example jsons changed/added

flexiprep/nbactions.xml

@@ -10,7 +10,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json</exec.args>
+                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
             </properties>
@@ -25,7 +25,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json</exec.args>
+                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json</exec.args>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
@@ -41,7 +41,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json</exec.args>
+                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
             </properties>

gatk/examples/test.json

 {
+    "inputtype": "rna",
     "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
     "bwa" : {"exe":"/home/pjvan_thof/pipelines/test/test"},
     "flexiprep": {

mapping/examples/test.json

+{
+    "referenceFile": "/blabla/blabla.fa",
+    "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
+    
+    "flexiprep": {
+        "fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"},
+        "cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},
+        "sickle": {"exe":"/home/pjvan_thof/pipelines/test/test"}
+    }
+}

mapping/nbactions.xml

@@ -10,7 +10,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping</exec.args>
+                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN star-2pass -skipflexiprep</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
             </properties>
@@ -25,7 +25,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping</exec.args>
+                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN star-2pass -skipflexiprep</exec.args>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
@@ -41,7 +41,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping</exec.args>
+                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN star-2pass -skipflexiprep</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
             </properties>