Introduction

This is an example Nextflow workflow to be used as the Technical exercise for the 2025 Bioinformatics Developer Position.

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

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 2025_BINFdev/main.nf \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR> \
   --projectID <projectID>

Alternatively you can use the run.sh script

bash run.sh <profiles> <outputdir> <projectID>

It is recommended to utilize the test profile with your computational environment, such as test,singularity or test,docker.

Credits

2025_BINFdev was originally written by S Sevilla.

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.