RareDisease_RNA_workflow

ARCHIVE

This repo and its functionality has been supersede by https://github.com/genomic-medicine-sweden/tomte This repo was therefor archived on 2024-04-18

nextflow main.nf --help

To test the pipeline run:

nextflow main.nf -profile test,<singularity/docker>

run a single sample:

nextflow main.nf -profile singularity --r1 read1.fq.gz --r2 read2.fq.gz --sample sampleID --output output_directory

run a single sample with multiple fastq files

nextflow main.nf -profile singularity --r1 "folder/*R1*.fq.gz" --r2 "folder/*R2*.fq.gz" --sample sampleID --output output_directory

NOTE: you need to add quotation marks around the search pattern

run all samples in a samplesheet:

nextflow main.nf -profile singularity --samplesheet sample.csv --output output_directory

The samplesheet is a comma-separated file with the following header:

id,r1,r2

Local profile

You can setup a custom config to facilitate running the pipeline on your local cluster. Here's how to run the pipeline with the pipeline on the Clinical Genomics Stockholm cluster called hasta with development priority.

nextflow main.nf -profile singularity,hasta,dev_prio --samplesheet sample.csv --output output_directory

Setup

Modify the config file:

Parameter	Description
reference_dir	specify the folder with all your references
star_index	the star reference index folder
fasta	the reference fasta file
gtf	gene annotations in gtf format
strandedness	library strandedness <forward/reverse>, optional
rrna_intervals	file with rrna postions in interval_list format. If not provided one will be generated automatically from the gtf gene annotaion file
downsample_regions	bed file with regions to be downsampled prior to variant calling. Only 0.1% of the reads will be kept
vep_cache	path to vep cache for offline use
reference_count_file	File with reference gene counts for aberrant expression analysis (drop)
run_drop_ae	Run the aberrant expression module from DROP (Turned off by default)
variantcaller	Specify variant caller. Available callers are: bcftools (default) and gatk

The pipeline will automatically download and cache the singularity/docker images.

You can also install all dependencies, as listed in dependencies

Dependencies

When using singularity/docker:

nextflow
singularity/docker

otherwise:

nextflow
bcftools
BootstrapAnn (https://github.com/J35P312/BootstrapAnn)
drop
fastp
gatk
gffcompare
multiQC
picard
samtools
STAR
stringtie
vep