Introduction

nf-core/dragenflow is a bioinformatics pipeline that runs a variety of dragen commands and workflows for downstream analysis

Pipeline Summary:

all workflows:

• samplesheet check
• make fasqlists (from reads/crams/bams)
• concatenate fastqlists
• run dragen

rna downstream analysis:

• get sizes file and strandedness
• annotate rnaseq
• bedtools genomecov
• ucsc bedclip, bedgraph to bigwig

tumor downstream analysis

• annotate small variants

Usage

Samplesheet Format

If running with mgi samplesheet:

Pass flag --mgi true, and use Samplemap2.csv with the following columns:

FASTQ Path - Read 1,FASTQ Path - Read 2,Flowcell ID,Index Sequence,Flowcell Lane,ESP ID,Pool Name,Species,Illumina Sample Type,Library Type,Library Name,Date Complete,Total Reads,Total Bases,Avg >Q Score Read 1,Avg Q Score Read 2,% >Q30 Read 1,% >Q30 Read 2,PhiX Error Rate Read 1,PhiX Error Rate Read 2,% Pass Filter Clusters Read 1,% Pass Filter Clusters Read 2

If running with custom samplesheet:

First column should be id, remaining columns are data type, or a combination of data types (read1,read2/bam/cram)

Examples:

id,read1,read2
sample1,sample1_R1.fastq.gz,sample1_R1.fastq.gz
sample2,sample2_R1.fastq.gz,sample2_R1.fastq.gz

id,bam,cram
sample1,,sample1.cram
sample2,sample2.bam,

Run Command

nextflow run dhslab/dragenflow -r dev \
-profile ris,<dragen2/dragen4/dragenaws> \
--input /path/to/samplesheet \
--outdir <OUTDIR> \ 
--workflow <rna/5mc/align/somatic/tumor/idtumis>

Optional Parameters

--dragen_args <dragen arguments> : provides additional arguments in dragen command

--mgi true : pass if mgi samplesheet is used

-bucket-dir <path to s3 bucket dir> : pass if aws is used

AWS

run the following commands:

nextflow secrets set AWS_ACCESS_KEY <aws access key>

nextflow secrets set AWS_SECRET_KEY <aws secret key>

export DRAGEN_USERNAME <dragen username>

export DRAGEN_PASSWORD <dragen password>

to check if secrets are set/exist in NXF_HOME, run:

nextflow secrets list