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CgpSomaticCore.java
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CgpSomaticCore.java
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package io.seqware.pancancer;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Calendar;
import java.util.List;
import java.util.Map;
import java.io.File;
import net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel;
import net.sourceforge.seqware.pipeline.workflowV2.model.Job;
import net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile;
import org.apache.commons.lang.StringUtils;
import io.seqware.pancancer.Version;
import java.util.UUID;
/**
* <p>For more information on developing workflows, see the documentation at
* <a href="http://seqware.github.io/docs/6-pipeline/java-workflows/">SeqWare Java Workflows</a>.</p>
*
* Quick reference for the order of methods called:
* 1. setupDirectory
* 2. setupFiles
* 3. setupWorkflow
* 4. setupEnvironment
* 5. buildWorkflow
*
* See the SeqWare API for
* <a href="http://seqware.github.io/javadoc/stable/apidocs/net/sourceforge/seqware/pipeline/workflowV2/AbstractWorkflowDataModel.html#setupDirectory%28%29">AbstractWorkflowDataModel</a>
* for more information.
*/
public class CgpSomaticCore extends AbstractWorkflowDataModel {
private static String OUTDIR = "outdir";
private static String TIMEDIR;
private static String COUNTDIR;
private static String BBDIR;
private boolean cleanup = false;
private boolean cleanupBams = false;
// datetime all upload files will be named with
DateFormat df = new SimpleDateFormat("yyyyMMdd");
String dateString = df.format(Calendar.getInstance().getTime());
private String workflowName = Version.WORKFLOW_SHORT_NAME_VERSION;
// MEMORY variables //
private String memGenerateBasFile, memPackageResults, memMarkTime,
memQcMetrics, memGenotype, memContam,
memBbMerge,
// ascat memory
memAlleleCount, memAscat, memAscatFinalise,
// pindel memory
memPindelInput, memPindelPerThread, memPindelVcf, memPindelMerge , memPindelFlag,
// brass memory
memBrassInput, memBrassCoverPerThread, memBrassCoverMerge, memBrassGroup, memBrassIsize,
memBrassNormCn, memBrassFilter, memBrassSplit,
memBrassAssemblePerThread, memBrassGrass, memBrassTabix,
// caveman memory
memCaveCnPrep,
memCavemanSetup, memCavemanSplit, memCavemanSplitConcat,
memCavemanMstepPerThread, memCavemanMerge, memCavemanEstepPerThread,
memCavemanMergeResults, memCavemanAddIds, memCavemanFlag
;
// workflow variables
private String // reference variables
species, assembly, refFrom, bbFrom,
// sequencing type/protocol
seqType, seqProtocol,
//GNOS identifiers
pemFile, uploadPemFile, gnosServer, uploadServer,
// ascat variables
gender,
// pindel variables
refExclude, pindelGermline,
//general variables
installBase, refBase, genomeFa, testBase,
//contamination variables
contamDownSampOneIn
;
private int coresAddressable, memWorkflowOverhead, memHostMbAvailable;
// UUID
private String uuid = UUID.randomUUID().toString().toLowerCase();
// if localFileMode, this is the path at which the workflow will find the XML files used for metadata in the upload of VCF
// private String localXMLMetadataPath = null;
// private String localBamFilePathPrefix = null;
// used for downloading from S3
// private boolean downloadBamsFromS3 = false;
// private String normalS3Url = "";
// private ArrayList<String> tumorS3Urls = null;
// private String S3DownloadKey = "";
// private String S3DownloadSecretKey = "";
private void init() {
try {
//optional properties
String outDir = OUTDIR;
String outPrefix = "";
if (hasPropertyAndNotNull("output_dir")) {
outDir = getProperty("output_dir");
}
if (hasPropertyAndNotNull("output_prefix")) {
outPrefix = getProperty("output_prefix");
}
if (!"".equals(outPrefix)) {
if (outPrefix.endsWith("/")) {
OUTDIR = outPrefix + outDir;
} else {
OUTDIR = outPrefix + "/" + outDir;
}
}
} catch (Exception e) {
throw new RuntimeException(e);
}
TIMEDIR = OUTDIR + "/timings";
COUNTDIR = OUTDIR + "/ngsCounts";
BBDIR = OUTDIR + "/bbCounts";
}
@Override
public void setupDirectory() {
//since setupDirectory is the first method run, we use it to initialize variables too.
init();
// creates a dir1 directory in the current working directory where the workflow runs
addDirectory(OUTDIR);
addDirectory(TIMEDIR);
addDirectory(COUNTDIR);
addDirectory(BBDIR);
}
@Override
public Map<String, SqwFile> setupFiles() {
try {
if(hasPropertyAndNotNull("cleanup")) {
cleanup = Boolean.valueOf(getProperty("cleanup"));
}
if(hasPropertyAndNotNull("cleanupBams")) {
cleanupBams = Boolean.valueOf(getProperty("cleanupBams"));
}
// used by steps that can use all available cores
coresAddressable = Integer.valueOf(getProperty("coresAddressable"));
// MEMORY //
memGenerateBasFile = getProperty("memGenerateBasFile");
memPackageResults = getProperty("memPackageResults");
memMarkTime = getProperty("memMarkTime");
memQcMetrics = getProperty("memQcMetrics");
memGenotype = getProperty("memGenotype");
memContam = getProperty("memContam");
memBbMerge = getProperty("memBbMerge");
memAlleleCount = getProperty("memAlleleCount");
memAscat = getProperty("memAscat");
memAscatFinalise = getProperty("memAscatFinalise");
memPindelInput = getProperty("memPindelInput");
memPindelPerThread = getProperty("memPindelPerThread");
memPindelVcf = getProperty("memPindelVcf");
memPindelMerge = getProperty("memPindelMerge");
memPindelFlag = getProperty("memPindelFlag");
memBrassInput = getProperty("memBrassInput");
memBrassCoverPerThread = getProperty("memBrassCoverPerThread");
memBrassCoverMerge = getProperty("memBrassCoverMerge");
memBrassGroup = getProperty("memBrassGroup");
memBrassIsize = getProperty("memBrassIsize");
memBrassNormCn = getProperty("memBrassNormCn");
memBrassFilter = getProperty("memBrassFilter");
memBrassSplit = getProperty("memBrassSplit");
memBrassAssemblePerThread = getProperty("memBrassAssemblePerThread");
memBrassGrass = getProperty("memBrassGrass");
memBrassTabix = getProperty("memBrassTabix");
memCaveCnPrep = getProperty("memCaveCnPrep");
memCavemanSetup = getProperty("memCavemanSetup");
memCavemanSplit = getProperty("memCavemanSplit");
memCavemanSplitConcat = getProperty("memCavemanSplitConcat");
memCavemanMstepPerThread = getProperty("memCavemanMstepPerThread");
memCavemanMerge = getProperty("memCavemanMerge");
memCavemanEstepPerThread = getProperty("memCavemanEstepPerThread");
memCavemanMergeResults = getProperty("memCavemanMergeResults");
memCavemanAddIds = getProperty("memCavemanAddIds");
memCavemanFlag = getProperty("memCavemanFlag");
memWorkflowOverhead = Integer.valueOf(getProperty("memWorkflowOverhead"));
memHostMbAvailable = Integer.valueOf(getProperty("memHostMbAvailable"));
contamDownSampOneIn = getProperty("contamDownSampOneIn");
// REFERENCE INFO //
species = getProperty("species");
assembly = getProperty("assembly");
refFrom = getProperty("refFrom");
bbFrom = getProperty("bbFrom");
// Sequencing info
seqType = getProperty("seqType");
if(seqType.equals("WGS")) {
seqProtocol = "genomic";
}
// Specific to ASCAT workflow //
gender = getProperty("gender");
// pindel specific
refExclude = getProperty("refExclude");
//environment
installBase = "/opt/wtsi-cgp";
refBase = OUTDIR + "/reference_files";
genomeFa = refBase + "/genome.fa";
} catch (Exception ex) {
throw new RuntimeException(ex);
}
return getFiles();
}
@Override
public void buildWorkflow() {
Job startDownload = markTime("workflow", "start");
startDownload.setMaxMemory(memMarkTime);
try {
List<String> rawBams = Arrays.asList(getProperty("tumourBams").split(":"));
if(rawBams.size() == 0) {
throw new RuntimeException("Property tumourBams has no list of BAM files");
}
List<Job> prepTumourBamJobs = new ArrayList<Job>();
List<String> tumourBams = new ArrayList<String>();
int tumBamCount = rawBams.size();
for(int i=0; i<tumBamCount; i++) {
File tumourBamFile = new File(rawBams.get(i));
String tumourBam = OUTDIR + "/" + tumourBamFile.getName();
tumourBams.add(tumourBam);
Job prepTumourBamJob = prepBam(rawBams.get(i), "tumour", i+1);
prepTumourBamJob.addParent(startDownload);
prepTumourBamJob.setMaxMemory(memMarkTime);
prepTumourBamJobs.add(prepTumourBamJob);
}
File controlBamFile = new File(getProperty("controlBam"));
String controlBam = OUTDIR + "/" + controlBamFile.getName();
Job prepControlBamJob = prepBam(getProperty("controlBam"), "control", 0);
prepControlBamJob.addParent(startDownload);
prepControlBamJob.setMaxMemory(memMarkTime);
Job genotypeJob = genoptypeBaseJob(tumourBams, controlBam);
genotypeJob.setMaxMemory(memGenotype);
genotypeJob.addParent(prepControlBamJob);
for(Job j : prepTumourBamJobs) {
genotypeJob.addParent(j);
}
Job genotypePackJob = packageGenotype(tumourBams, controlBam);
genotypePackJob.setMaxMemory("4000");
genotypePackJob.addParent(genotypeJob);
Job contaminationJob = contaminationBaseJob(tumBamCount, controlBam, "control");
contaminationJob.setMaxMemory(memContam);
contaminationJob.addParent(prepControlBamJob);
for(Job j : prepTumourBamJobs) {
contaminationJob.addParent(j);
}
String tmpRef = OUTDIR + "/" + "ref.tar.gz";
Job pullRef = pullRef(refFrom, tmpRef);
pullRef.addParent(startDownload);
pullRef.setMaxMemory(memMarkTime);
String tmpBbRef = OUTDIR + "/" + "bb.tar.gz";
Job pullBbRef = pullRef(bbFrom, tmpBbRef);
pullBbRef.addParent(startDownload);
pullBbRef.setMaxMemory(memMarkTime);
Job unpackRef = unpackRef(tmpRef, null);
unpackRef.addParent(pullRef);
unpackRef.setMaxMemory(memMarkTime);
Job unpackBbRef = unpackRef(tmpBbRef, "reference_files");
unpackBbRef.addParent(pullBbRef);
unpackBbRef.addParent(unpackRef);
unpackBbRef.setMaxMemory(memMarkTime);
List<Job> basBbAlleleCountJobsList = new ArrayList<Job>();
Job controlBasJob = basFileBaseJob(0, controlBam, "control", 0);
controlBasJob.setMaxMemory(memGenerateBasFile);
controlBasJob.addParent(unpackRef);
controlBasJob.addParent(prepControlBamJob);
basBbAlleleCountJobsList.add(controlBasJob);
for(int i=0; i<tumBamCount; i++) {
String tumourBam = rawBams.get(i);
Job tumourBasJob = basFileBaseJob(tumBamCount, tumourBam, "tumours", i+1);
tumourBasJob.setMaxMemory(memGenerateBasFile);
tumourBasJob.addParent(unpackRef);
tumourBasJob.addParent(prepTumourBamJobs.get(i));
basBbAlleleCountJobsList.add(tumourBasJob);
}
// packaging must have parent cavemanTbiCleanJob
// these are not paired but per individual sample
List<Job> bbAlleleCountJobs = new ArrayList<Job>();
for(int i=0; i<23; i++) { // not 1-22+X
for(int j=0; j<tumBamCount; j++) {
Job bbAlleleCountJob = bbAlleleCount(j, tumourBams.get(j), "tumour", i);
bbAlleleCountJob.setMaxMemory(memAlleleCount);
bbAlleleCountJob.addParent(unpackBbRef);
bbAlleleCountJob.addParent(prepTumourBamJobs.get(j));
bbAlleleCountJobs.add(bbAlleleCountJob);
basBbAlleleCountJobsList.add(bbAlleleCountJob);
}
Job bbAlleleCountJob = bbAlleleCount(1, controlBam, "control", i);
bbAlleleCountJob.setMaxMemory(memAlleleCount);
bbAlleleCountJob.addParent(unpackBbRef);
bbAlleleCountJob.addParent(prepControlBamJob);
bbAlleleCountJobs.add(bbAlleleCountJob);
basBbAlleleCountJobsList.add(bbAlleleCountJob);
}
Job bbAlleleMergeJob = bbAlleleMerge(controlBam);
bbAlleleMergeJob.setMaxMemory(memBbMerge);
for(Job j : bbAlleleCountJobs) {
bbAlleleMergeJob.addParent(j);
}
// donor based workflow section
Job[] cavemanFlagJobs = new Job [tumBamCount];
for(int i=0; i<tumBamCount; i++) {
Job cavemanFlagJob = buildPairWorkflow(unpackRef, basBbAlleleCountJobsList, controlBam, tumourBams.get(i), i);
cavemanFlagJobs[i] = cavemanFlagJob;
}
Job endWorkflow = markTime("workflow", "end");
endWorkflow.setMaxMemory(memMarkTime);
for(Job cavemanFlagJob : cavemanFlagJobs) {
endWorkflow.addParent(cavemanFlagJob);
}
Job metricsJob = getMetricsJob(tumourBams, controlBam);
metricsJob.setMaxMemory(memQcMetrics);
metricsJob.addParent(endWorkflow);
Job renameGenotypeJob = renameSampleFile(tumourBams, OUTDIR, "genotype.tar.gz");
renameGenotypeJob.setMaxMemory("4000");
renameGenotypeJob.addParent(genotypePackJob);
Job renameGenotypeMd5Job = renameSampleFile(tumourBams, OUTDIR, "genotype.tar.gz.md5");
renameGenotypeMd5Job.setMaxMemory("4000");
renameGenotypeMd5Job.addParent(genotypePackJob);
Job packageContamJob = packageContam(tumourBams, controlBam);
packageContamJob.setMaxMemory("4000");
for(Job cavemanFlagJob : cavemanFlagJobs) {
packageContamJob.addParent(cavemanFlagJob);
}
Job renameContamJob = renameSampleFile(tumourBams, OUTDIR, "verifyBamId.tar.gz");
renameContamJob.setMaxMemory("4000");
renameContamJob.addParent(packageContamJob);
Job renameContamMd5Job = renameSampleFile(tumourBams, OUTDIR, "verifyBamId.tar.gz.md5");
renameContamMd5Job.setMaxMemory("4000");
renameContamMd5Job.addParent(packageContamJob);
Job renameImputeJob = renameSampleFile(tumourBams, OUTDIR + "/bbCounts", "imputeCounts.tar.gz");
renameImputeJob.setMaxMemory("4000");
renameImputeJob.addParent(bbAlleleMergeJob);
Job renameImputeMd5Job = renameSampleFile(tumourBams, OUTDIR + "/bbCounts", "imputeCounts.tar.gz.md5");
renameImputeMd5Job.setMaxMemory("4000");
renameImputeMd5Job.addParent(bbAlleleMergeJob);
// delete just the BAM inputs and not the output dir
if (cleanup || cleanupBams) {
Job cleanInputsJob = cleanJob();
cleanInputsJob.addParent(metricsJob);
}
} catch(Exception e) {
throw new RuntimeException(e);
}
}
/**
* This builds the workflow for a pair of samples
* The generic buildWorkflow section will choose the pair to be processed and
* setup the control sample download
*/
private Job buildPairWorkflow(Job refUnpackJob, List dependencyJobsList, String controlBam, String tumourBam, int tumourCount) {
/**
* ASCAT - Copynumber
* Depends on
* - tumour/control BAMs
* - Gender, will attempt to determine if not specified
*/
Job[] alleleCountJobs = new Job[2];
for(int i=0; i<2; i++) {
Job alleleCountJob = cgpAscatBaseJob(tumourCount, tumourBam, controlBam, "ASCAT", "allele_count", i+1);
alleleCountJob.setMaxMemory(memAlleleCount);
addJobParents(alleleCountJob, dependencyJobsList);
alleleCountJobs[i] = alleleCountJob;
}
Job ascatJob = cgpAscatBaseJob(tumourCount, tumourBam, controlBam, "ASCAT", "ascat", 1);
ascatJob.setMaxMemory(memAscat);
ascatJob.addParent(alleleCountJobs[0]);
ascatJob.addParent(alleleCountJobs[1]);
Job ascatFinaliseJob = cgpAscatBaseJob(tumourCount, tumourBam, controlBam, "ASCAT", "finalise", 1);
ascatFinaliseJob.setMaxMemory(memAscatFinalise);
ascatFinaliseJob.addParent(ascatJob);
Job ascatPackage = packageResults(tumourCount, "ascat", "cnv", tumourBam, "copynumber.caveman.vcf.gz", workflowName, "somatic", dateString);
ascatPackage.setMaxMemory(memPackageResults);
ascatPackage.addParent(ascatFinaliseJob);
Job contaminationJob = contaminationBaseJob(tumourCount, tumourBam, "tumour");
contaminationJob.setMaxMemory(memContam);
contaminationJob.addParent(ascatFinaliseJob);
/**
* CaVEMan setup is here to allow better workflow graph
* Messy but necessary
*/
Job caveCnPrepJobs[] = new Job[2];
for(int i=0; i<2; i++) {
Job caveCnPrepJob;
if(i==0) {
caveCnPrepJob = caveCnPrep(tumourCount, "tumour");
}
else {
caveCnPrepJob = caveCnPrep(tumourCount, "normal");
}
caveCnPrepJob.addParent(refUnpackJob);
caveCnPrepJob.addParent(ascatFinaliseJob); // ASCAT dependency!!!
caveCnPrepJobs[i] = caveCnPrepJob;
}
Job cavemanSetupJob = cavemanBaseJob(tumourCount, tumourBam, controlBam, "CaVEMan", "setup", 1);
cavemanSetupJob.setMaxMemory(memCavemanSetup);
cavemanSetupJob.addParent(caveCnPrepJobs[0]);
cavemanSetupJob.addParent(caveCnPrepJobs[1]);
// some dependencies handled by ascat step
/**
* Pindel - InDel calling
* Depends on:
* - tumour/control BAMs
*/
Job[] pindelInputJobs = new Job[2];
for(int i=0; i<2; i++) {
Job inputParse = pindelBaseJob(tumourCount, tumourBam, controlBam, "cgpPindel", "input", i+1);
// If you tell SGE you are using ,multiple cores it multiplies the requested memory for you
inputParse.setMaxMemory( memPindelInput );
addJobParents(inputParse, dependencyJobsList);
pindelInputJobs[i] = inputParse;
}
int pindelNormalisedThreads = pindelNormalisedThreads(memPindelPerThread, coresAddressable);
int totalPindelMem = Integer.valueOf(memPindelPerThread) + (Integer.valueOf(memWorkflowOverhead) / pindelNormalisedThreads);
Job pindelJob = pindelBaseJob(tumourCount, tumourBam, controlBam, "cgpPindel", "pindel", 1);
pindelJob.getCommand().addArgument("-l " + pindelNormalisedThreads);
pindelJob.getCommand().addArgument("-c " + pindelNormalisedThreads);
pindelJob.setMaxMemory(Integer.toString(totalPindelMem));
pindelJob.setThreads(pindelNormalisedThreads);
pindelJob.addParent(pindelInputJobs[0]);
pindelJob.addParent(pindelInputJobs[1]);
// determine number of refs to process
// we know that this is static for PanCancer so be lazy 24 jobs (1-22,X,Y)
// but pindel needs to know the exclude list so hard code this
Job pinVcfJobs[] = new Job[24];
for(int i=0; i<24; i++) {
Job pinVcfJob = pindelBaseJob(tumourCount, tumourBam, controlBam, "cgpPindel", "pin2vcf", i+1);
pinVcfJob.setMaxMemory(memPindelVcf);
pinVcfJob.addParent(pindelJob);
pinVcfJobs[i] = pinVcfJob;
}
Job pindelMergeJob = pindelBaseJob(tumourCount, tumourBam, controlBam, "cgpPindel", "merge", 1);
pindelMergeJob.setMaxMemory(memPindelMerge);
for (Job parent : pinVcfJobs) {
pindelMergeJob.addParent(parent);
}
Job pindelFlagJob = pindelBaseJob(tumourCount, tumourBam, controlBam, "cgpPindel", "flag", 1);
pindelFlagJob.setMaxMemory(memPindelFlag);
pindelFlagJob.addParent(pindelMergeJob);
pindelFlagJob.addParent(cavemanSetupJob);
Job pindelPackage = packageResults(tumourCount, "pindel", "indel", tumourBam, "flagged.vcf.gz", workflowName, "somatic", dateString);
pindelPackage.setMaxMemory(memPackageResults);
pindelPackage.addParent(pindelFlagJob);
/**
* BRASS - BReakpoint AnalySiS
* Depends on:
* - tumour/control BAMs
* - ASCAT output at filter step
*/
Job brassInputJobs[] = new Job[2];
for(int i=0; i<2; i++) {
int index = i+1;
Job brassInputJob = brassBaseJob(tumourCount, tumourBam, controlBam, "BRASS", "input", index);
brassInputJob.getCommand().addArgument("-i " + index);
brassInputJob.setMaxMemory(memBrassInput);
addJobParents(brassInputJob, dependencyJobsList);
brassInputJobs[i] = brassInputJob;
}
int localCores = coresAddressable / 2;
if(localCores == 0) { localCores = 1; }
int totalBrassCoverMem = Integer.valueOf(memBrassCoverPerThread) + (Integer.valueOf(memWorkflowOverhead) / localCores);
Job brassCoverJob = brassBaseJob(tumourCount, tumourBam, controlBam, "BRASS", "cover", 1);
brassCoverJob.getCommand().addArgument("-l " + localCores);
brassCoverJob.getCommand().addArgument("-c " + localCores);
brassCoverJob.setMaxMemory(Integer.toString(totalBrassCoverMem));
brassCoverJob.setThreads(localCores);
brassCoverJob.addParent(brassInputJobs[0]);
brassCoverJob.addParent(brassInputJobs[1]);
Job brassCoverMergeJob = brassBaseJob(tumourCount, tumourBam, controlBam, "BRASS", "merge", 1);
brassCoverMergeJob.setMaxMemory(memBrassCoverMerge);
brassCoverMergeJob.addParent(brassCoverJob);
brassCoverMergeJob.addParent(brassInputJobs[0]);
brassCoverMergeJob.addParent(brassInputJobs[1]);
Job brassGroupJob = brassBaseJob(tumourCount, tumourBam, controlBam, "BRASS", "group", 1);
brassGroupJob.setMaxMemory(memBrassGroup);
brassGroupJob.addParent(brassCoverMergeJob);
Job brassIsizeJob = brassBaseJob(tumourCount, tumourBam, controlBam, "BRASS", "isize", 1);
brassIsizeJob.setMaxMemory(memBrassIsize);
brassIsizeJob.addParent(brassCoverMergeJob);
Job brassNormCnJob = brassBaseJob(tumourCount, tumourBam, controlBam, "BRASS", "normcn", 1);
brassNormCnJob.setMaxMemory(memBrassNormCn);
brassNormCnJob.addParent(brassCoverMergeJob);
Job brassFilterJob = brassBaseJob(tumourCount, tumourBam, controlBam, "BRASS", "filter", 1);
brassFilterJob.setMaxMemory(memBrassFilter);
brassFilterJob.addParent(brassGroupJob);
brassFilterJob.addParent(brassIsizeJob);
brassFilterJob.addParent(brassNormCnJob);
brassFilterJob.addParent(ascatFinaliseJob); // NOTE: dependency on ASCAT!!
Job brassSplitJob = brassBaseJob(tumourCount, tumourBam, controlBam, "BRASS", "split", 1);
brassSplitJob.setMaxMemory(memBrassSplit);
brassSplitJob.addParent(brassFilterJob);
int brassAssNormalisedThreads = getMemNormalisedThread(memBrassAssemblePerThread, coresAddressable);
int totalBrassAssMem = Integer.valueOf(memBrassAssemblePerThread) + (Integer.valueOf(memWorkflowOverhead) / brassAssNormalisedThreads);
Job brassAssembleJob = brassBaseJob(tumourCount, tumourBam, controlBam, "BRASS", "assemble", 1);
brassAssembleJob.getCommand().addArgument("-l " + brassAssNormalisedThreads);
brassAssembleJob.getCommand().addArgument("-c " + brassAssNormalisedThreads);
brassAssembleJob.setMaxMemory(Integer.toString(totalBrassAssMem));
brassAssembleJob.setThreads(brassAssNormalisedThreads);
brassAssembleJob.addParent(brassSplitJob);
Job brassGrassJob = brassBaseJob(tumourCount, tumourBam, controlBam, "BRASS", "grass", 1);
brassGrassJob.setMaxMemory(memBrassGrass);
brassGrassJob.addParent(brassAssembleJob);
Job brassTabixJob = brassBaseJob(tumourCount, tumourBam, controlBam, "BRASS", "tabix", 1);
brassTabixJob.setMaxMemory(memBrassTabix);
brassTabixJob.addParent(brassGrassJob);
Job brassPackage = packageResults(tumourCount, "brass", "sv", tumourBam, "annot.vcf.gz", workflowName, "somatic", dateString);
brassPackage.setMaxMemory(memPackageResults);
brassPackage.addParent(brassTabixJob);
/**
* CaVEMan - SNV analysis
* !! see above as setup done earlier to help with workflow structure !!
* Depends on:
* - tumour/control BAMs (but depend on BAS for better workflow)
* - ASCAT from outset
* - pindel at flag step
*/
// should really line count the fai file
Job cavemanSplitJobs[] = new Job[86];
for(int i=0; i<86; i++) {
Job cavemanSplitJob = cavemanBaseJob(tumourCount, tumourBam, controlBam, "CaVEMan", "split", i+1);
cavemanSplitJob.setMaxMemory(memCavemanSplit);
cavemanSplitJob.addParent(cavemanSetupJob);
cavemanSplitJobs[i] = cavemanSplitJob;
}
Job cavemanSplitConcatJob = cavemanBaseJob(tumourCount, tumourBam, controlBam, "CaVEMan", "split_concat", 1);
cavemanSplitConcatJob.setMaxMemory(memCavemanSplitConcat);
for (Job cavemanSplitJob : cavemanSplitJobs) {
cavemanSplitConcatJob.addParent(cavemanSplitJob);
}
int mstepNormalisedThreads = getMemNormalisedThread(memCavemanMstepPerThread, coresAddressable);
int totalMstepMem = Integer.valueOf(memCavemanMstepPerThread) + (Integer.valueOf(memWorkflowOverhead) / mstepNormalisedThreads);
Job cavemanMstepJob = cavemanBaseJob(tumourCount, tumourBam, controlBam, "CaVEMan", "mstep", 1);
cavemanMstepJob.getCommand().addArgument("-l " + mstepNormalisedThreads);
cavemanMstepJob.getCommand().addArgument("-t " + mstepNormalisedThreads);
cavemanMstepJob.setMaxMemory(Integer.toString(totalMstepMem));
cavemanMstepJob.setThreads(mstepNormalisedThreads);
cavemanMstepJob.addParent(cavemanSplitConcatJob);
Job cavemanMergeJob = cavemanBaseJob(tumourCount, tumourBam, controlBam, "CaVEMan", "merge", 1);
cavemanMergeJob.setMaxMemory(memCavemanMerge);
cavemanMergeJob.addParent(cavemanMstepJob);
int estepNormalisedThreads = getMemNormalisedThread(memCavemanEstepPerThread, coresAddressable);
int totalEstepMem = Integer.valueOf(memCavemanEstepPerThread) + (Integer.valueOf(memWorkflowOverhead) / estepNormalisedThreads);
Job cavemanEstepJob = cavemanBaseJob(tumourCount, tumourBam, controlBam, "CaVEMan", "estep", 1);
cavemanEstepJob.getCommand().addArgument("-l " + estepNormalisedThreads);
cavemanEstepJob.getCommand().addArgument("-t " + estepNormalisedThreads);
cavemanEstepJob.setMaxMemory(Integer.toString(totalEstepMem));
cavemanEstepJob.setThreads(estepNormalisedThreads);
cavemanEstepJob.addParent(cavemanMergeJob);
Job cavemanMergeResultsJob = cavemanBaseJob(tumourCount, tumourBam, controlBam, "CaVEMan", "merge_results", 1);
cavemanMergeResultsJob.setMaxMemory(memCavemanMergeResults);
cavemanMergeResultsJob.addParent(cavemanEstepJob);
Job cavemanAddIdsJob = cavemanBaseJob(tumourCount, tumourBam, controlBam, "CaVEMan", "add_ids", 1);
cavemanAddIdsJob.setMaxMemory(memCavemanAddIds);
cavemanAddIdsJob.addParent(cavemanMergeResultsJob);
Job cavemanFlagJob = cavemanBaseJob(tumourCount, tumourBam, controlBam, "CaVEMan", "flag", 1);
cavemanFlagJob.setMaxMemory(memCavemanFlag);
cavemanFlagJob.addParent(pindelFlagJob); // PINDEL dependency
cavemanFlagJob.addParent(cavemanAddIdsJob);
cavemanFlagJob.addParent(contaminationJob);
Job cavemanPackage = packageResults(tumourCount, "caveman", "snv_mnv", tumourBam, "flagged.muts.vcf.gz", workflowName, "somatic", dateString);
cavemanPackage.setMaxMemory(memPackageResults);
cavemanPackage.addParent(cavemanFlagJob);
return cavemanFlagJob;
}
private void addJobParents(Job child, List<Job> parents) {
for(int i=0; i<parents.size(); i++) {
child.addParent(parents.get(i));
}
}
/**
* This allows for other processes to run along side if the number of cores
* will allow. Added in an attempt to prevent increased wall time for the
* whole workflow.
*
* @param memPerThread Memory in MB consumed by each thread
* @param totalCores Total number of cores available to the workflow
* @return Number of threads usable based on per-thread and system overhead.
*/
private int pindelNormalisedThreads(String memPerThread, int totalCores) {
int sensibleCores = totalCores;
if(sensibleCores > 12) {
sensibleCores = totalCores - 2;
}
int pindelNormalisedThreads = getMemNormalisedThread(memPerThread, sensibleCores);
return pindelNormalisedThreads;
}
private Job bbAlleleCount(int sampleIndex, String bam, String process, int index) {
Job thisJob = prepTimedJob(sampleIndex, "bbAllele", process, index);
int chr = index+1;
thisJob.getCommand()
.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
.addArgument(installBase)
.addArgument(getWorkflowBaseDir()+ "/bin/execute_with_sample.pl " + bam)
.addArgument("alleleCounter")
.addArgument("-l " + refBase + "/battenberg/1000genomesloci/1000genomesloci2012_chr" + chr + ".txt")
.addArgument("-o " + BBDIR + "/%SM%." + chr + ".tsv")
.addArgument("-b " + bam)
;
return thisJob;
}
private Job bbAlleleMerge(String controlBam) {
Job thisJob = prepTimedJob(0, "bbAllele", "merge", 1);
thisJob.getCommand()
.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
.addArgument(installBase)
.addArgument(getWorkflowBaseDir()+ "/bin/packageImpute.pl")
.addArgument(controlBam)
.addArgument(BBDIR)
;
return thisJob;
}
private Job renameSampleFile(List<String> bams, String dir, String extension) {
Job thisJob = getWorkflow().createBashJob("renameSampleFile");
for(String bam : bams) {
thisJob.getCommand()
.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
.addArgument(installBase)
.addArgument(getWorkflowBaseDir()+ "/bin/execute_with_sample.pl " + bam)
.addArgument("cp " + dir + "/" + "%SM%." + extension)
.addArgument(OUTDIR + "/" + "%SM%." + workflowName + "." + dateString + ".somatic." + extension)
.addArgument(";");
;
}
return thisJob;
}
private Job packageResults(int tumourCount, String algName, String resultType, String tumourBam, String baseVcf, String workflowName, String somaticOrGermline, String date) {
//#packageResults.pl outdir 0772aed3-4df7-403f-802a-808df2935cd1/c007f362d965b32174ec030825262714.bam outdir/caveman snv_mnv flagged.muts.vcf.gz
Job thisJob = getWorkflow().createBashJob("packageResults");
thisJob.getCommand()
.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
.addArgument(installBase)
.addArgument(getWorkflowBaseDir() + "/bin/packageResults.pl")
.addArgument(OUTDIR)
.addArgument(tumourBam)
.addArgument(OUTDIR + "/" + tumourCount + "/" + algName)
.addArgument(resultType)
.addArgument(baseVcf)
.addArgument(workflowName)
.addArgument(somaticOrGermline)
.addArgument(date)
;
return thisJob;
}
private int getMemNormalisedThread(String perThreadMemory, int threads) {
int usableThreads = 0;
// memWorkflowOverhead, memHostMbAvailable
int memoryAvail = memHostMbAvailable - memWorkflowOverhead;
if((memoryAvail / threads) >= Integer.valueOf(perThreadMemory)) {
usableThreads = threads;
}
else {
usableThreads = memoryAvail / Integer.valueOf(perThreadMemory);
}
if(usableThreads == 0) {
throw new RuntimeException("memHostMbAvailable - memWorkflowOverhead = memoryAvail (" +
memHostMbAvailable + " - " + memWorkflowOverhead + " = " + memoryAvail +
") is less than one of the mem*PerThread parameters in provided ini file.");
}
return usableThreads;
}
private Job basFileBaseJob(int tumourCount, String sampleBam, String process, int index) {
Job thisJob = prepTimedJob(tumourCount, "basFileGenerate", process, index);
File f = new File(sampleBam);
thisJob.getCommand()
.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
.addArgument(installBase)
.addArgument("bam_stats")
.addArgument("-i " + sampleBam)
.addArgument("-o " + OUTDIR + "/" + f.getName() + ".bas")
;
return thisJob;
}
private Job getMetricsJob(List<String> tumourBams, String controlBam) {
//die "USAGE: rootOfOutdir ordered.bam [ordered.bam2]";
Job thisJob = getWorkflow().createBashJob("metrics");
thisJob.getCommand()
.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
.addArgument(installBase)
.addArgument(getWorkflowBaseDir()+ "/bin/qc_and_metrics.pl")
.addArgument(OUTDIR)
.addArgument(controlBam);
for(String bam : tumourBams) {
thisJob.getCommand().addArgument(bam);
}
return thisJob;
}
private Job caveCnPrep(int tumourCount, String type) {
String cnPath = OUTDIR + "/" + tumourCount + "/ascat/*.copynumber.caveman.csv";
Job thisJob = getWorkflow().createBashJob("CaveCnPrep" + type);
int offset = 0;
if(type.equals("tumour")) {
offset = 6;
}
else if(type.equals("normal")) {
offset = 4;
}
thisJob.getCommand()
.addArgument("perl -ne '@F=(split q{,}, $_)[1,2,3," + offset + "]; $F[1]-1; print join(\"\\t\",@F).\"\\n\";'")
.addArgument("< " + cnPath)
.addArgument("> " + OUTDIR + "/" + tumourCount + "/" + type + ".cn.bed")
;
thisJob.setMaxMemory(memCaveCnPrep);
return thisJob;
}
private Job cleanJob() {
Job thisJob = getWorkflow().createBashJob("GeneralCleanup");
// this just removes the contents of the working directory and not OUTDIR which may point to another filesystem for archival purposes
if (cleanupBams) {
thisJob.getCommand().addArgument("rm -f ./*/*.bam; ");
}
// this removes the whole working directory
if (cleanup) {
thisJob.getCommand().addArgument("rm -rf *; ");
}
// cleans up the downloaded reference
thisJob.getCommand().addArgument("rm -rf " + OUTDIR + "/reference_files");
return thisJob;
}
private Job cavemanBaseJob(int tumourCount, String tumourBam, String controlBam, String alg, String process, int index) {
String ascatContamFile = OUTDIR + "/" + tumourCount + "/ascat/*.samplestatistics.csv";
Job thisJob = prepTimedJob(tumourCount, alg, process, index);
thisJob.getCommand()
.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
.addArgument(installBase)
.addArgument("caveman.pl")
.addArgument("-p " + process)
.addArgument("-ig " + refBase + "/caveman/ucscHiDepth_0.01_merge1000_no_exon.tsv")
.addArgument("-b " + refBase + "/caveman/flagging")
.addArgument("-np " + seqType)
.addArgument("-tp " + seqType)
.addArgument("-sa " + assembly)
.addArgument("-s " + species)
.addArgument("-st " + seqProtocol)
.addArgument("-o " + OUTDIR + "/" + tumourCount + "/caveman")
.addArgument("-tc " + OUTDIR + "/" + tumourCount + "/tumour.cn.bed")
.addArgument("-nc " + OUTDIR + "/" + tumourCount + "/normal.cn.bed")
.addArgument("-k " + ascatContamFile)
.addArgument("-tb " + tumourBam)
.addArgument("-nb " + controlBam)
.addArgument("-r " + genomeFa + ".fai")
.addArgument("-u " + refBase + "/caveman");
if(!process.equals("mstep") && !process.equals("estep")) {
thisJob.getCommand().addArgument("-i " + index);
}
if(process.equals("flag")) {
thisJob.getCommand().addArgument("-in " + OUTDIR + "/" + tumourCount + "/pindel/*.germline.bed");
}
return thisJob;
}
private Job genoptypeBaseJob(List<String> tumourBams, String controlBam) {
Job thisJob = prepTimedJob(0, "compareBamGenotypes", "all", 0);
thisJob.getCommand()
.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
.addArgument(installBase)
.addArgument("compareBamGenotypes.pl")
.addArgument("-o " + OUTDIR + "/genotype")
.addArgument("-nb " + controlBam)
.addArgument("-j " + OUTDIR + "/genotype/summary.json")
;
for(String tumourBam : tumourBams) {
thisJob.getCommand().addArgument("-tb " + tumourBam);
}
return thisJob;
}
private Job packageGenotype(List<String> tumourBams, String controlBam) {
Job thisJob = getWorkflow().createBashJob("packageGenotype");
thisJob.getCommand()
.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
.addArgument(installBase)
.addArgument(getWorkflowBaseDir() + "/bin/packageGenotype.pl")
.addArgument(OUTDIR)
.addArgument(controlBam)
;
for(String tumour : tumourBams) {
thisJob.getCommand().addArgument(tumour);
}
return thisJob;
}
private Job contaminationBaseJob(int tumourCount, String inBam, String process) {
Job thisJob = prepTimedJob(tumourCount, "verifyBamHomChk", process, 0);
thisJob.getCommand()
.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
.addArgument(installBase)
.addArgument("verifyBamHomChk.pl")
.addArgument("-o " + OUTDIR + "/" + tumourCount + "/contamination")
.addArgument("-b " + inBam)
.addArgument("-d " + contamDownSampOneIn)
.addArgument("-j " + OUTDIR + "/" + tumourCount + "/contamination/summary.json")
;
if(process.equals("tumour")) {
thisJob.getCommand().addArgument("-a " + OUTDIR + "/" + tumourCount + "/ascat/*.copynumber.caveman.csv"); // not the best approach but works
}
return thisJob;
}
private Job packageContam(List<String> tumourBams, String controlBam) {
Job thisJob = getWorkflow().createBashJob("packageContam");
thisJob.getCommand()
.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
.addArgument(installBase)
.addArgument(getWorkflowBaseDir() + "/bin/packageContam.pl")
.addArgument(OUTDIR)
.addArgument(controlBam)
;
for(String tumour : tumourBams) {
thisJob.getCommand().addArgument(tumour);
}
return thisJob;
}
private Job cgpAscatBaseJob(int tumourCount, String tumourBam, String controlBam, String alg, String process, int index) {
Job thisJob = prepTimedJob(tumourCount, alg, process, index);
thisJob.getCommand()
.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
.addArgument(installBase)
.addArgument("ascat.pl")
.addArgument("-p " + process)
.addArgument("-i " + index)
.addArgument("-r " + genomeFa)
.addArgument("-s " + refBase + "/ascat/SnpLocus.tsv")
.addArgument("-sp " + refBase + "/ascat/SnpPositions.tsv")
.addArgument("-sg " + refBase + "/ascat/SnpGcCorrections.tsv")
.addArgument("-pr " + seqType)
.addArgument("-ra " + assembly)
.addArgument("-rs " + species)
.addArgument("-pl " + "ILLUMINA") // should be in BAM header
.addArgument("-o " + OUTDIR + "/" + tumourCount + "/ascat")
.addArgument("-t " + tumourBam)
.addArgument("-n " + controlBam)
.addArgument("-f") // force completion, even when ascat fails
;
thisJob.getCommand().addArgument("-g " + gender);
return thisJob;
}
private Job pindelBaseJob(int tumourCount, String tumourBam, String controlBam, String alg, String process, int index) {
Job thisJob = prepTimedJob(tumourCount, alg, process, index);
thisJob.getCommand()
.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
.addArgument(installBase)
.addArgument("pindel.pl")
.addArgument("-p " + process)
.addArgument("-r " + genomeFa)
.addArgument("-e " + refExclude)
.addArgument("-st " + seqType)
.addArgument("-as " + assembly)
.addArgument("-sp " + species)
.addArgument("-s " + refBase + "/pindel/simpleRepeats.bed.gz")
.addArgument("-f " + refBase + "/pindel/genomicRules.lst")
.addArgument("-g " + refBase + "/pindel/human.GRCh37.indelCoding.bed.gz")
.addArgument("-u " + refBase + "/pindel/pindel_np.gff3.gz")
.addArgument("-sf " + refBase + "/pindel/softRules.lst")
.addArgument("-b " + refBase + "/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz")
.addArgument("-o " + OUTDIR + "/" + tumourCount + "/pindel")
.addArgument("-t " + tumourBam)
.addArgument("-n " + controlBam)
;
if(!process.equals("pindel")) {
thisJob.getCommand().addArgument("-i " + index);
}
if(process.equals("input")) {
int pindelInputThreads;
if(coresAddressable > 4) {
pindelInputThreads = 4;
}
else {
pindelInputThreads = coresAddressable;
}
thisJob.getCommand().addArgument("-c " + pindelInputThreads);
thisJob.setThreads(pindelInputThreads);
}
return thisJob;
}
private Job markTime(String name, String item) {
String timeFile = TIMEDIR + "/" + name + "_" + item;
Job thisJob = getWorkflow().createBashJob("mark_" + item);