Analysis of bulk RNA-Seq data from the Germinal Center.
Paper: Holmes, A. B., Corinaldesi, C., Shen, Q., Kumar, R., Compagno, N., Wang, Z., ... & Basso, K. (2020). Single-cell analysis of germinal-center B cells informs on lymphoma cell of origin and outcome. Journal of Experimental Medicine, 217(10). Chicago
To get DAG:
snakemake --profile profiles/aws --forceall --dag | dot -Tpdf > dag.pdf
To get rule graph:
snakemake --profile profiles/aws --forceall --rulegraph | dot -Tpdf > rulegraph.pdf
To get file graph:
snakemake --profile profiles/aws --forceall --filegraph | dot -Tpdf > filegraph.pdf
To run pipeline:
snakemake --profile profiles/aws/ all
To modify pipeline:
Change SRA sample table.