Snakemake workflow: snakemake_rnaseq_combined_workflow

This workflow performs trimming with trimmomatic sliding window, runs alignment with STAR and/or HISAT2, produces a featureCounts file and then runs QC before and after trimming to generate 3 multiqc reports..

Authors

Hans Vasquez-Gross (@hansvg)

Usage

Simple

Step 1: Install workflow

clone this workflow to your local computer

Step 2: Configure workflow

Configure the workflow according to your needs via editing the file config.yaml and units.tsv.

To help fill out the units.tsv, you can use MS Excel to create the 4 columns sample,units,fq1,fq2

Then in the directory where you have your fastq files, run the following command to get the full path to the files. This can be easily copy/pasted into the correct column. ls -d1 $PWD/*R1.fastq.gz

Likewise, once the worksheet is filled out, copy the table and paste it into an empty units.tsv file.

Step 3: Execute workflow

Test your configuration by performing a dry-run via

snakemake --use-conda -n

Execute the workflow locally via

snakemake --use-conda --cores $N

using $N cores or run it in a cluster environment via

snakemake --use-conda --cluster qsub --jobs 100

snakemake --use-conda --drmaa --jobs 100

See the Snakemake documentation for further details.