Merge pull request #72 from VEuPathDB/repeat-masker-root-and-sl-fix

RepeatMasker Root and SL Fix

Author: weili-apidb

Main/lib/perl/WorkflowSteps/TouchFile.pm

@@ -0,0 +1,25 @@
+package ApiCommonWorkflow::Main::WorkflowSteps::TouchFile;
+
+@ISA = (ApiCommonWorkflow::Main::WorkflowSteps::WorkflowStep);
+
+use strict;
+use ApiCommonWorkflow::Main::WorkflowSteps::WorkflowStep;
+
+
+sub run {
+  my ($self, $test, $undo) = @_;
+
+  my $fileName = $self->getParamValue('fileName');
+
+  my $workflowDataDir = $self->getWorkflowDataDir();
+
+  my $cmd = "touch $workflowDataDir/$fileName";
+
+  if ($undo) {
+    $self->runCmd(0, "rm -f $workflowDataDir/$fileName");
+  } else {
+    $self->runCmd($test, $cmd);
+  }
+}
+
+1;

Main/lib/xml/workflow/globalGraph.xml

@@ -37,6 +37,11 @@
     <depends name="initUserGroupProject"/>
   </step>
 
+  <step name="repeatMaskerRoot" stepClass="ApiCommonWorkflow::Main::WorkflowSteps::TouchFile">
+    <paramValue name="fileName">$$dataDir$$/repeatMaskerRootFile</paramValue>
+    <depends name="initUserGroupProject"/>
+  </step>
+
 
   <subgraph name="GO_RSRC" xmlFile="loadDataset.xml">
     <paramValue name="datasetName">GO_RSRC</paramValue>
@@ -330,4 +335,6 @@
     <depends name="registerPlugins"/>
   </subgraph>
 
+
+
 </workflowGraph>

Main/lib/xml/workflow/makeAndBlockAssemblySeqs.xml

@@ -75,6 +75,7 @@
       <paramValue name="analysisDir">$$analysisDirectory$$</paramValue>
       <paramValue name="entry"></paramValue>
       <depends name="makeRepeatMaskerNextflowConfig"/>
+      <dependsGlobal name="repeatMaskerRoot"/>
     </subgraph>
 
 

Main/lib/xml/workflow/mapClonedInsertEnds.xml

@@ -79,6 +79,7 @@
     <paramValue name="nextflowWorkflow">VEuPathDB/repeat-masker-nextflow</paramValue>
     <paramValue name="entry"></paramValue>
     <depends name="makeRepeatMaskerNextflowConfig"/>
+    <dependsGlobal name="repeatMaskerRoot"/>
   </subgraph>
 
   <subgraph name="blat" xmlFile="blatDnaAgainstGenome.xml">

Main/lib/xml/workflow/maskGenome.xml

@@ -84,6 +84,7 @@
     <paramValue name="nextflowWorkflow">VEuPathDB/repeat-masker-nextflow</paramValue>
     <paramValue name="entry"></paramValue>
     <depends name="makeRepeatMaskerNextflowConfig"/>
+    <dependsGlobal name="repeatMaskerRoot"/>
   </subgraph>
 
 

Main/lib/xml/workflow/rnaSeqSplicedLeaderAndPolyASitesProfiles.xml

@@ -12,7 +12,7 @@
     <param name="gusConfigFile"/>
 
 
-    <constant name="dataDir">$$parentDataDir$$/processSplicedLeaderAndPolyASitesExperiment</constant>
+    <constant name="dataDir">$$parentDataDir$$/processSplicedLeaderAndPolyASitesExperiment/profiles</constant>
     <constant name="analysisDirectory">$$dataDir$$/analysisDir</constant>
     <constant name="resultsDirectory">$$analysisDirectory$$/results</constant>
 
@@ -23,8 +23,15 @@
     <constant name="nextflowResultsDir">$$nextflowAnalysisDir$$/nextflow_output</constant>
     <constant name="analysisOutputDir">$$nextflowResultsDir$$/analysis_output</constant>
 
+
+    <step name="makeDataDir" stepClass="ReFlow::StepClasses::MakeDataDir">
+        <paramValue name="dataDir">$$dataDir$$</paramValue>
+    </step>
+
+
     <step name="makeAnslysisDir" stepClass="ReFlow::StepClasses::MakeDataDir">
       <paramValue name="dataDir">$$nextflowAnalysisDir$$</paramValue>
+      <depends name="makeDataDir"/>
     </step>
 
     <!-- This step makes the nextflow config file -->