Enables use of 1 param runs with --config - Githubissues

sheynkman-lab / Long-Read-Proteogenomics

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

MIT License

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Enables use of 1 param runs with --config #132

Closed cgpu closed 3 years ago

cgpu commented 3 years ago

Overview

This PR implements a parameterised way to make use of Nextflow profiles, that allows for using the config files instead of passing parameters.

Example:

git clone https://github.com/sheynkman-lab/Long-Read-Proteogenomics
git checkout cgpu-parameterise-configs
nextflow run main.nf --config conf/test.config --max_cpus 2

PR checklist

[X] This comment contains a description of changes (with reason)
[ ] CHANGELOG.md is updated
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] Documentation in docs is updated

cgpu commented 3 years ago

Noted updated formatting of main.nf and config files.

Awesome, thanks for reviewing @gsheynkman 👍 !