Invalid workflow defniiton

[DNA-Bioboss]

Description of the bug

I ran Phoenix pipeline and I got the following error:

starting ph

 N E X T F L O W   ~  version 26.04.4

Launching `/epi_data/home/epi_shared/Documents/GitHub/phoenix/main.nf` [evil_newton] revision: e6acfab07a

Error main.nf:38:1: Invalid workflow definition -- check for missing or out-of-order section labels
│  36 | // -------------------------------------------------------------------
│  37 | 
│  38 | workflow PHOENIX {
│     | ^^^^^^^^^^^^^^^^^^
│  39 | 
╰  40 |     if (!params.input)


WARN: Failed to render execution report -- see the log file for details
WARN: Failed to render execution timeline -- see the log file for details
ERROR ~ Script compilation failed

 -- Check '.nextflow.log' file for details

I'm using the following Nextflow version: 26.04.4 and Phoenix version 2.1.1.

I have attached the nextflow log message for your reference.
.nextflow.log

What might be the issue causing this error? I am guessing it is the nextflow version which I am currently using.

Thank you for your time and support.

-Mayra

Command used and terminal output

Relevant files

No response

System information

No response

[jvhagey]

There was a lot of changes in Nextflow v26 and we don't tested the old versions of phx with the newer versions of Nextflow.
I would try updating your PHX version to the latest to see if that resolves the issue.

[DNA-Bioboss]

I updated the Phoenix software with the most recent version v 2.3.1 but I am still experiencing some errors. Which can be seen below:

What next steps do you suggest I take?

[vascokarla]

Did you enable the nextflow v1 syntax parser? It seems that it's expecting the v2 nextflow syntax. Try setting this before running Phoenix with nextflow v26

export NXF_SYNTAX_PARSER=v1

https://training.nextflow.io/latest/info/nxf_versions/

[jvhagey]

@DNA-Bioboss can you confirm the change vascokarla suggested worked?