From 0aa8cad6884a953f9c89a2fdd7af397e4e9ccf3e Mon Sep 17 00:00:00 2001
From: Max Schubach <max.schubach@bih-charite.de>
Date: Thu, 10 Nov 2022 11:19:04 +0100
Subject: [PATCH] feature: replace merging by NGmerge

close replace MergeTrimReadsBAM.py #57
---
 config/sbatch.yml                   |  6 +++---
 workflow/rules/assignment.smk       | 15 +++++++++------
 workflow/rules/common.smk           |  2 +-
 workflow/schemas/config.schema.yaml | 19 +++++++++++++++++++
 4 files changed, 32 insertions(+), 10 deletions(-)

diff --git a/config/sbatch.yml b/config/sbatch.yml
index cbb2fe3..4127599 100644
--- a/config/sbatch.yml
+++ b/config/sbatch.yml
@@ -13,7 +13,7 @@ assignment_merge:
   time: "0-08:00"
   queue: medium
 assignment_fastq_split:
-  time: "0-02:00"
+  time: "0-04:00"
   threads: 1
   mem: 10G
   queue: medium
@@ -28,9 +28,9 @@ assignment_collect:
   mem: 10G
   queue: medium
 assignment_getBCs:
-  time: "0-04:00"
+  time: "1-08:00"
   threads: 1
-  queue: short
+  queue: medium
 assignment_statistic_totalCounts:
   time: "0-01:00"
   threads: 1
diff --git a/workflow/rules/assignment.smk b/workflow/rules/assignment.smk
index 8d257fc..3684acd 100644
--- a/workflow/rules/assignment.smk
+++ b/workflow/rules/assignment.smk
@@ -1,6 +1,3 @@
-SPLIT_FILES_NUMBER = 1
-
-
 include: "assignment/statistic.smk"
 
 
@@ -78,9 +75,15 @@ rule assignment_merge:
             "results/assignment/{assignment}/fastq/merge_split{split}.join.fastq.gz"
         ),
     params:
-        min_overlap=20,
-        frac_mismatches_allowed=0.10,
-        min_dovetailed_overlap=50,
+        min_overlap=lambda wc: config["assignments"][wc.assignment]["NGmerge"][
+            "min_overlap"
+        ],
+        frac_mismatches_allowed=lambda wc: config["assignments"][wc.assignment][
+            "NGmerge"
+        ]["frac_mismatches_allowed"],
+        min_dovetailed_overlap=lambda wc: config["assignments"][wc.assignment][
+            "NGmerge"
+        ]["min_dovetailed_overlap"],
     log:
         temp("results/logs/assignment/merge.{assignment}.{split}.log"),
     shell:
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 7ca7661..21563ac 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -408,7 +408,7 @@ def withoutZeros(project, conf):
 
 
 def getSplitNumber():
-    split = SPLIT_FILES_NUMBER
+    split = 1
 
     if "global" in config:
         if "assignments" in config["global"]:
diff --git a/workflow/schemas/config.schema.yaml b/workflow/schemas/config.schema.yaml
index 7a7db67..6c4b3ea 100644
--- a/workflow/schemas/config.schema.yaml
+++ b/workflow/schemas/config.schema.yaml
@@ -68,6 +68,24 @@ properties:
               type: string
             minItems: 1
             uniqueItems: true
+          NGmerge:
+            type: object
+            properties:
+              min_overlap:
+                type: integer
+                default: 20
+              frac_mismatches_allowed:
+                type: number
+                default: 0.1
+              min_dovetailed_overlap:
+                type: integer
+                default: 20
+            required:
+              - min_overlap
+              - frac_mismatches_allowed
+              - min_dovetailed_overlap
+            default: {}
+            additionalProperties: false
           reference:
             type: string
           configs:
@@ -106,6 +124,7 @@ properties:
           - configs
           - alignment_start
           - sequence_length
+          - NGmerge
         additionalProperties: false
     additionalProperties: false
     minProperties: 1