feat: expand cluster resourcing for new rna rules and better tailor d…

…na ones
OpenOmics · Feb 27, 2024 · 07ea12b · 07ea12b
1 parent d6dcf75
commit 07ea12b
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Showing 3 changed files with 59 additions and 26 deletions.
diff --git a/config/cluster.json b/config/cluster.json
@@ -1,32 +1,60 @@
 {
     "__default__": {
         "threads": 4,
-        "mem": "8g",
+        "mem": "8G",
         "partition": "norm",
         "time": "0-04:00:00",
         "gres": "lscratch:64"
     },
+    "concat_reads": {
+        "threads": 28,
+        "mem": "16G",
+        "partition": "norm",
+        "time": "1-00:00:00",
+        "gres": "lscratch:400"
+    },
+    "concat_rna_reads": {
+        "threads": 28,
+        "mem": "16G",
+        "partition": "norm",
+        "time": "1-00:00:00",
+        "gres": "lscratch:400"
+    },
     "metawrap_read_qc": {
         "threads": 16,
-        "mem": "32g",
+        "mem": "32G",
+        "partition": "norm",
+        "time": "1-00:00:00",
+        "gres": "lscratch:400"
+    },
+    "rna_read_qc": {
+        "threads": 16,
+        "mem": "32G",
         "partition": "norm",
-        "time": "1-00:00:00"
+        "time": "1-00:00:00",
+        "gres": "lscratch:400"
     },
     "metawrap_genome_assembly": {
-        "threads": 24,
-        "mem": "128g",
+        "threads": 48,
+        "mem": "128G",
         "partition": "norm",
-        "time": "2-00:00:00"
+        "time": "5-00:00:00"
     },
     "metawrap_tax_classification": {
-        "threads": 12,
-        "mem": "32g",
-        "partition": "quick",
-        "time": "0-04:00:00"
-    },
-    "metawrap_assembly_binning": {
-        "threads": 16,
-        "mem": "64g",
+        "threads": 32,
+        "mem": "64G",
+        "partition": "norm",
+        "time": "5-00:00:00"
+    }, 
+    "metawrap_binning": {
+        "threads": 32,
+        "mem": "64G",
+        "partition": "norm",
+        "time": "2-00:00:00"
+    }, 
+    "derep_bins": {
+        "threads": 32,
+        "mem": "32G",
         "partition": "norm",
         "time": "2-00:00:00"
     }

diff --git a/config/images.json b/config/images.json
@@ -1,10 +1,10 @@
 {
     "images": {
-        "metawrap": "docker://rroutsong/metamorph_metawrap:0.0.2",
+        "metawrap": "docker://rroutsong/metamorph_metawrap:0.0.4",
         "metagenome": "docker://rroutsong/metamorph_metagenome:0.0.1"
     }, 
     "containers": {
-        "metawrap": "/data/OpenOmics/SIFs/metamorph_metawrap_0.0.2.sif",
+        "metawrap": "/data/OpenOmics/SIFs/metamorph_metawrap_0.0.4.sif",
         "metagenome": "/data/OpenOmics/SIFs/metamorph_metagenome_0.0.1.sif"
     }
 }
diff --git a/config/resources.json b/config/resources.json
@@ -1,10 +1,10 @@
 {
     "databases": [
         {
-            "name": "KRAKEN_DB2",
+            "name": "KRAKEN2_DB",
             "to": "/data2/KRAKEN_DB2",
-            "from": "/data/OpenOmics/references/metamorph/kraken2/k2_pluspfp_08gb_20230605",
-            "mode": "ro"
+            "from": "/data/OpenOmics/references/metamorph/kraken2/k2_pluspfp_08gb_20240112",
+            "mode": "rw"
         }, {
             "name": "KRAKEN_DB",
             "to": "/data2/KRAKEN_DB",
@@ -26,19 +26,24 @@
             "from": "/data/OpenOmics/references/metamorph/GUNC/gunc_1.0.5db",
             "mode": "ro"
         }, {
-            "name": "CHECKM_DB",
-            "to": "/data2/checkm",
-            "from": "/data/OpenOmics/references/metamorph/checkm",
-            "mode": "rw"
-        },  {
             "name": "NCBI_NT",
             "to": "/data2/NCBI_NT_DB",
             "from": "/data/OpenOmics/references/metamorph/NCBI_nt",
             "mode": "rw"
-        },  {
+        }, {
             "name": "NCBI_TAX",
             "to": "/data2/NCBI_TAX_DB",
-            "from": "/data/OpenOmics/references/metamorph/NCBI_tax",
+            "from": "/data/OpenOmics/references/metamorph/taxonomy",
+            "mode": "rw"
+        }, {
+            "name": "CHECKM_DB",
+            "to": "/data2/CHECKM_DB",
+            "from": "/data/OpenOmics/references/metamorph/checkm",
+            "mode": "rw"
+        },  {
+            "name": "CHECKM_CONFIG",
+            "to": "/opt/conda/envs/metawrap-env/lib/python2.7/site-packages/checkm/DATA_CONFIG",
+            "from": "/data/OpenOmics/references/metamorph/checkm/DATA_CONFIG",
             "mode": "rw"
         }
     ]