main.nf error

[shelgueta]

Operating System

Windows 10

Other Linux

Ubuntu

Workflow Version

v24.04

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

./nextflow run wf-transcriptomes
--fastq differential_expression/fastq_pass
--de_analysis --ref_genome differential_expression/Homo_sapiens.GRCh38.cdna.all.fa
--transcriptome-source reference-guided
--ref_annotation differential_expression/Homo_sapiens.GRCh38.109.gtf
--direct_rna --minimap2_index_opts '-k 15' --sample_sheet differential_expression/sample_sheet_Sergio.csv
-profile singularity

Workflow Execution - CLI Execution Profile

None

What happened?

When trying ./nextflow run hello it works, but then, when running the command above, I cannot run nextflow

Relevant log output

Launching `wf-transcriptomes/main.nf` [backstabbing_marconi] DSL2 - revision: eda4699855

ERROR ~ Script compilation error
- file : /massstorage/HOME/u242938/wf-transcriptomes/main.nf
- cause: Invalid output definition @ line 824, column 9.
           output(pipeline.out.results)
           ^

1 error


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

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

[shelgueta]

Please, any help of which could be the error I am getting? Yesterday it worked for the demo of EPI2ME but today it does not...

[Brynjar-H]

I got the same error, it was fixed with by typing this in the command line: export NXF_VER=23.10.1
#90

[sarahjeeeze]

Thanks for letting us know, we will fix this shortly.