A repository of independently testable NextFlow DSL2 modules and sub-workflows for EDTA. Over time these components should be submitted to nf-core/modules.

Use the dev version of the nf-core/tools

pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev

• Search: Search on nf-core/modules, GitHub issues and GitHub PRs
• Issue: Create a new issue on GitHub issues for module or sub-workflow
• Create: Create nf-core -v modules create tool/subtool on a tool specific branch
• Lint: Lint nf-core -v modules lint tool/subtool
• Test: Test nf-core -v modules -g [email protected]:GallVp/edta-components.git test tool/subtool
• Commit: Commit to this repo
• Install: Install nf-core -v modules -g [email protected]:GallVp/edta-components.git install tool/subtool
• PR: Create a PR on nf-core/modules from a personal fork of nf-core/modules
• Status: Update submission status below
• Remove: Once the PR is accepted at nf-core/modules, remove the module from this repo and update submission status below

Following modules have been submitted and added (✅︎) to nf-core/modules and may be removed (⛔) from this repository without notice.

And more...

Hybrid sub-workflows are not supported by nf-core/tools. See: nf-core/tools#1927

The workaround is to install nf-core modules in the nf-core-modules which is setup as a dummy pipeline. The nf-core modules needed for testing are then symlinked to modules/nf-core and the nf-core modules needed for sub-workflows are symlinked to modules/edta-components. See: nf-core-hybridisation.sh

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.