wf-bacterial-genomes workflow not working

bunnu27 commented 4 months ago

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

N E X T F L O W ~ version 24.04.3

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-bacterial-genomes –-help

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

I have been using wf-bacterial-genomes workflow for last 2 years. It worked fine till date. However, now it started showing following erros

"ERROR ~ Script compilation error

file : /home/hmn/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/main.nf
cause: Invalid output definition @ line 862, column 5. output(results.all_out) ^ I checked main.nf file fow syntax error but it is perfectly fine. Still I downloaded new file from source "https://github.com/epi2me-labs/wf-bacterial-genomes/blob/master/main.nf"

Upgraded nextflow for latest version too. Still not working for me. Need suggestions to troubleshoot.

Relevant log output

na

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

cjalder commented 4 months ago

Hi @bunnu27 - The problem is actually with the latest version of the nextflow, which is incompatible with the workflow. We will update this in the next release cycle, but for now you can run the workflow by changing the Nextflow version used to execute the workflow e.g NXF_VER=23.10.1 nextflow run epi2me-labs/wf-bacterial-genomes .... Hope that helps!

julibeg commented 3 months ago

Hi @bunnu27, this should be fixed with the most recent release (v1.3.0). Please reopen this issue and let us know if you still run into the same problem. Thanks!

epi2me-labs / wf-bacterial-genomes