workflow fails with Nextflow 24.04.1

angelovangel commented 4 months ago

Operating System

macOS

Other Linux

No response

Workflow Version

1.2.0

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

The pipeline fails to start after updating nextflow to 24.04.1 It runs OK with NXF_VER=23.04.3

ERROR ~ Script compilation error
- file : /Users/angelangelov/.nextflow/assets/epi2me-labs/wf-clone-validation/main.nf
- cause: Invalid output definition @ line 652, column 5.
       output(results[0])
       ^

1 error

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

Relevant log output

May-27 08:18:52.998 [main] ERROR nextflow.cli.Launcher - Script compilation error
- file : /Users/angelangelov/.nextflow/assets/epi2me-labs/wf-clone-validation/main.nf
- cause: Invalid output definition @ line 652, column 5.
       output(results[0])
       ^



### Application activity log entry

_No response_

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

no

### Other demo data information

_No response_

sarahjeeeze commented 4 months ago

Thanks for letting us know, we will update this soon. For now if you could stick with NXF_VER=23.04.3 that would be great

ryandward commented 3 months ago

Getting the same problem across a variety of Linux distros. Something unusual about the usage of output here.

cjw85 commented 3 months ago

@ryandward You are correct. Nextflow 24.04 has introduced new keywords into the Nextflow DSL grammar. These conflict with the use of output as a process name (in some contexts). In essence we need to rename the output process in the workflow to something else.

epi2me-labs / wf-clone-validation