--stage end-prg causes premature exit

[IanGBrennan]

Description of the bug

Heya @SiddhantAttavar

running --stage end-prg using the dev branch causes the pipeline to exit without completing any steps.

Lines 544/545 of workflows/pipesnake.nf appear to tell the pipeline to exit immediately?

    if (params.stage == "end-prg") {
        exit 0
    }

Any idea what happened here?
I've confirmed that --stage end-prg still works in the main branch, just not in dev.

Command used and terminal output

nextflow run pipesnake_dev_28072025 -profile singularity --input data/ToyData_SampleInfo.csv --blat_db data/ToyData_SqCL_25Targets.fasta --stage end-prg --outdir ToyData_end-prg

Relevant files

No response

System information

nextflow version 24.10.0
ausarg/pipesnake dev branch from 27/07/2025

[IanGBrennan]

Resolved this issue with help from @SiddhantAttavar

changed exit 0 to return on line 545.

Workflow executes properly and completes up to the PRG stage when --stage end-prg is run.