snakemake_gbs_sorghum_mapping_workflow

This workflow performs fastqc on an input PROJECT directory downloaded from basespace. It will merge the FASTQ files between lanes, then run fastqc on all merged data and compile an aggregate report with multiqc.

Authors

• Hans Vasquez-Gross (@hans-vg)

Usage

Simple

Step 1: Install workflow

clone this workflow to your local computer

Step 2: Configure workflow

Configure the workflow according to your needs by editing the config.yaml to configure your input basespace PROJECT directory.

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

or

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

See the Snakemake documentation for further details.