Add autodetect multithreading

nextstrain · Nov 19, 2024 · ae9354b · ae9354b
1 parent 68d122c
commit ae9354b
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Showing 5 changed files with 12 additions and 6 deletions.
diff --git a/ingest/profiles/default/config.yaml b/ingest/profiles/default/config.yaml
@@ -0,0 +1,3 @@
+cores: all
+printshellcmds: true
+rerun-incomplete: true
diff --git a/ingest/rules/nextclade.smk b/ingest/rules/nextclade.smk
@@ -65,11 +65,13 @@ rule nextclade_classify:
         dataset=config["nextclade"]["nextclade_dataset_path"],
     output:
         nextclade_tsv="data/nextclade_results/nextclade.tsv",
+    threads: workflow.cores,
     shell:
         """
         nextclade3 run \
           --input-dataset {input.dataset} \
           --output-tsv {output.nextclade_tsv} \
+          --jobs {threads:q} \
           --silent \
           {input.sequences}
         """

diff --git a/phylogenetic/profiles/default/config.yaml b/phylogenetic/profiles/default/config.yaml
@@ -0,0 +1,3 @@
+cores: all
+printshellcmds: true
+rerun-incomplete: true
diff --git a/phylogenetic/rules/construct_phylogeny.smk b/phylogenetic/rules/construct_phylogeny.smk
@@ -29,15 +29,14 @@ rule tree:
         "logs/tree.txt",
     benchmark:
         "benchmarks/tree.txt"
-    params:
-        threads = workflow.cores,
+    threads: workflow.cores
     shell:
         """
         augur tree \
             --alignment {input.alignment} \
             --output {output.tree} \
             --method raxml \
-            --nthreads {threads} 2>&1 | tee {log}
+            --nthreads {threads:q} 2>&1 | tee {log}
         """
 
 rule refine:

diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk
@@ -61,14 +61,13 @@ rule align:
         "logs/align.txt",
     benchmark:
         "benchmarks/align.txt"
-    params:
-        threads = workflow.cores
+    threads: workflow.cores
     shell:
         """
         augur align \
             --sequences {input.sequences} \
             --output {output.alignment} \
             --fill-gaps \
             --reference-sequence {input.reference} \
-            --nthreads {threads} 2>&1 | tee {log}
+            --nthreads {threads:q} 2>&1 | tee {log}
         """