Commit dad2ef53 authored by Jasper Koehorst's avatar Jasper Koehorst
Browse files

reformatting

parent c35a91ca
......@@ -6,15 +6,15 @@ import java.util.Arrays;
import java.util.List;
import java.util.concurrent.TimeUnit;
public class Amplicon {
public class AmpliconRuns {
String referenceDB = "/unlock/references/databases/Silva/SILVA_138.1_SSURef_tax_silva.fasta.gz";
String project = "P_RIVM"; // "P_TKI_BO3B"; //
String investigation = "%";
String study = "S_DRP005906"; // "%"; //
String project = "%"; //P_RIVM"; // "P_TKI_BO3B"; //
String investigation = "I_Mocks";
String study = "%"; // S_SRP148840";
String observationUnit = "%";
String assay = "%";
String limit = "2";
String[] ngtaxReadLength = {"70","100","120"};
String limit = "100";
String[] ngtaxReadLength = {"100"}; // {"70","100","120"};
private String reset = "-reset";
// Performing the NGTAX workflow test
......@@ -24,8 +24,8 @@ public class Amplicon {
try {
for (String readLength : ngtaxReadLength) {
String[] args = {
"-cwl", "workflow_ngtax.cwl",
"-wid", "AmpliconAnalysis_NGTAX_Silva138.1",
"-cwl", "workflow_ngtax_picrust2.cwl", // "workflow_ngtax.cwl",
"-wid", "NGTAX_Silva138.1",
"-project", project,
"-investigation", investigation,
"-study", study,
......@@ -34,13 +34,13 @@ public class Amplicon {
"-referenceDB", referenceDB,
"-overwrite",
// For Entrez datasets primers might not be removed
"-primersRemoved",
"-memory", "6000",
"-primersRemoved",
"-memory", "10000",
"-threads", "2",
"-debug",
"-nomock"
// "-debug",
// "-nomock"
};
// App.main(args);
App.main(args);
runKubernetes();
}
return;
......
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