remove explicit threading restrictions (#453)

vector-engineering · Nov 30, 2021 · 7a578b4 · 7a578b4
1 parent a7beca5
commit 7a578b4
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Showing 3 changed files with 0 additions and 11 deletions.
diff --git a/workflow_main/Snakefile b/workflow_main/Snakefile
@@ -194,7 +194,6 @@ rule build_location_tree:
         )
     output:
         geo_select_tree = os.path.join(data_folder, "geo_select_tree.json")
-    threads: workflow.cores / 2
     run:
         geo_select_tree = build_location_tree(
             input.case_data, input.metadata_map, input.emoji_map_file,
@@ -232,7 +231,6 @@ rule consensus_mutations:
     output:
         group_consensus_mutations = os.path.join(data_folder, "group_consensus_mutations.json"),
         group_mutation_frequencies = os.path.join(data_folder, "group_mutation_frequencies.json")
-    threads: workflow.cores / 2
     run:
         get_all_consensus_mutations(
             input.case_data, output.group_consensus_mutations, output.group_mutation_frequencies,
@@ -252,7 +250,6 @@ rule global_group_counts:
         global_group_counts = os.path.join(
             data_folder, "global_group_counts.json"
         )
-    threads: workflow.cores / 2
     run:
         global_group_counts(
             input.case_data, output.global_group_counts,
@@ -272,7 +269,6 @@ rule assemble_data_package:
         metadata_map = rules.combine_all_data.output.metadata_map
     output:
         data_package = os.path.join(data_folder, "data_package.json.gz")
-    threads: workflow.cores / 2
     run:
         assemble_data_package(
             **input,
@@ -285,7 +281,6 @@ rule build_full_dataframe:
         metadata_map = rules.combine_all_data.output.metadata_map
     output:
         full_df = os.path.join(data_folder, 'data_complete.csv')
-    threads: workflow.cores / 2
     run:
         build_full_dataframe(input.case_data, input.metadata_map, output.full_df)
 

diff --git a/workflow_main/analyses/Snakefile b/workflow_main/analyses/Snakefile
@@ -32,7 +32,6 @@ rule az_reports:
         spike_cooc_region = os.path.join(az_report_out, 'spike_cooc_region.csv'),
         lineage_global = os.path.join(az_report_out, 'lineage_global.csv'),
         lineage_region = os.path.join(az_report_out, 'lineage_region.csv'),
-    threads: workflow.cores / 2
     run:
         generate_az_reports(input.case_data, input.metadata_map, output.report_out)
 
@@ -55,7 +54,6 @@ rule surveillance_data:
         end_date_days_ago = config.get('surv_end_date_days_ago', 30),
         min_combo_count = config['surv_min_combo_count'],
         min_single_count = config['surv_min_single_count']
-    threads: workflow.cores / 2
     output:
         group_counts = os.path.join(data_folder, 'surveillance', 'group_counts2.csv'),
         group_regression = os.path.join(data_folder, 'surveillance', 'group_regression2.csv'),
@@ -75,7 +73,6 @@ rule global_sequencing_efforts:
         metadata_map = os.path.join(data_folder, "metadata_map.json"),
     output:
         country_score = os.path.join(data_folder, "country_score.json")
-    threads: workflow.cores / 2
     run:
         global_sequencing_efforts(
             input.case_data, input.metadata_map,
@@ -104,7 +101,6 @@ rule global_seq_data:
         sequences_per_month = os.path.join(data_folder, "new_global_data", "sequences_per_month.json"),
         turnaround_per_month = os.path.join(data_folder, "new_global_data", "turnaround_per_month.json"),
         iso_lookup = os.path.join(data_folder, "new_global_data", "iso_lookup.json")
-    threads: workflow.cores / 2
     shell:
         """
         python3 analyses/scripts/global_seq_data.py --case-data {input.case_data} --metadata-map {input.metadata_map} -o {params.out_folder}

diff --git a/workflow_main/phylotree/Snakefile b/workflow_main/phylotree/Snakefile
@@ -32,7 +32,6 @@ rule get_representative_sequences:
         representatives = os.path.join(data_folder, "lineage_representatives.fa"),
         datefile = os.path.join(data_folder, "lineage_representative_dates.csv"),
         table = os.path.join(data_folder, 'lineage_representative_table.csv')
-    threads: workflow.cores / 2
     run:
         get_representative_seqs(
             input.case_data, input.metadata_map, input.ref_seq,
@@ -85,7 +84,6 @@ rule build_phylotree_graph:
         representative_table = rules.get_representative_sequences.output.table
     output:
         graph_table = os.path.join(data_folder, 'lineage_tree_graph.json')
-    threads: workflow.cores / 2
     run:
         build_graph_table(
             input.case_data,