Add feature to disable mpa heatmap plot

CHANGELOG.md

@@ -19,6 +19,8 @@ situations.
 - Added a new Slurm profile for use on CTMR Gandalf, also intended to be useful
   as a starting point for creating custom Slurm profiles.
 - Added a README with basic instructions for how to configure the workflow.
+- Added function to disable MetaPhlAn heatmap plots, which may be useful when
+  processing very large numbers of samples.
 
 ### Fixed
 - Fixed missing interactive Kaiju Krona plots for all samples in final report.

config/config.yaml

@@ -126,6 +126,7 @@ metaphlan:
     keep_sam: False          # Keep the sam files, set this to True if you want to run StrainPhlAn.
     run_krona: True
     heatmap:
+        create_plot: True        # Whether to create the MetaPhlAn heatmap plot, set to False to disable
         level: "Species"         # Taxononomic level: Kingdom, Phylum, Class, Order, Family, Genus, Species, or Strain
         topN: 50                 # Number of top taxa to include in heatmap.
         pseudocount: -1          # Negative value means to autocompute pseudocount

workflow/rules/taxonomic_profiling/metaphlan.smk

@@ -27,7 +27,8 @@ if config["taxonomic_profile"]["metaphlan"] or config["functional_profile"]["hum
     mpa_outputs = expand(f"{OUTDIR}/metaphlan/levels/{{taxlvl}}.tsv",
         taxlvl=("species", "genus", "family", "order"))
 
-    all_outputs.append(heatmap)
+    if mpa_config["heatmap"]["create_plot"]:
+        all_outputs.append(heatmap)
     all_outputs.append(mpa_area_plot)
     all_outputs.append(mpa_outputs)