nextflow_RS2_star

About

This repository contains a nextflow workflow treating RNAseq data. It consits of the following steps:

• fastq (preprocessing)
• check strandedness (determine the strandedness of the input data)
• STAR index reference
• split reads
• STAR Align to reference
• sort and convert alignement to BAM
• merge alignements of chunks
• cufflinks (transcript abuundance)

Input

References:

• Reference genome (fasta)
• reference transcriptome (fasta)
• genome annotation (gtf) To call the check strandedness, ensembl references are necessary. Input reads:
• paired-ends FASTQ files (single end for the moment not supported)

Output

• Quality control file from fastp
• transcripts abundance from cufflinks

How to run the workflow

nextflow run path/to/nextflow_RS2_star -c nextflow.config -w /path/to/workdir

How to run on the FONDA cluster:

nextflow kuberun Nine-s/nextflow_RS2_star -r main -c nextflow.config -v nextflow-ninon:/workdir

The configuration files are available in the config directory.