[BUG] Setting the diann_speclib to an empty string breaks the pipeline

[jspaezp]

Description of the bug

Hey there!

Setting the diann_speclib to an empty string breaks the pipeline with

[main] DEBUG nextflow.Session - Session aborted -- Cause: Missing `fromPath` parameter

quantms/workflows/dia.nf

Line 59 in e3c95f0

if (params.diann_speclib != null) {

A while ago I had it as if (...) (https://github.com/bigbio/quantms/blame/e3c95f038192db53b41bd9b072687b549dfff5db/workflows/dia.nf#L59) and later it was changed to if (... == Null), which makes it such that having an empty string WAS but IS NO LONGER equivalent to not setting the parameter.

I think both should be supported but its not critical (TBH i think its more of a nextflow issue ... where the error is very bad at fromPath).

LMK if you think we should invest some time supporting both the empty and the null as options to generate a new library.

TLDR:
-> Situation: When the parameter diann_speclib is set to ""
-> Outcome: the pipeline fails with a cryptic error message.
-> Expected outcome: A new library is generated as if diann_speclib was not set at all.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[ypriverol]

@jspaezp Do you think you can tackle the issue? I guess is to validate the path variable for null and empty?

[jspaezp]

It is IN THEORY an easy fix. I dont think I will have time to tackle it in the next week or so. I can do it after that though! I just wanted to make sure I left the report once I figured out the error.

[jspaezp]

Thanks for squeezing the fix in!