Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Running the pipeline with only "--help" returns error #89

Open
travis-m-blimkie opened this issue Nov 27, 2024 · 0 comments
Open

Running the pipeline with only "--help" returns error #89

travis-m-blimkie opened this issue Nov 27, 2024 · 0 comments
Labels
bug Something isn't working

Comments

@travis-m-blimkie
Copy link

Description of the bug

When downloading/running the pipeline, it returns an error (missing database) when trying to print the help message.

Command used and terminal output

# On Cedar, load the relevant modules (`StdEnv` & `nextflow`). The following command generates an error:
$ nextflow run cidgoh/bacpaq -r v1.0.1 --help
Nextflow 24.10.1 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 24.04.4

Launching `https://github.com/cidgoh/bacpaq` [pensive_watson] DSL2 - revision: 3c48b98202 [v1.0.1]

ERROR ~ Path to Kraken2 database is not valid

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

Relevant files

nextflow.log

System information

Nextflow version: 24.04.4
Hardware: Cedar
Executor: Local (salloc)
OS: Linux
Version of bacpaq: 1.0.1

@travis-m-blimkie travis-m-blimkie added the bug Something isn't working label Nov 27, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

1 participant