fix: increase mem for some rules; gatk contamination not run as localrule

CHANGELOG.md

@@ -7,6 +7,7 @@
   - Previously, `xavier_gui` (with an underscore) was a command in the `ccbrpipeliner` module.
 - Provide default exome targets for hg38 and mm10, which can be overridden by the optional `--targets` argument. (#102, @kelly-sovacool)
   - Previously, the `--targets` argument was required with no defaults.
+- Increased memory for rules: BWA mem, qualimap, kraken. gatk_contamination is not localrule. (#89, @samarth8392)
 
 ## XAVIER 3.0.3
 

config/cluster.biowulf.json

@@ -22,13 +22,17 @@
         "threads": "2",
         "time": "4:00:00"
     },
-
+    "kraken": {
+        "mem": "64G"
+    },
     "strelka": {
         "threads": "16",
         "time": "16:00:00",
         "mem": "32G"
     },
-
+    "qualimap_bamqc": {
+        "mem": "32G"
+    },
     "strelka_filter": {
         "threads": "4",
         "time": "8:00:00",
@@ -57,7 +61,7 @@
         "mem": "32G"
     },
 
-    "merge_somatic_callers": {
+    "somatic_merge_callers": {
         "threads": "16",
         "time": "18:00:00",
         "mem": "32G"
@@ -116,7 +120,7 @@
     },
     "bwa_mem": {
         "threads": "24",
-        "mem": "32G"
+        "mem": "64G"
     },
     "picard_headers": {
         "threads": "2",

config/cluster.frce.json

@@ -21,13 +21,17 @@
         "threads": "2",
         "time": "4:00:00"
     },
-
+    "kraken": {
+        "mem": "64G"
+    },
     "strelka": {
         "threads": "16",
         "time": "16:00:00",
         "mem": "32G"
     },
-
+    "qualimap_bamqc": {
+        "mem": "32G"
+    },
     "strelka_filter": {
         "threads": "4",
         "time": "8:00:00",
@@ -56,7 +60,7 @@
         "mem": "32G"
     },
 
-    "merge_somatic_callers": {
+    "somatic_merge_callers": {
         "threads": "16",
         "time": "18:00:00",
         "mem": "32G"
@@ -115,7 +119,7 @@
     },
     "bwa_mem": {
         "threads": "24",
-        "mem": "32G"
+        "mem": "64G"
     },
     "picard_headers": {
         "threads": "2",

workflow/rules/somatic_snps.paired.smk

@@ -73,7 +73,6 @@ rule pileup_paired:
     wait
     """
 
-localrules: contamination_paired
 rule contamination_paired:
     input:
         tumor = os.path.join(output_somatic_snpindels, "mutect2_out", "pileup_summaries", "{samples}_tumor.pileup.table"),

workflow/rules/somatic_snps.tumor_only.smk

@@ -67,7 +67,6 @@ rule pileup_single:
         -O {output.pileup}
     """
 
-localrules: contamination_single
 rule contamination_single:
     input:
         pileup = os.path.join(output_somatic_snpindels, "mutect2_out", "pileup_summaries", "{samples}.pileup.table")