fixed path database and update emmtyper params

Daniel-VM · Sep 12, 2024 · 07a3eb1 · 07a3eb1
1 parent 7839afa
commit 07a3eb1
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog
@@ -53,7 +53,7 @@ cat <<EOF > _01_emmtyper.sbatch
 # create results folder
 mkdir -p 01-typing
 mkdir -p 01-typing/tmps
-blastdb_path=/data/bi/references/cdc_emm_blastdb
+blastdb_path=/data/bi/references/cdc_emm_blastdb/20240509
 
 # Run emmtyper
 singularity exec \\
@@ -63,9 +63,9 @@ singularity exec \\
     /data/bi/pipelines/singularity-images/singularity-emmtyper.0.2.0--py_0 emmtyper \\
     -w blast \\
     --keep \\
-    --blast_db "\${blastdb_path}/cdc_emm_database29042024" \\
-    --percent-identity 95 \\
-    --culling-limit 5 \\
+    --blast_db "\${blastdb_path}/cdc_emm_database" \\
+    --percent-identity 100 \\
+    --culling-limit 5 \
     --output 01-typing/results_emmtyper.out \\
     --output-format verbose \\
     ./fasta_inputs/*.fasta