Introduction

medgen/directrna is a bioinformatics pipeline that is still in the works........ everyting below here is part of the TEMPLATE scaffold

1. Read QC (FastQC)
2. Present QC for raw reads (MultiQC)

Official nextflow sample test data for directRNA is here. Sequencing summary files, bams, fast5's even! Unfortunately there aren't enough dRNA data, so additional datasets will be included.

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Now, you can run the pipeline using:

nextflow run medgen/directrna \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

medgen/directrna was originally written by Dean Bašić.

We thank the following people for their extensive assistance in the development of this pipeline:

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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.