Missing "paired" input for fastp tool

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1

Hi! I’d like to ask if there’s a bug in the fastp tool. When I tried to create a workflow manually and used this tool, the input only included “single” and “paired collection”. Thank you very much in advance.

Screenshot 2025-02-17 012823
Screenshot 2025-02-17 0128231867×889 173 KB

Regards,
John Kim

2

I noticed the same, was going to post about it, but saw your post.

1 Like
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Great, thanks @John_Kim for reporting the issue and @Jon_Colman for confirming it. The brand new tool wrapper does seem to have a problem.

What to do

Toggle the tool version to the prior version in the pull down menu.

Input menu with buggy display (tool panel or workflow)

  • fastp fast all-in-one preprocessing for FASTQ files(Galaxy Version 0.24.0+galaxy4)

Correct input menu

  • fastp fast all-in-one preprocessing for FASTQ files(Galaxy Version 0.24.0+galaxy3)

This is where to toggle in the workflow editor. (or on the tool form)

fastp-input-select
fastp-input-select818×496 53.4 KB

Tracking ticket → Correction: fastp is missing an input type on the form select menu · Issue #6781 · galaxyproject/tools-iuc · GitHub

Thanks again! :hammer_and_wrench:

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4

Hi @jennaj,

I hope you’re doing well mate, thank you very much for your immediate response.

Regards,
John Kim

5

As mentioned in the linked ticket the removal of the option was intentional. The reason for the removal was to simplify the complexity of the tool wrapper.

Since paired data can still be used, no functionality is lost in my opinion. You “just” need to organize the data as paired collection.

Would you agree with my argumentation? I would be happy to discuss. What is your use case?

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6

I agree since I am a collection user, so I’ll let others explain what they are needing. I’ll also remember that this was on purpose. Thanks @bernt-matthias !

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Hello @jennaj and @bernt-matthias, I hope everything is going well. To be fair, I also use paired-collection when I have a large number of reads to analyze. However, I noticed that using paired-collection for only two FASTQ files consistently resulted in an error. I was only able to resolve this by uploading them using the ‘paired’ strategy.

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Thanks for the reply. Good to know. I assume that currently there is no issue with issuing a pair as input?

2 Likes
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Hi @John_Kim

For this part

would you like to troubleshoot this? A small example would be helpful. Maybe something else is going on. A paired collection with just one pair should work fine. And if it isn’t, that would be worth investigating. The Upload collection builder is just like the history collection builder, or should be.

Thanks!