plasmidfinder task bugfix and updates (#191)

* plasmidfinder task updates: decrease cpus to 2, memory to 8, and disk_size to 50. Also fixed bug with output string of plasmid replicons found. Also made some move commands verbose * update CI
theiagen · Sep 19, 2023 · f229903 · f229903
1 parent 9aa16ba
commit f229903
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Showing 3 changed files with 11 additions and 11 deletions.
diff --git a/tasks/gene_typing/task_plasmidfinder.wdl b/tasks/gene_typing/task_plasmidfinder.wdl
@@ -4,10 +4,10 @@ task plasmidfinder {
   input {
     File assembly
     String samplename
-    Int cpu = 8
-    Int memory = 16
+    Int cpu = 2
+    Int memory = 8
     String docker = "us-docker.pkg.dev/general-theiagen/staphb/plasmidfinder:2.1.6"
-    Int disk_size = 100
+    Int disk_size = 50
     String? database
     String? database_path
     String? method_path
@@ -41,15 +41,15 @@ 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
 
-  mv results_tab.tsv ~{samplename}_results.tsv
-  mv Hit_in_genome_seq.fsa ~{samplename}_seqs.fsa
+  mv -v results_tab.tsv ~{samplename}_results.tsv
+  mv -v Hit_in_genome_seq.fsa ~{samplename}_seqs.fsa
 
   >>>
   output {

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -264,7 +264,7 @@
     - path: miniwdl_run/call-merlin_magic/workflow.log
       contains: ["wdl", "theiaprok_illumina_pe", "merlin", "done"]
     - path: miniwdl_run/call-plasmidfinder/command
-      md5sum: 61f7be9cfd36e3a48585e7f64cbcfe35
+      md5sum: 3b70033058bf91c04337e38bfd038b5a
     - path: miniwdl_run/call-plasmidfinder/inputs.json
     - path: miniwdl_run/call-plasmidfinder/outputs.json
     - path: miniwdl_run/call-plasmidfinder/stderr.txt
@@ -556,7 +556,7 @@
     - path: miniwdl_run/wdl/tasks/gene_typing/task_bakta.wdl
       md5sum: 0bed8fb60786095843a67b1ad03051dc
     - path: miniwdl_run/wdl/tasks/gene_typing/task_plasmidfinder.wdl
-      md5sum: 6ca295b4dcdbe95dd86516ba0a4073f8
+      md5sum: 8730e07b1c7ab9d2434a7838ddb1fc72
     - path: miniwdl_run/wdl/tasks/gene_typing/task_prokka.wdl
       md5sum: 8e8423b99d5cd3e92bb89b3c3211d432
     - path: miniwdl_run/wdl/tasks/gene_typing/task_resfinder.wdl

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -261,7 +261,7 @@
     - path: miniwdl_run/call-merlin_magic/workflow.log
       contains: ["wdl", "theiaprok_illumina_se", "merlin", "done"]
     - path: miniwdl_run/call-plasmidfinder/command
-      md5sum: 61f7be9cfd36e3a48585e7f64cbcfe35
+      md5sum: 3b70033058bf91c04337e38bfd038b5a
     - path: miniwdl_run/call-plasmidfinder/inputs.json
     - path: miniwdl_run/call-plasmidfinder/outputs.json
     - path: miniwdl_run/call-plasmidfinder/stderr.txt
@@ -526,7 +526,7 @@
     - path: miniwdl_run/wdl/tasks/gene_typing/task_bakta.wdl
       md5sum: 0bed8fb60786095843a67b1ad03051dc
     - path: miniwdl_run/wdl/tasks/gene_typing/task_plasmidfinder.wdl
-      md5sum: 6ca295b4dcdbe95dd86516ba0a4073f8
+      md5sum: 8730e07b1c7ab9d2434a7838ddb1fc72
     - path: miniwdl_run/wdl/tasks/gene_typing/task_prokka.wdl
       md5sum: 8e8423b99d5cd3e92bb89b3c3211d432
     - path: miniwdl_run/wdl/tasks/gene_typing/task_resfinder.wdl