config and slurm update

config/config.yaml

@@ -39,10 +39,11 @@ data:
     # Meta-transcriptomics
     metat:
         sr:
-            r1: "data/metaT/FastSelectFull1_MT_Rashi_S14_R1_001.fastq.gz"
-            r2: "data/metaT/FastSelectFull1_MT_Rashi_S14_R2_001.fastq.gz"
+            r1: "data/metaT/FastSelectFull1_MT_Rashi_S14_R1_001.fastq.gz" # leave empty if no data, i.e. ""
+            r2: "data/metaT/FastSelectFull1_MT_Rashi_S14_R2_001.fastq.gz" # leave empty if no data, i.e. ""
     # Meta-proteomics
     metap:
+        # TODO
 
 # binning_samples: ["flye", "megahit", "bwa_sr_metaspades_hybrid", "bwa_lr_metaspades_hybrid", "bwa_merged_metaspades_hybrid", "mmi_sr_metaspades_hybrid", "mmi_lr_metaspades_hybrid", "mmi_merged_metaspades_hybrid"]
 

config/slurm.yaml

@@ -19,13 +19,13 @@ guppy_gpu_basecalling:
     n: 1
     explicit: "--gres=gpu:1"
 
-# fastp_sr:
-#     time: "00-01:00:00"
-#     partition: "batch"
-#     qos: "qos-batch"
-#     nodes: 1
-#     n: 1
-#     explicit: ""
+fastp_sr:
+    time: "00-01:00:00"
+    partition: "batch"
+    qos: "qos-batch"
+    nodes: 1
+    n: 1
+    explicit: ""
 
 # Assembly
 assembly_lr_flye:
@@ -78,7 +78,7 @@ bwa_index_assembly:
     explicit: ""
 
 bwa_mem_assembly_sr:
-    time: "00-06:00:00"
+    time: "00-02:00:00"
     partition: "batch"
     qos: "qos-batch"
     nodes: 1
@@ -94,7 +94,7 @@ bwa_mem_assembly_lr:
     explicit: ""
 
 bwa_mem_assembly_hy:
-    time: "00-06:00:00"
+    time: "00-02:00:00"
     partition: "batch"
     qos: "qos-batch"
     nodes: 1
@@ -119,7 +119,7 @@ bwa_mem_assembly_polishing:
     explicit: ""
 
 polishing_lr_racon:
-    time: "00-06:00:00"
+    time: "00-04:00:00"
     partition: "bigmem"
     qos: "qos-bigmem"
     nodes: 1
@@ -127,7 +127,7 @@ polishing_lr_racon:
     explicit: ""
 
 polishing_lr_medaka:
-    time: "01-00:00:00"
+    time: "00-12:00:00"
     partition: "bigmem"
     qos: "qos-bigmem"
     nodes: 1