Running

The main entrypoint is the tourmaline.sh script. Run from the tourmaline directory.

Usage

conda activate snakemake-tour2
./tourmaline.sh --step [qaqc,repseqs,taxonomy] --configfile [config1,config2,config3] --cores N

Notes:

  • The number of --step entries must match the number of --configfile entries.
  • Provide steps and configs in the same order.
  • Each Snakemake rule uses --use-conda to pull the qiime2-amplicon-2024.10 env as needed.

Examples

Run a single step (taxonomy):

./tourmaline.sh -s taxonomy -c config_03_taxonomy.yaml -n 6

Run all steps with one command:

./tourmaline.sh -s qaqc,repseqs,taxonomy -c config_01_qaqc.yaml,config_02_repseqs.yaml,config_03_taxonomy.yaml -n 6

Tips

  • Use --printshellcmds and --dryrun when calling Snakemake directly to see planned commands and DAG.
  • Choose rarefaction depth after inspecting table summaries in Repseqs step.
  • Optionally filter by taxonomy/length/abundance/prevalence before final visualizations.

Output structure

v2-results/
├── [run_name]-samples/
├── [run_name]-repseqs/
└── [run_name]-taxonomy/

See Configuration for parameters and Steps for per-step details.