From c438562a5167dbc1574aa4721f10dc4997abad43 Mon Sep 17 00:00:00 2001
From: samarth8392 <samarth.mathur@nih.gov>
Date: Fri, 9 Aug 2024 11:58:58 -0400
Subject: [PATCH 1/3] fix: removed localrule for gatk_contamination

---
 config/cluster.biowulf.json                | 6 ++++--
 config/cluster.frce.json                   | 6 ++++--
 workflow/rules/somatic_snps.paired.smk     | 1 -
 workflow/rules/somatic_snps.tumor_only.smk | 1 -
 4 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/config/cluster.biowulf.json b/config/cluster.biowulf.json
index 184b3fa..1b2fc00 100644
--- a/config/cluster.biowulf.json
+++ b/config/cluster.biowulf.json
@@ -22,7 +22,9 @@
         "threads": "2",
         "time": "4:00:00"
     },
-
+    "kraken": {
+        "mem": "64G"
+    },
     "strelka": {
         "threads": "16",
         "time": "16:00:00",
@@ -116,7 +118,7 @@
     },
     "bwa_mem": {
         "threads": "24",
-        "mem": "32G"
+        "mem": "64G"
     },
     "picard_headers": {
         "threads": "2",
diff --git a/config/cluster.frce.json b/config/cluster.frce.json
index 3ddeb16..afc6726 100644
--- a/config/cluster.frce.json
+++ b/config/cluster.frce.json
@@ -21,7 +21,9 @@
         "threads": "2",
         "time": "4:00:00"
     },
-
+    "kraken": {
+        "mem": "64G"
+    },
     "strelka": {
         "threads": "16",
         "time": "16:00:00",
@@ -115,7 +117,7 @@
     },
     "bwa_mem": {
         "threads": "24",
-        "mem": "32G"
+        "mem": "64G"
     },
     "picard_headers": {
         "threads": "2",
diff --git a/workflow/rules/somatic_snps.paired.smk b/workflow/rules/somatic_snps.paired.smk
index ce8071f..1f5427b 100644
--- a/workflow/rules/somatic_snps.paired.smk
+++ b/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"),
diff --git a/workflow/rules/somatic_snps.tumor_only.smk b/workflow/rules/somatic_snps.tumor_only.smk
index 650e3b9..826b07f 100644
--- a/workflow/rules/somatic_snps.tumor_only.smk
+++ b/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")

From 885f10085e18951e366b9feaa62c5b68cb9a8bdc Mon Sep 17 00:00:00 2001
From: samarth8392 <samarth.mathur@nih.gov>
Date: Tue, 13 Aug 2024 00:56:07 -0400
Subject: [PATCH 2/3] fix: add more mem to qualimap and somatic_merge rules

---
 config/cluster.biowulf.json | 6 ++++--
 config/cluster.frce.json    | 6 ++++--
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/config/cluster.biowulf.json b/config/cluster.biowulf.json
index 1b2fc00..a647265 100644
--- a/config/cluster.biowulf.json
+++ b/config/cluster.biowulf.json
@@ -30,7 +30,9 @@
         "time": "16:00:00",
         "mem": "32G"
     },
-
+    "qualimap_bamqc": {
+        "mem": "32G"
+    },
     "strelka_filter": {
         "threads": "4",
         "time": "8:00:00",
@@ -59,7 +61,7 @@
         "mem": "32G"
     },
 
-    "merge_somatic_callers": {
+    "somatic_merge_callers": {
         "threads": "16",
         "time": "18:00:00",
         "mem": "32G"
diff --git a/config/cluster.frce.json b/config/cluster.frce.json
index afc6726..6c7773d 100644
--- a/config/cluster.frce.json
+++ b/config/cluster.frce.json
@@ -29,7 +29,9 @@
         "time": "16:00:00",
         "mem": "32G"
     },
-
+    "qualimap_bamqc": {
+        "mem": "32G"
+    },
     "strelka_filter": {
         "threads": "4",
         "time": "8:00:00",
@@ -58,7 +60,7 @@
         "mem": "32G"
     },
 
-    "merge_somatic_callers": {
+    "somatic_merge_callers": {
         "threads": "16",
         "time": "18:00:00",
         "mem": "32G"

From 8c1964f119e8308d9b79dc6e605545a522790541 Mon Sep 17 00:00:00 2001
From: samarth8392 <samarth.mathur@nih.gov>
Date: Tue, 13 Aug 2024 14:05:50 -0400
Subject: [PATCH 3/3] chore: update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index aae5dfd..946855e 100644
--- a/CHANGELOG.md
+++ b/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