config: GDB update

config/GDB/config.yaml

@@ -3,7 +3,7 @@
 
 # Steps to be done
 # steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
-steps: ["preprocessing", "assembly", "polishing"]
+steps: ["preprocessing", "assembly", "mapping"]
 steps_annotation: ["rgi", "plasflow", "minced", "barrnap"] # prodigal is run in any case
 steps_analysis: ["quast", "cdhit", "diamond", "mash"]
 steps_taxonomy: ["kraken2", "kaiju"]

config/GDB/slurm.yaml

@@ -135,7 +135,7 @@ polishing_medaka_lr:
     explicit: ""
 
 # Mapping
-mapping_bwa_idx_assembly:
+mapping_bwa_idx_asm:
     time: "00-02:00:00"
     partition: "batch"
     qos: "qos-batch"
@@ -143,7 +143,7 @@ mapping_bwa_idx_assembly:
     n: 1
     explicit: ""
 
-mapping_bwa_mem_assembly_sr_metag:
+mapping_bwa_mem_asm_sr:
     time: "00-02:00:00"
     partition: "batch"
     qos: "qos-batch"
@@ -151,31 +151,15 @@ mapping_bwa_mem_assembly_sr_metag:
     n: 1
     explicit: ""
 
-mapping_bwa_mem_assembly_sr_metat:
-    time: "00-02:00:00"
-    partition: "batch"
-    qos: "qos-batch"
-    nodes: 1
-    n: 1
-    explicit: ""
-
-mapping_bwa_mem_assembly_lr:
-    time: "00-06:00:00"
-    partition: "batch"
-    qos: "qos-batch"
-    nodes: 1
-    n: 1
-    explicit: ""
-
-mapping_bwa_mem_assembly_hy:
-    time: "00-02:00:00"
+mapping_bwa_mem_asm_lr:
+    time: "00-12:00:00"
     partition: "batch"
     qos: "qos-batch"
     nodes: 1
     n: 1
     explicit: ""
 
-mapping_bwa_mem_assembly_hyhy:
+mapping_bwa_mem_asm_hy:
     time: "00-02:00:00"
     partition: "batch"
     qos: "qos-batch"
@@ -247,4 +231,4 @@ tax_kaiju_summary:
     qos: "qos-batch"
     nodes: 1
     n: 1
-    explicit: ""
\ No newline at end of file
+    explicit: ""