private Job statInputFiles(Job parent) {
Job statFiles = this.getWorkflow().createBashJob("stat downloaded input files");
String moveToFailed =
GitUtils.gitMoveCommand(
"running-jobs",
"failed-jobs",
this.JSONlocation + "/" + this.JSONrepoName + "/" + this.JSONfolderName,
this.JSONfileName,
this.gitMoveTestMode,
this.getWorkflowBaseDir() + "/scripts/");
String statFilesCMD = "( ";
for (VcfInfo vcfInfo : this.vcfs) {
boolean useGnosIdInPath =
vcfInfo.getOriginatingPipeline() != Pipeline.smufin
&& this.pipelineDownloadMethods.get(vcfInfo.getOriginatingPipeline())
!= DownloadMethod.filesystemCopy;
// Remember: smufin won't have a gnos ID so don't try to use that in the path for stat.
String prefix =
"stat /datastore/vcf/"
+ vcfInfo.getOriginatingPipeline().toString()
+ "/"
+ (useGnosIdInPath ? vcfInfo.getPipelineGnosID() + "/" : "");
statFilesCMD += prefix + vcfInfo.getFileName() + " && \\\n";
statFilesCMD += prefix + vcfInfo.getIndexFileName() + " && \\\n";
}
// stat all tumour BAMS
for (int i = 0; i < this.tumours.size(); i++) {
String prefix =
"stat /datastore/bam/"
+ BAMType.tumour.toString()
+ "/"
+ (!this.bamDownloadMethod.equals(DownloadMethod.filesystemCopy.toString())
? this.tumours.get(i).getTumourBamGnosID() + "/"
: "");
statFilesCMD += prefix + this.tumours.get(i).getTumourBAMFileName() + " && \\\n";
statFilesCMD += prefix + this.tumours.get(i).getTumourBamIndexFileName() + " && \\\n";
}
String normalPrefix =
"stat /datastore/bam/"
+ BAMType.normal.toString()
+ "/"
+ (!this.bamDownloadMethod.equals(DownloadMethod.filesystemCopy.toString())
? this.normalBamGnosID + "/"
: "");
statFilesCMD += normalPrefix + this.normalBAMFileName + " && \\\n";
statFilesCMD += normalPrefix + this.normalBamIndexFileName + " \\\n";
statFilesCMD += " ) || " + moveToFailed;
statFiles.setCommand(statFilesCMD);
statFiles.addParent(parent);
return statFiles;
}
