fix: using correct threads

kircherlab · Jul 16, 2024 · 6dcad7d · 6dcad7d
1 parent 1ca36e1
commit 6dcad7d
Showing 1 changed file with 4 additions and 12 deletions.
diff --git a/profiles/default/config.yaml b/profiles/default/config.yaml
@@ -4,69 +4,61 @@ default-resources:
   slurm_account: hpc-ag-kircher
   slurm_partition: debug
   mem: 2G
-  threads: 1
   runtime: 60
 # error: "logs/%x_%j_%N.err"
 # output: "logs/%x_%j_%N.log"
 ##################
 ### ASSIGNMENT ###
 ##################
+set-threads:
+  assignment_mapping_bwa: 30
+  assignment_collect: 30
+  assignment_collectBCs: 20
 set-resources:
   assignment_hybridFWRead_get_reads_by_length:
     runtime: 1140
-    threads: 1
     mem: 2G
     slurm_partition: medium
   assignmemt_hybridFWRead_get_reads_by_cutadapt:
     runtime: 1200
-    threads: 1
     mem: 4G
     slurm_partition: medium
   assignment_merge:
     runtime: 480
     slurm_partition: medium
   assignment_fastq_split:
     runtime: 1440
-    threads: 1
     mem: 10G
     slurm_partition: medium
   assignment_mapping_bwa:
     runtime: 120
-    threads: 30
     mem: 10G
     slurm_partition: medium
   assignment_collect:
     runtime: 2160
-    threads: 30
     mem: 10G
     slurm_partition: medium
   assignment_getBCs:
     runtime: 240
-    threads: 1
     slurm_partition: medium
   assignment_collectBCs:
     runtime: 3120
-    threads: 20
     mem: 10G
     slurm_partition: medium
   assignment_mapping_exact:
     runtime: 60
-    threads: 1
     mem: 10G
     slurm_partition: debug
   assignment_statistic_totalCounts:
     runtime: 60
-    threads: 1
     slurm_partition: medium
     mem: 60G
   assignment_statistic_assignedCounts:
     runtime: 60
-    threads: 1
     slurm_partition: medium
     mem: 10G
   assignment_statistic_assignment:
     runtime: 60
-    threads: 1
     slurm_partition: medium
     mem: 40G
   ##############