refactor!: No min max length for bbmap. default mapq is 30. (kircherl…

…ab#131) Changes for bbmap * no min an max for sequence length and start. (like exact matching) * using default of 30 mapq instead of 35
visze · Oct 28, 2024 · 1e9157b · 1e9157b
1 parent 2d80faf
commit 1e9157b
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Showing 6 changed files with 20 additions and 52 deletions.
diff --git a/config/example_assignment_bbmap.yaml b/config/example_assignment_bbmap.yaml
@@ -8,13 +8,9 @@ assignments:
     alignment_tool:
       tool: bbmap
       configs:
-        min_mapping_quality: 35 # integer >=0. 35 is default
-        sequence_length: # sequence length of design excluding adapters.
-          min: 166
-          max: 175
-        alignment_start: # start of an alignment in the reference/design_file. Here using 15 bp adapters. Can be different when using adapter free approaches
-          min: 1 # integer
-          max: 3 # integer
+        min_mapping_quality: 30 # integer >=0. 30 is default for bbmap
+        sequence_length: 171 # sequence length of design excluding adapters.
+        alignment_start: 1 # start of an alignment in the reference/design_file. Here using 15 bp adapters. Can be different when using adapter free approaches
     FW:
       - resources/Assignment_BasiC/R1.fastq.gz
     BC:

diff --git a/config/example_config.yaml b/config/example_config.yaml
@@ -6,9 +6,9 @@ assignments:
   exampleAssignment: # name of an example assignment (can be any string)
     bc_length: 15
     alignment_tool:
-      tool: exact # bbbmap, bwa or exact
+      tool: exact # bbmap, bwa or exact
       configs:
-        sequence_length: 170 # sequence length of design excluding adapters.
+        sequence_length: 171 # sequence length of design excluding adapters.
         alignment_start: 1 # start of the alignment in the reference/design_file
     FW:
       - resources/assoc_basic/data/SRR10800986_1.fastq.gz

diff --git a/resources/assoc_basic/config.yml b/resources/assoc_basic/config.yml
@@ -8,12 +8,8 @@ assignments:
     alignment_tool:
       tool: bbmap
       configs:
-        sequence_length:
-          min: 166
-          max: 175
-        alignment_start:
-          min: 1
-          max: 3
+        sequence_length: 171
+        alignment_start: 1
     FW:
       - data/SRR10800986_1.fastq.gz
     BC:

diff --git a/resources/combined_basic/config.yml b/resources/combined_basic/config.yml
@@ -8,12 +8,8 @@ assignments:
     alignment_tool:
       tool: bbmap
       configs:
-        sequence_length:
-          min: 166
-          max: 175
-        alignment_start:
-          min: 1
-          max: 3
+        sequence_length: 171
+        alignment_start: 1
     FW:
       - data/SRR10800986_1.fastq.gz
     BC:

diff --git a/workflow/rules/assignment.smk b/workflow/rules/assignment.smk
@@ -29,28 +29,24 @@ rule assignment_check_design:
         start=lambda wc: (
             config["assignments"][wc.assignment]["alignment_tool"]["configs"][
                 "alignment_start"
-            ]
-            if config["assignments"][wc.assignment]["alignment_tool"]["tool"]
-            == "exact"
+            ]["max"]
+            if config["assignments"][wc.assignment]["alignment_tool"]["tool"] == "bwa"
             else config["assignments"][wc.assignment]["alignment_tool"]["configs"][
                 "alignment_start"
-            ]["max"]
+            ]
         ),
         length=lambda wc: (
             config["assignments"][wc.assignment]["alignment_tool"]["configs"][
                 "sequence_length"
-            ]
-            if config["assignments"][wc.assignment]["alignment_tool"]["tool"]
-            == "exact"
+            ]["min"]
+            if config["assignments"][wc.assignment]["alignment_tool"]["tool"] == "bwa"
             else config["assignments"][wc.assignment]["alignment_tool"]["configs"][
                 "sequence_length"
-            ]["min"]
+            ]
         ),
         fast_check=lambda wc: (
             "--fast-dict"
             if config["assignments"][wc.assignment]["design_check"]["fast"]
-            or config["assignments"][wc.assignment]["alignment_tool"]["tool"]
-            == "bbmap"
             else "--slow-string-search"
         ),
         check_sequence_collitions=lambda wc: (

diff --git a/workflow/schemas/config.schema.yaml b/workflow/schemas/config.schema.yaml
@@ -99,29 +99,13 @@ properties:
                         min_mapping_quality:
                           type: integer
                           minimum: 0
-                          default: 35
+                          default: 30
                         sequence_length:
-                          type: object
-                          properties:
-                            min:
-                              type: integer
-                            max:
-                              type: integer
-                          additionalProperties: false
-                          required:
-                            - min
-                            - max
+                          type: integer
+                          minimum: 1
                         alignment_start:
-                          type: object
-                          properties:
-                            min:
-                              type: integer
-                            max:
-                              type: integer
-                          additionalProperties: false
-                          required:
-                            - min
-                            - max
+                          type: integer
+                          minimum: 1
                       additionalProperties: false
                       required:
                         - min_mapping_quality