A set of Nextflow configs commonly used across pipelines.
- Add this repository as a submodule in the pipeline of interest
- Include the required config files and call necessary functions
| Module | Description |
|---|---|
| retry.config | Enable Nextflow's process retry mechanism (How to enable retry) |
| schema.config | Automatic parameter validation (How to perform validation) |
| csv_parser.config | CSV parsing (How to parse a CSV) |
| bam_parser.config | BAM parsing (How to parse a BAM) |
| common_methods.config | Collection of commonly used config functions (How to use common functions) |
| pipeline_selector.config | Functions for resolving pipeline dependencies (How to resolve pipeline dependencies) |
| align_methods.config | Collection of commonly used config functions for align-DNA and -RNA (How to use common align pipeline functions) |
Regression tests for the functions supplied by this repository are located in the tests directory. The tests are automatically run on every pull request, and can be run locally with the ./tests/run_tests.sh script.
The tests are written for compatibility with JUnit4 and Groovy testing. New tests can be added using ExampleTests.groovy as a template.
nf-core- https://nf-co.re/nf-code modules- https://github.com/nf-core/sarek/blob/ad2b34f39fead34d7a09051e67506229e827e892/conf/modules.config
Author: Yash Patel (YashPatel@mednet.ucla.edu)
pipeline-Nextflow-config is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
pipeline-Nextflow-config comprises a set of commonly used Nextflow configs.
Copyright (C) 2022 University of California Los Angeles ("Boutros Lab") All rights reserved.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.