I don't remember if the relevant values were something I did manually or automatically by nf-core tools.
The relevant sleuthing and fix by @robsyme is documented here https://github.com/socialgene/sgnf/pull/37/files#diff-4ec6c97fca07ea9b1ff300c0c4488d0f097ae32a78f0e0b01e00b9df0c346eb6

@chasemc
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chasemc commented Jun 20, 2023

So this seems to have turn from a bug to feature request. It would be nice if an array/list type was supported as an input type

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