GDB config: more cores and time for sortmerna

config/GDB/config.yaml

@@ -74,7 +74,7 @@ fastp:
 
 # rRNA gene filtering
 sortmerna:
-    threads: 20
+    threads: 30
     # References to be used (w/ md5sums)
     refs: [
         # db6e72022cf650c4b33bd888b92a0391  silva-bac-16s-id90.fasta
@@ -95,7 +95,7 @@ fastqc:
 # List of assemblers for different read types: assembler names MUST be UNIQUE
 assemblers:
     sr: ["megahit", "metaspades"]
-    lr: ["flye", "wtdbg2", "canu"]
+    lr: ["flye", "wtdbg2"]
     hy: ["metaspadeshybrid", "operams"]
     hyhy: []
 

config/GDB/slurm.yaml

@@ -28,7 +28,7 @@ fastp_sr:
     explicit: ""
 
 sortmerna_filt:
-    time: "00-12:00:00"
+    time: "01-00:00:00"
     partition: "batch"
     qos: "qos-batch"
     nodes: 1
@@ -101,7 +101,15 @@ mapping_bwa_idx_assembly:
     n: 1
     explicit: ""
 
-mapping_bwa_mem_assembly_sr:
+mapping_bwa_mem_assembly_sr_metag:
+    time: "00-02:00:00"
+    partition: "batch"
+    qos: "qos-batch"
+    nodes: 1
+    n: 1
+    explicit: ""
+
+mapping_bwa_mem_assembly_sr_metat:
     time: "00-02:00:00"
     partition: "batch"
     qos: "qos-batch"
@@ -125,6 +133,14 @@ mapping_bwa_mem_assembly_hy:
     n: 1
     explicit: ""
 
+mapping_bwa_mem_assembly_hy_hy:
+    time: "00-02:00:00"
+    partition: "batch"
+    qos: "qos-batch"
+    nodes: 1
+    n: 1
+    explicit: ""
+
 # Assembly polishing
 mapping_bwa_idx_polishing:
     time: "00-02:00:00"