config: updated rumen

config/rumen/config.yaml

@@ -2,10 +2,9 @@
 # STEPS
 
 # Steps to be done
-# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
-steps: ["preprocessing", "assembly", "mapping"]
-steps_annotation: ["rgi", "plasflow", "minced", "barrnap", "kegg"] # prodigal is run in any case
-steps_analysis: ["quast", "mash", "mashmap", "fastani", "mummer", "cdhit", "diamond", "cov"]
+steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
+steps_annotation: ["rgi", "plasflow", "minced", "barrnap"] # prodigal is run in any case; excluded: kegg
+steps_analysis: ["quast", "mash", "mashmap", "fastani", "cdhit", "diamond", "cov"] # excluded: mummer
 steps_taxonomy: ["kraken2", "kaiju"]
 
 ############################################################

config/rumen/slurm.yaml

@@ -79,11 +79,11 @@ mapping_bwa_idx_asm:
 
 mapping_bwa_mem_asm_sr:
     time: "00-02:00:00"
-    partition: "batch"
+    partition: "bigmem"
 
 mapping_bwa_mem_asm_lr:
     time: "00-08:00:00"
-    partition: "batch"
+    partition: "bigmem"
 
 mapping_bwa_mem_asm_hy:
     time: "00-02:00:00"
@@ -99,72 +99,72 @@ annotation_rgi:
     partition: "batch"
 
 annotation_minced:
-    time: "00-00:05:00"
+    time: "00-00:20:00"
     partition: "batch"
 
 annotation_plasflow:
-    time: "00-00:10:00"
+    time: "00-00:30:00"
     partition: "bigmem"
 
 annotation_barrnap:
-    time: "00-00:10:00"
+    time: "00-00:20:00"
     partition: "batch"
 
 annotation_hmm_kegg:
     time: "00-08:00:00"
-    partition: "batch"
+    partition: "bigmem"
 
 # Analysis
 analysis_quast:
-    time: "00-00:05:00"
+    time: "00-00:10:00"
     partition: "batch"
 
 analysis_mash_sketch_sr:
-    time: "00-00:15:00"
+    time: "00-00:40:00"
     partition: "batch"
 
 analysis_mash_sketch_lr:
-    time: "00-00:15:00"
+    time: "00-00:40:00"
     partition: "batch"
 
 analysis_mash_reads:
-    time: "00-00:05:00"
+    time: "00-00:10:00"
     partition: "batch"
 
 analysis_mash_sketch_asm:
-    time: "00-00:05:00"
+    time: "00-00:10:00"
     partition: "batch"
 
 analysis_mash_asm:
-    time: "00-00:05:00"
+    time: "00-00:10:00"
     partition: "batch"
 
 analysis_mashmap_one2one:
-    time: "00-00:30:00"
+    time: "00-01:00:00"
     partition: "batch"
 
 analysis_fastani_one2one:
-    time: "00-00:20:00"
+    time: "00-01:00:00"
     partition: "batch"
 
 analysis_mummer_dnadiff:
-    time: "00-01:00:00"
-    partition: "batch"
+    time: "00-02:00:00"
+    partition: "bigmem"
 
 analysis_cdhit:
-    time: "00-00:05:00"
+    time: "00-01:00:00"
     partition: "batch"
 
 analysis_diamond:
-    time: "00-00:10:00"
+    time: "00-01:00:00"
     partition: "batch"
 
 analysis_diamond_db:
-    time: "00-02:00:00"
+    time: "00-06:00:00"
     partition: "batch"
 
 analysis_genomecov_pergene:
-    time: "00-02:00:00"
+    time: "00-12:00:00"
     partition: "batch"
 
 analysis_genomecov_segmentation: