How to solve Nextflow error: "Trace file already exists"?

Question

When trying to run epi2me-labs/wf-artic, I get the following error:

❯ nextflow run epi2me-labs/wf-artic \
 -r v0.3.18 --fastq  ~/Downloads/barcode95.fastq.gz \
 --scheme_version Midnight-ONT/V3 

N E X T F L O W  ~  version 22.10.1
Launching `https://github.com/epi2me-labs/wf-artic` [ecstatic_marconi] DSL2 - revision: a60a1e1e73 [v0.3.18]
Trace file already exists: /Users/corneliusromer/Downloads/BJGMC_ONT_Run71/output/execution/trace.txt

It seems that nextflow doesn't like to rerun after it failed. Is there a convenient way to force nextflow to rerun, in a similar way to snakemake --force-rerun? Or do I need to manually delete the trace file every time? That works, but it's tedious.

Answer 1

Rotation of report files (trace, execution, timeline etc) was removed recently (since version 22.10.0 in a762ed5). To overwrite the existing trace file you will need to add the following to your Nextflow config:

trace.overwrite = true

See: https://github.com/nextflow-io/nextflow/issues/3317