updated version of parsnp

NorwegianVeterinaryInstitute · Feb 7, 2024 · 7d35d4d · 7d35d4d
1 parent 70daa43
commit 7d35d4d
Showing 1 changed file with 7 additions and 4 deletions.
diff --git a/modules/PARSNP.nf b/modules/PARSNP.nf
@@ -1,6 +1,6 @@
 process PARSNP {
-	conda (params.enable_conda ? 'bioconda::parsnp=1.7.4' : null)
-	container 'quay.io/biocontainers/parsnp:1.7.4--hdcf5f25_2'
+	conda (params.enable_conda ? 'bioconda::parsnp=2.0.0' : null)
+	container 'quay.io/biocontainers/parsnp:2.0.3--hdcf5f25_0'
 
 	label 'process_long'
 
@@ -15,8 +15,11 @@ process PARSNP {
         script:
         """
 	parsnp --version > parsnp.version
-        parsnp -d *.fasta -p 4 --skip-phylogeny -u -o results -r $params.parsnp_ref -v -c &> parsnp.log
-	mv results/* .
+        parsnp -d *.fasta -p $task.cpus --skip-phylogeny -u -o results -r $params.parsnp_ref -v -c &> parsnp.log
+	mv results/log/parsnpAligner.log .
+	mv results/parsnp.ggr .
+	mv results/parsnp.xmfa .
+	mv results/parsnp.unalign . 
 	harvesttools -x *xmfa -M parsnp_alignment.fasta
         """
 }