Merge pull request rhysnewell#171 from rhysnewell/set-pplacer-threads

Set pplacer threads
AroneyS · Nov 15, 2023 · 1457755 · 1457755
2 parents 5067303 + d664178
commit 1457755
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/aviary/modules/annotation/annotation.smk b/aviary/modules/annotation/annotation.smk
@@ -188,7 +188,7 @@ rule gtdbtk:
         done = "data/gtdbtk/done"
     params:
         gtdbtk_folder = config['gtdbtk_folder'],
-        pplacer_threads = config["pplacer_threads"],
+        pplacer_threads = lambda wildcards, threads: min(threads, config["pplacer_threads"]),
         extension = config['mag_extension']
     conda:
         "../../envs/gtdbtk.yaml"

diff --git a/aviary/modules/binning/binning.smk b/aviary/modules/binning/binning.smk
@@ -397,7 +397,7 @@ rule checkm_rosella:
     input:
         done = ancient("data/rosella_bins/done")
     params:
-        pplacer_threads = config["pplacer_threads"],
+        pplacer_threads = lambda wildcards, threads: min(threads, config["pplacer_threads"]),
         checkm2_db_path = config["checkm2_db_folder"],
         bin_folder = "data/rosella_bins/",
         extension = "fna",
@@ -422,7 +422,7 @@ rule checkm_metabat2:
     input:
         done = ancient("data/metabat_bins_2/done")
     params:
-        pplacer_threads = config["pplacer_threads"],
+        pplacer_threads = lambda wildcards, threads: min(threads, config["pplacer_threads"]),
         checkm2_db_path = config["checkm2_db_folder"],
         bin_folder = "data/metabat_bins_2/",
         extension = "fa",
@@ -447,7 +447,7 @@ rule checkm_semibin:
     input:
         done = ancient("data/semibin_bins/done")
     params:
-        pplacer_threads = config["pplacer_threads"],
+        pplacer_threads = lambda wildcards, threads: min(threads, config["pplacer_threads"]),
         checkm2_db_path = config["checkm2_db_folder"],
         bin_folder = "data/semibin_bins/output_recluster_bins/",
         extension = "fa",
@@ -485,7 +485,7 @@ rule refine_rosella:
         output_folder = "data/rosella_refined/",
         min_bin_size = config["min_bin_size"],
         max_iterations = config["refinery_max_iterations"],
-        pplacer_threads = config["pplacer_threads"],
+        pplacer_threads = lambda wildcards, threads: min(threads, config["pplacer_threads"]),
         max_contamination = 15,
         final_refining = False
     threads:
@@ -522,7 +522,7 @@ rule refine_metabat2:
         output_folder = "data/metabat2_refined/",
         min_bin_size = config["min_bin_size"],
         max_iterations = config["refinery_max_iterations"],
-        pplacer_threads = config["pplacer_threads"],
+        pplacer_threads = lambda wildcards, threads: min(threads, config["pplacer_threads"]),
         max_contamination = 15,
         final_refining = False
     log:
@@ -554,7 +554,7 @@ rule refine_semibin:
         output_folder = "data/semibin_refined/",
         min_bin_size = config["min_bin_size"],
         max_iterations = config["refinery_max_iterations"],
-        pplacer_threads = config["pplacer_threads"],
+        pplacer_threads = lambda wildcards, threads: min(threads, config["pplacer_threads"]),
         max_contamination = 15,
         final_refining = False
     log:
@@ -673,7 +673,7 @@ rule refine_dastool:
         output_folder = "data/refined_bins/",
         min_bin_size = config["min_bin_size"],
         max_iterations = config["refinery_max_iterations"],
-        pplacer_threads = config["pplacer_threads"],
+        pplacer_threads = lambda wildcards, threads: min(threads, config["pplacer_threads"]),
         max_contamination = 15,
         final_refining = True
     log: