add thread param

PacificBiosciences · Jan 12, 2023 · 88a5a5d · 88a5a5d
1 parent e9668ac
commit 88a5a5d
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diff --git a/Taxonomic-Profiling-Sourmash/Snakefile-sourmash b/Taxonomic-Profiling-Sourmash/Snakefile-sourmash
@@ -65,7 +65,7 @@ rule sourmash_gather:
         gather_txt=os.path.join(out_dir, '2-gather', '{sample}.k{ksize}.gather.txt'),
     params:
         threshold_bp = sourmash_params.get('threshold_bp', '50000'),
-    threads: 1
+    threads: sourmash_params['threads']
     resources:
         mem_mb=lambda wildcards, attempt: attempt *100000,
         time=10000,

diff --git a/Taxonomic-Profiling-Sourmash/config.yaml b/Taxonomic-Profiling-Sourmash/config.yaml
@@ -35,3 +35,10 @@ sourmash:
     - databases/genbank-2022.03-fungi.lineages.csv.gz
     - databases/genbank-2022.03-protozoa.lineages.csv.gz
     - databases/genbank-2022.03-viral.lineages.csv.gz
+
+  # sourmash is not multi-threaded so this is default set to 1.
+  # There may be cases where changing thread number helps with
+  # HPC resource allocation. The sourmash_gather step in particular
+  # can require substantial memory, and this thread number will only 
+  # be applied to that rule.
+  threads: 1