Fix 'Value is string but should be boolean' | Nextflow | nf-core

Description:
#nextflow #nfcorernaseq #boolean #string #error #pipeline #parameters

ERROR ~ Validation of pipeline parameters failed!

-- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --save_reference (true): Value is [string] but should be [boolean]
* --skip_alignment (true): Value is [string] but should be [boolean]


What the variable does?

The strict syntax was added in 25.04 and was opt-in via NXF_SYNTAX_PARSER=v2. In 26.04 it became the default, and you can disable it by setting NXF_SYNTAX_PARSER=v1.

So export NXF_SYNTAX_PARSER=v1 is a way to turn off strict parsing and go back to the legacy behavior.

00:00 Huston we have a problem :D
00:14 Running nf-core/rnaseq
01:30 Value is [string] but should be [boolean] error is thrown
01:51 Fix of the problem on theory
02:33 Fix of the problem in practice
03:26 Test the solution

Don't worry, be happy!!!

On my channel find also:

Full set up of nextflow for running nf-core pieplines:

https://studio.youtube.com/playlist/PLf3cOsCKqW6w

The role of the human microbiome in health and disease
https://www.youtube.com/watch?v=twPyAroCLEc&list=PL2y6qTW3Stzk7qMUoWDPL5ygnOOUdLBf8

Tutorial for Estimation of relative abundance of species in metagenome data
https://www.youtube.com/watch?v=LoMORt9u1ys&list=PL2y6qTW3StzmxmNvtLWOHYro2oliTtq2_

Tutorial for building co-expression network from gene expression data
https://www.youtube.com/playlist?list=PL2y6qTW3Stzmy6Zyn6A20vmi77BitGc00

Tutorial for analyses of bulk RNA-seq - from raw counts, up to GO enriched categories
https://www.youtube.com/watch?v=kR_iHVau8GI&t=129s (beginners)


#NXF_SYNTAX_PARSER, #nextflowtutorial, #nextflowv2parser, #strictsyntax, #workflowmanager, #nextflowsyntaxerror, #nfcore