snakehive

Tutorial and best practices for snakemake and hive

Goals

• Minimal pre-installation (snakemake, conda)
• Examples of progressively more sophisticated snakemake pipelines
• Changing conda environments
• With and without slurm jobs
• Singularity/apptainer

Pipeline Diagram

                  /---> Step 3a --- \
                 /                   \
Step 1 ---> Step 2                   Step 4 ---> Step X, Y, Z
                 \                   /
                  \---> Step 3b --- /

Ideas

• Make a conda environment for the project
• Make other conda environments for running specific programs
• Pipeline ideas:
  • Proteins, BLAST, multiple-alignment, phylogenetic tree
  • Mini RNA-Seq or ChIP-seq: trimming, deduplication, alignment, post-process sam something