Issue with Nextflow 26.04.6's new parser (Parser v2)

[xavier-j]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.2.6

Workflow Execution

Command line (Local)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-alignment

Workflow Execution - CLI Execution Profile

None

What happened?

Wf-alignment is not compatible with nextflow v26.

import groovy.json.JsonBuilder
nextflow.enable.dsl = 2

The new Script Parser v2 in Nextflow 26 no longer accepts top-level Groovy import statements, resulting in:

Groovy import declarations are not supported

The legacy parser (NXF_SYNTAX_PARSER=v1) still supports them, so the workflow runs normally.

Relevant log output

N E X T F L O W   ~  version 26.04.6

Launching `https://github.com/epi2me-labs/wf-alignment` [serene_kowalevski] revision: c84a379070 [master]

WARN: Unrecognized config option 'epi2melabs.tags'
Error main.nf:3:1: Groovy `import` declarations are not supported -- use fully-qualified name inline instead
│   3 | import groovy.json.JsonBuilder
╰     | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^


ERROR ~ Script compilation failed

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

Application activity log entry

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

yes

Other demo data information

[github-actions]

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[BKthePerson]

Same issue here. Rolling back to nextflow v25 allowed me to get the pipeline up.