Closed
Description
Have you checked the docs?
Description of the bug
Processes that include lines like: 2> >(tee output.log >&2) break if run with conda. Specifically discovered when working with fastp.
Switching them to 2>| >(tee output.log >&2) will fix the issue.
Command used and terminal output
unzip fulcrumgenomics-example.zip
cd fulcrumgenomics-example/
nextflow run main.nf -profile "docker" # works!
nextflow run main.nf -profile "conda" # fails!
Command error:
.command.sh: line 5: /dev/fd/63: cannot overwrite existing fileRelevant files
System information
Nextflow version: 24.10.6
nf-core/tools version: 3.2.1
Hardware: M3 mac
Executor: local
Container engine: conda 24.11.3
OS: macOS 14.5