Supported pipelines in OpenMind for PILM community.
We use Nextflow to run our pipelines.
Our pipelines are in our GitHub repository with the naming: pipelines-ng-*:
For instance, to run the RNAseq pipeline you can do the following (assuming you have nextflow already):
nextflow pilm-bioinformatics/pipelines-nf-rnaseq -prodile docker,test
If you want to run the development pipeline:
nextflow pilm-bioinformatics/pipelines-nf-rnaseq -r pilm-devel -prodile docker,test
To know the difference, look at the CHANGELONG file: https://github.com/pilm-bioinformatics/pipelines-nf-rnaseq/blob/pilm-devel/CHANGELOG.md
Our pipelines are synchronize with nf-core pipelines, and in the majority of the cases will be the same. We updated a little bit before them but in general, the changes will be merged at some point.
To know the differences, look at the README file.