Merge pull request #3 from Kincekara/dev

version 1.2.1
Kincekara · Oct 3, 2023 · b7966f3 · b7966f3
2 parents ff4155d + 3e08969
commit b7966f3
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/tasks/task_mlst.wdl b/tasks/task_mlst.wdl
@@ -7,7 +7,7 @@ task ts_mlst {
   input {
     File assembly
     String samplename
-    String docker = "staphb/mlst:2.23.0"
+    String docker = "staphb/mlst:2.23.0-2023-08"
     Int? cpu = 4
     # Parameters
     # --nopath          Strip filename paths from FILE column (default OFF)

diff --git a/tasks/task_plasmidfinder.wdl b/tasks/task_plasmidfinder.wdl
@@ -33,12 +33,12 @@ task plasmidfinder {
     if [ ! -f results_tab.tsv ]; then
       PF="No plasmids detected in database"
     else
-      PF="$(tail -n +2 results_tab.tsv | cut -f 2 | sort | uniq -u | paste -s -d, - )"
+      PF="$(tail -n +2 results_tab.tsv | uniq | cut -f 2 | sort | paste -s -d, - )"
         if [ "$PF" == "" ]; then
           PF="No plasmids detected in database"
         fi  
     fi
-    echo $PF | tee PLASMIDS
+    echo "$PF" | tee PLASMIDS
 
     # rename results
     mv results_tab.tsv ~{samplename}.plasmid.tsv

diff --git a/tasks/task_spades.wdl b/tasks/task_spades.wdl
@@ -4,7 +4,7 @@ task spades_pe {
   input {
     File read1
     File read2
-    Int? contig_threshold = 500
+    Int? contig_threshold = 300
     String samplename
     String docker = "kincekara/spades:3.15.5"
 

diff --git a/tasks/task_version.wdl b/tasks/task_version.wdl
@@ -8,7 +8,7 @@ task version_capture {
     volatile: true
   }
   command {
-    cbird_version="C-BIRD v1.1.0"
+    cbird_version="C-BIRD v1.2.1"
     ~{default='' 'export TZ=' + timezone}
     date +"%Y-%m-%d" > TODAY
     echo "$cbird_version" > CBIRD_VERSION