This workflow performs trimming with trimmomatic sliding window, runs alignment with STAR, produces a featureCounts file and then runs QC before and after trimming to generate 3 multiqc reports..
- Hans Vasquez-Gross (@hansvg), https://hansvg.github.io
clone this workflow to your local computer
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.
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.
After successful execution, you can create a self-contained interactive HTML report with all results via:
snakemake --report report.html
This report can, e.g., be forwarded to your collaborators. An example (using some trivial test data) can be seen here.