wf-artic incompatible with nextflow version >24

[ammaraziz]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.2.2

Workflow Execution

Command line (Local)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run vidrl/wf-artic -r v1.2.2 \
-c covid.cfg \
--fastq dataset/fastq_pass \
--out_dir results/ \
--sample_sheet dataset/samplesheet.csv \
--scheme_name SARS-CoV-2 \
--scheme_version ARTIC-ONT/V5.2 \
--basecaller_cfg dna_r10.4.1_e8.2_400bps_hac \
--update_data \
--normalise 400 \
--min_len 150 \
--max_len 1200

Workflow Execution - CLI Execution Profile

None

What happened?

This pipeline is incompatible with nextflow version 24 and above. The error produced:

ERROR ~ Script compilation error
- file : .../.nextflow/assets/vidrl/wf-artic/main.nf
- cause: Invalid output definition @ line 638, column 5.
       output(results)
       ^

1 error


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

Downgrading nextflow verson to 23.10.1 fixes this issue.

Tested nextflow version nextflow version 24.10.4 and 24.10.1

Relevant log output

N E X T F L O W   ~  version 24.10.4

Launching `https://github.com/vidrl/wf-artic` [disturbed_dubinsky] DSL2 - revision: 672be102cc [v1.1.0.r4]

ERROR ~ Script compilation error
- file : .../.nextflow/assets/vidrl/wf-artic/main.nf
- cause: Invalid output definition @ line 638, column 5.
       output(results)
       ^

1 error


 -- 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