GDB config: sortmerna/bbmap update

config/GDB/config.yaml

@@ -3,7 +3,7 @@
 
 # Steps to be done
 # steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
-steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
+steps: ["preprocessing", "assembly", "annotation", "analysis", "taxonomy"]
 steps_annotation: ["diamond", "rgi", "plasflow", "minced", "barrnap"] # prodigal is run in any case
 steps_analysis: ["quast", "cdhit", "mash_dist"]
 steps_taxonomy: ["kraken2", "kaiju"]
@@ -72,19 +72,6 @@ fastp:
     threads: 10
     min_length: 40
 
-# rRNA gene filtering
-sortmerna:
-    threads: 28
-    # References to be used (w/ md5sums)
-    refs: [
-        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-16s-id95.fasta",
-        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-23s-id98.fasta",
-        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-16s-id90.fasta",
-        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-23s-id98.fasta",
-        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-18s-id95.fasta",
-        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-28s-id98.fasta"
-    ]
-
 # FastQ QC
 # https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
 fastqc:
@@ -99,7 +86,7 @@ assemblers:
     sr: ["megahit", "metaspades"]
     lr: ["flye", "wtdbg2", "canu"]
     hy: ["metaspadeshybrid", "operams"]
-    hyhy: []
+    hyhy: ["imp3"]
 
 # https://github.com/fenderglass/Flye
 flye:
@@ -204,9 +191,29 @@ barrnap:
 cdhit:
     threads: 10
 
-# XXX
+# https://sourceforge.net/projects/bbmap/
+# https://github.com/BioInfoTools/BBMap/
 bbmap:
     threads: 10
+    # References to be used (w/ md5sums)
+    rrna_refs: [
+        # c0cd2aa2e84e3e3977859c34feb63cd5  /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5.8s-database-id98.fasta
+        # 703e4c270ab0a578deb4800c33b36367  /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5s-database-id98.fasta
+        # 8b4e6c6f17f6f35444a60fdc915e052c  /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-16s-id95.fasta
+        # ca4edcdddb98d7868f93e2308e297704  /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-23s-id98.fasta
+        # db6e72022cf650c4b33bd888b92a0391  /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-16s-id90.fasta
+        # f347d2f8f8ffbfa28c785e3a9fe3db79  /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-23s-id98.fasta
+        # 878a413765d09c3ec75409fb1d1573f1  /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-18s-id95.fasta
+        # cbb973e63f52981bd591de0404df5839  /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-28s-id98.fast
+        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5.8s-database-id98.fasta",
+        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5s-database-id98.fasta",
+        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-16s-id95.fasta",
+        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-23s-id98.fasta",
+        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-16s-id90.fasta",
+        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-23s-id98.fasta",
+        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-18s-id95.fasta",
+        "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-28s-id98.fasta"
+    ]
 
 # Assembly quality
 # https://github.com/ablab/quast

config/GDB/slurm.yaml

@@ -27,8 +27,8 @@ fastp_sr:
     n: 1
     explicit: ""
 
-sortmerna_filt:
-    time: "01-12:00:00"
+rm_rrna_bbmap:
+    time: "00-6:00:00"
     partition: "batch"
     qos: "qos-batch"
     nodes: 1