added samtools_depth

UPHL-BioNGS · Jun 4, 2021 · edcc2db · edcc2db
1 parent 6daaa2a
commit edcc2db
Showing 1 changed file with 11 additions and 5 deletions.
diff --git a/configs/example.config b/configs/example.config
@@ -47,7 +47,6 @@
 //params.primer_bed = "Cecret/configs/artic_V3_nCoV-2019.bed"
 //params.amplicon_bed = "Cecret/configs/nCoV-2019.insert.bed"
 
-
 //# Tool toggles
 //params.trimmer = 'ivar'
 //params.trimmer = 'samtools'
@@ -120,6 +119,10 @@ iqtree_container = 'staphb/iqtree:latest'
 //params.samtools_coverage_options = ''
 //params.samtools_coverage = true
 
+//# For process samtools_depth
+//params.samtools_depth_options = ''
+//params.samtools_depth = true
+
 //# For process samtools_flagstat
 //params.samtools_flagstat_options = ''
 //params.samtools_flagstat = true
@@ -138,7 +141,7 @@ iqtree_container = 'staphb/iqtree:latest'
 //params.samtools_ampliconstats_options = ''
 //params.samtools_ampliconstats = true
 
-//# For process samtools_ampliconstats
+//# For process samtools_plot_ampliconstats
 //params.samtools_plot_ampliconstats_options = '-size 1200,900 -size2 1200,900 -size3 1200,900'
 //params.samtools_plot_ampliconstats = true
 
@@ -247,7 +250,7 @@ process {
   }
 
   withName:bamsnap{
-    cpus = 'params.medpus'
+    cpus = 'params.medcpus'
     errorStrategy = 'ignore'
     container = bamsnap_container
     time = '1h'
@@ -265,6 +268,10 @@ process {
     container = samtools_container
   }
 
+  withName:samtools_depth{
+    container = samtools_container
+  }
+
   withName:kraken2{
     cpus = "params.maxcpus"
     container = kraken2_container
@@ -287,14 +294,13 @@ process {
     container = pangolin_container
   }
 
-
   withName:nextclade{
     cpus = "params.maxcpus"
     container = nextclade_container
   }
 
   withName:vadr{
-    cpus = 'params.medpus'
+    cpus = 'params.medcpus'
     memory = 'params.maxmem'
     container = 'staphb/vadr:latest'
   }