fix db path in RDS threshold calculation script

oschwengers · Sep 30, 2020 · cff6af0 · cff6af0
1 parent 83a335d
commit cff6af0
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/db-scripts/compute-rds-thresholds.nf b/db-scripts/compute-rds-thresholds.nf
@@ -6,9 +6,9 @@ import java.nio.file.*
 
 
 // Parameters
-mpsPath         = Paths.get( params.mps ).toRealPath()
-contigsPath    = Paths.get( params.contigs ).toRealPath()
-pcDb            = Paths.get( params.pcDb ).toRealPath()
+mpsPath     = Paths.get( params.mps ).toRealPath()
+contigsPath = Paths.get( params.contigs ).toRealPath()
+pcDb        = Paths.get( params.pcDb ).toRealPath()
 
 
 // Constants
@@ -38,7 +38,7 @@ process searchProts {
     errorStrategy 'retry'
     maxRetries 3
     cpus 1
-    memory '2 GB'
+    memory '2.5 GB'
 
     input:
     set val(type), val(id), val(subSequence) from chContigs
@@ -52,7 +52,7 @@ process searchProts {
     prodigal -i seq.fna -a cdss.faa -p meta
     if [ -s cdss.faa ]
     then
-        diamond blastp --query cdss.faa --db ${pcDB}/mps.dmnd --threads ${task.cpus} --out output.tsv --max-target-seqs 1 --id 90 --query-cover 80 --subject-cover 80
+        diamond blastp --query cdss.faa --db ${pcDb} --threads ${task.cpus} --out output.tsv --max-target-seqs 1 --id 90 --query-cover 80 --subject-cover 80
     else
         touch output.tsv
     fi