Adding resources and allocation information for sqanti rules

OpenOmics · Sep 18, 2023 · 3dd245d · 3dd245d
1 parent 5eb3ede
commit 3dd245d
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Showing 2 changed files with 18 additions and 4 deletions.
diff --git a/config/cluster.json b/config/cluster.json
@@ -132,5 +132,15 @@
         "threads": "8",
         "mem": "16g",
         "time": "0-06:00:00"
+    },
+    "sqanti_qc": {
+        "threads": "16",
+        "mem": "64g",
+        "time": "0-12:00:00"
+    },
+    "sqanti_ml_filter": {
+        "threads": "16",
+        "mem": "64g",
+        "time": "0-12:00:00"
     }
 }
diff --git a/config/genome.json b/config/genome.json
@@ -3,20 +3,24 @@
         "hg38_41": {
             "GENOME_FA":      "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/GRCh38.primary_assembly.genome.fa.gz",
             "TRANSCRIPTS_FA": "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/gencode.v42.transcripts.fa.gz",
-            "GTF_FILE":       "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/gencode.v42.primary_assembly.annotation.gtf.gz"
+            "GTF_FILE":       "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/gencode.v42.primary_assembly.annotation.gtf.gz",
+            "SQANTI_CAGEPEAK": "/data/OpenOmics/references/modr/sqanti3/data/ref_TSS_annotation/human.refTSS_v3.1.hg38.bed"
         },
         "mm39_M31": {
             "GENOME_FA":      "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M31/GRCm39.primary_assembly.genome.fa.gz",
             "TRANSCRIPTS_FA": "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M31/gencode.vM31.transcripts.fa.gz",
-            "GTF_FILE":       "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M31/gencode.vM31.primary_assembly.annotation.gtf.gz"
+            "GTF_FILE":       "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M31/gencode.vM31.primary_assembly.annotation.gtf.gz",
+            "SQANTI_CAGEPEAK": "/data/OpenOmics/references/modr/sqanti3/data/ref_TSS_annotation/mouse.refTSS_v3.1.GRCm39.bed"
         },
         "mm10_M25": {
             "GENOME_FA":      "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/GRCm38.primary_assembly.genome.fa.gz",
             "TRANSCRIPTS_FA": "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.transcripts.fa.gz",
-            "GTF_FILE":       "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.primary_assembly.annotation.gtf.gz"
+            "GTF_FILE":       "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.primary_assembly.annotation.gtf.gz",
+            "SQANTI_CAGEPEAK": "/data/OpenOmics/references/modr/sqanti3/data/ref_TSS_annotation/mouse.refTSS_v3.1.mm10.bed"
         },
         "DINOPORE_CLASSREF": "/data/OpenOmics/references/modr/truthsets/groundtruth_class_regression.tsv",
         "DINOPORE_MODELS": "/data/OpenOmics/references/modr/model",
-        "DINOPORE_CODE": "/data/OpenOmics/references/modr/code"
+        "DINOPORE_CODE": "/data/OpenOmics/references/modr/code",
+        "SQANTI_POLYA_MOTIF_LIST": "/data/OpenOmics/references/modr/sqanti3/data/polyA_motifs/mouse_and_human.polyA_motif.txt"
     }
 }