fix memory allocation for samtool multithreading rules

snakemodules/contigmap.smk

@@ -96,7 +96,8 @@ rule name_sort_unsorted:
     conda:
         os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
     resources:
-        mem_mb = resources["samtools"]["mem"],
+        # mem_mb = resources["samtools"]["mem"],
+        mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
         runtime = resources["samtools"]["time"]
     threads: 
         threads["multi"]["samtools"]
@@ -170,7 +171,8 @@ rule coordinate_sort_unsorted:
     conda:
         os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
     resources:
-        mem_mb = resources["samtools_25G"]["mem"],
+        # mem_mb = resources["samtools_25G"]["mem"],
+        mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
         runtime = resources["samtools_25G"]["time"]
     threads: 
         threads["multi"]["samtools"]

snakemodules/crop_remapped.smk

@@ -60,7 +60,8 @@ if config["SICKLE"]=="no":
         conda:
             os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
         resources:
-            mem_mb = resources["samtools"]["mem"],
+            # mem_mb = resources["samtools"]["mem"],
+            mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
             runtime = resources["samtools"]["time"]
         threads: 
             threads["multi"]["samtools"]
@@ -112,7 +113,8 @@ elif config["SICKLE"]=="yes":
         conda:
             os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
         resources:
-            mem_mb = resources["samtools"]["mem"],
+            # mem_mb = resources["samtools"]["mem"],
+            mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
             runtime = resources["samtools"]["time"]
         threads: 
             threads["multi"]["samtools"]

snakemodules/crop_unmapped.smk

@@ -58,7 +58,8 @@ if config["SICKLE"]=="no":
         conda:
             os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
         resources:
-            mem_mb = resources["samtools"]["mem"],
+            # mem_mb = resources["samtools"]["mem"],
+            mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
             runtime = resources["samtools"]["time"]
         threads: 
             threads["multi"]["samtools"]
@@ -108,7 +109,8 @@ elif config["SICKLE"]=="yes":
         output:
             WORK_DIR + "/{sample}/non_ref.bam"
         resources:
-            mem_mb = resources["samtools"]["mem"],
+            # mem_mb = resources["samtools"]["mem"],
+            mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
             runtime = resources["samtools"]["time"]
         threads: 
             threads["multi"]["samtools"]

snakemodules/kraken.smk

@@ -150,7 +150,8 @@ rule samtools_remap_classified_human:
     conda:
         os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
     resources:
-        mem_mb = resources["samtools"]["mem"],
+        # mem_mb = resources["samtools"]["mem"],
+        mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
         runtime = resources["samtools"]["time"]
     threads: 
         threads["multi"]["samtools"]
@@ -223,7 +224,8 @@ rule remapping_samsort_mates:
     conda:
         os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
     resources:
-        mem_mb = resources["samtools"]["mem"],
+        # mem_mb = resources["samtools"]["mem"],
+        mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
         runtime = resources["samtools"]["time"]
     threads: 
         threads["multi"]["samtools"]