WIP: Checkpoint snakefile

2019_GDB/config/CONFIG.yaml

-# steps: "assembly_annotation mapping metaT mmseq binning taxonomy"
-steps: "mapping metaT mmseq binning taxonomy"
+# steps: "assembly_annotation mapping metaT mmseq binning taxonomy analysis"
+steps: "binning taxonomy analysis"
 data_dir: "data"
 results_dir: "results"
 db_dir: "dbs"
@@ -91,7 +91,8 @@ rebaler:
     threads: 28
 diamond:
     threads: 28
-    db: "/mnt/isilon/projects/ecosystem_biology/NOMIS/DIAMOND/new_nr.dmnd"
+    #db: "/mnt/isilon/projects/ecosystem_biology/NOMIS/DIAMOND/new_nr.dmnd"
+    db: "/work/projects/ecosystem_biology/local_tools/databases/nr_uniprot_trembl.dmnd"
 metaspades:
     threads: 28
 mmseq2:
@@ -151,3 +152,11 @@ mmseqs:
      createdb: "/home/users/sbusi/apps/mmseqs/bin/mmseqs createdb"
      rbh: "/home/users/sbusi/apps/mmseqs/bin/mmseqs rbh"
      convertalis: "/home/users/sbusi/apps/mmseqs/bin/mmseqs convertalis"
+
+# Paths to CASC and minced for CRISPR
+CASC:
+    PATH: "$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/bin"
+    PERL5LIB: "/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/lib/site_perl"
+
+minced:
+    PATH: "$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/minced/"