NXF-COMPONENTS

A repository of developmental NextFlow DSL2 components meant to be used with nf-core/tools. As soon as a component meets all the nf-core guidelines, it should be submitted to nf-core/modules.

Setup

Use the dev version of the nf-core/tools

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

Steps for Adding a New Component

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 https://github.com/GallVp/nxf-components.git test tool/subtool
Commit: Commit to this repo
Install: Install nf-core -v modules -g https://github.com/GallVp/nxf-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

Submitted to nf-core/modules

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

Module	Pull request
pbtk/pbindex ✅︎ ⛔	#5901
fastq_bwa_mem_samblaster	#5582

And more...

Hybrid Testing and Hybrid Sub-workflows

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 module testing are copied to modules/gallvp, those needed for sub-workflow testing are copied to modules/nf-core, and those needed for sub-workflows are also copied to modules/gallvp. See: nf-core-hybridisation.sh

References