Commit 081cde4c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

example jsons changed/added

parent c8269286
...@@ -10,7 +10,7 @@ ...@@ -10,7 +10,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal> <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals> </goals>
<properties> <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.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir> <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties> </properties>
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal> <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals> </goals>
<properties> <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> <exec.executable>java</exec.executable>
<jpda.listen>true</jpda.listen> <jpda.listen>true</jpda.listen>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir> <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
...@@ -41,7 +41,7 @@ ...@@ -41,7 +41,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal> <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals> </goals>
<properties> <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.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir> <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties> </properties>
......
{ {
"inputtype": "rna",
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" }, "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"bwa" : {"exe":"/home/pjvan_thof/pipelines/test/test"}, "bwa" : {"exe":"/home/pjvan_thof/pipelines/test/test"},
"flexiprep": { "flexiprep": {
......
{
"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"}
}
}
...@@ -10,7 +10,7 @@ ...@@ -10,7 +10,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal> <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals> </goals>
<properties> <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.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir> <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties> </properties>
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal> <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals> </goals>
<properties> <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> <exec.executable>java</exec.executable>
<jpda.listen>true</jpda.listen> <jpda.listen>true</jpda.listen>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir> <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
...@@ -41,7 +41,7 @@ ...@@ -41,7 +41,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal> <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals> </goals>
<properties> <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.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir> <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties> </properties>
......
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