nf-cmgg/preprocessing

Introduction

nf-cmgg/preprocessing is a bioinformatics pipeline that demultiplexes and aligns raw sequencing data. It also performs basic QC and coverage analysis.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Steps include:

• Demultiplexing using BCLconvert
• Run QC using MultiQC SAV
• Read QC and trimming using fastp or falco
• Alignment using either bwa, bwa-mem2, bowtie2, dragmap, snap or strobe for DNA-seq and STAR for RNA-seq
• Duplicate marking using bamsormadup or samtools markdup
• Coverage analysis using mosdepth and samtools coverage
• Alignment QC using samtools flagstat, samtools stats, samtools idxstats and picard CollectHsMetrics, picard CollectWgsMetrics, picard CollectMultipleMetrics
• QC aggregation using 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.

The full documentation can be found here

First, prepare a samplesheet with your input data. Check the usage docs for details on the required format and example files.

Now, you can run the pipeline using:

nextflow run nf-cmgg/preprocessing \
   -profile <docker/singularity/...> \
   --igenomes_base /path/to/genomes \
   --input samplesheet.<csv|yaml|json> \
   --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

nf-cmgg/preprocessing was originally written by the CMGG ICT team.

Support

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.