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 inlcude:

1. Demultiplexing using BCLconvert
2. Read QC and trimming using fastp
3. Alignment using either bwa, bwa-mem2, bowtie2, dragmap or snap for DNA-seq and STAR for RNA-seq
4. Duplicate marking using bamsormadup or samtools markdup
5. Coverage analysis using mosdepth and samtools coverage
6. Alignment QC using samtools flagstat, samtools stats, samtools idxstats and picard CollecHsMetrics, picard CollectWgsMetrics, picard CollectMultipleMetrics
7. 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 that looks as follows:

samplesheet.csv for fastq inputs:

id,samplename,organism,library,fastq_1,fastq_2
sample1,sample1,Homo sapiens,Library_Name,reads1.fq.gz,reads2.fq.gz

samplesheet.csv for flowcell inputs:

id,samplesheet,lane,flowcell,sample_info
flowcell_id,/path/to/illumina_samplesheet.csv,1,/path/to/sequencer_uploaddir,/path/to/sampleinfo.csv

sampleinfo.csv for use with flowcell inputs:

samplename,library,organism,tag
fc_sample1,test,Homo sapiens,WES

Now, you can run the pipeline using:

nextflow run nf-cmgg/preprocessing \
   -profile <docker/singularity/.../institute> \
   --igenomes_base /path/to/genomes \
   --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

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.