thejacksonlaboratory / cs-nf-pipelines

The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines

JAX NGS Operations Nextflow DSL2 Pipelines

This repository contains production bioinformatic analysis pipelines.

Pipeline Level Documentation, Quick Start, and Developer Documentation:

Please see the Wiki documentation associated with this repository for all documentation.

cs-nf-pipelines's Issues

Gold Standard SNP and Indel files

Hello! I understand that this resource is meant for use on the compute clusters in Jackson Lab but I'm trying to setup my own docker containerised pipelines based on yours.
I have been looking at the list of gold standard SNP and indel files you have listed in the config files for WES, can you help me understand what it means when the file is annotated GATK formatted? Is there a particular formatting for VCF files that GATK prefers?

Pre-release and/or compatibility with `nextflow pull/run`

Hey CS team, this is a great resource!

Would it be possible to add a (pre-)release to the GitHub repo? Currently there's a tag 0.1.0 from a week ago and you just need to create a release from it (which could be automated in the future if needed).

This would allow compatibility with

nextflow pull -r 0.1.0 --workflow wgs ...
# and
nextflow run -r 0.1.0 --workflow wgs ...

I'd argue this is preferred over encouraging users to git clone the repo because
(a) nextflow can assert the pipeline being run corresponds to a specific version (it can manage multiple versions of pipeline)
(b) depending on when the repo was cloned, it may not be in a stable state or may be in a developmental state, and you have to rely on the end user to manage git pull/fetch

Cheers