Unable to Run DGE2 Test - WorkflowDGE2 Class Not Found

[zilov]

Description of the bug

I am trying to run the test for DGE2 but encountering an error stating that the WorkflowDge class is not found. I attempted to include the class explicitly in the dge.nf file, but the error persists.

Command used and terminal output

nextflow run lconde-ucl/DGE2 -profile test --outdir ./test

ERROR ~ No such variable: WorkflowDge

 -- Check script 'DGE2/./workflows/dge.nf' at line: 16 or see '.nextflow.log' file for more details

Relevant files

nextflow_log.txt

System information

• Nextflow both 23.04.01 and 24.04.02
• HPC
• running locally
• profiles Docker/Singularity/Test
• os - Ubuntu 22.04
• DGE2 1.0

[lconde-ucl]

Hi @zilov,

Thank you for reporting this issue. There was a small typo which has now been corrected, so please feel free to try again. Please note that the test profile does not include the containers, so you will need to include a singularity or docker profile as well, for example:

nextflow run lconde-ucl/DGE2 -profile test,singularity --outdir results

The above works well for me with nextflow 23.04.4.

Thanks,
Lucia

[zilov]

Lucia, thank you for the fast reply and fix! Everything works now!