Path	Lines of Code
CONTRIBUTING.md	72
README.md	146
config/checkstyle/checkstyle.xml	115
doc/Bam2FastqWorkflow.md	87
doc/DnaAmpliconVarBamWorkflow.md	252
doc/DnaAmpliconVarFastqWorkflow.md	310
doc/DnaCaptureVarBamWorkflow.md	252
doc/DnaCaptureVarFastqWorkflow.md	319
doc/DnaWgsVarBamWorkflow.md	160
doc/DnaWgsVarFastqWorkflow.md	246
doc/HlaTypingFastqWorkflow.md	184
doc/RnaCaptureVarFastqWorkflow.md	198
doc/RnaExpressionBamWorkflow.md	152
doc/RnaExpressionFastqWorkflow.md	235
doc/RnaFusionFastqWorkflow.md	196
doc/SCRnaExpressionCellRangerFastqWorkflow.md	185
doc/ScRnaExpressionBamWorkflow.md	152
doc/ScRnaExpressionFastqWorkflow.md	227
doc/TcrRepertoireFastqWorkflow.md	139
doc/User_guide.md	141
example/global_config/QC/global_config_DnaCaptureVar_Fastq_v1.1_PairEnd.txt	27
example/global_config/QC/global_config_DnaCaptureVar_Fastq_v1.1_PairEnd_mouse.txt	27
example/global_config/QC/global_config_DnaCaptureVar_Fastq_v1.1_SingleEnd.txt	27
example/global_config/QC/global_config_DnaCaptureVar_Fastq_v1.1_SingleEnd_mouse.txt	27
example/global_config/QC/global_config_RnaExpression_Fastq_v1.1_PairEnd.txt	28
example/global_config/QC/global_config_RnaExpression_Fastq_v1.1_SingleEnd.txt	28
example/global_config/QC/global_config_RnaExpression_Fastq_v1.1_SingleEnd_mouse.txt	28
example/global_config/global_config_Bam2Fastq_v1.1.txt	20
example/global_config/global_config_Bam2Fastq_v1.2.txt	20
example/global_config/global_config_DnaAmpliconVar_Bam_v1.1.txt	31
example/global_config/global_config_DnaAmpliconVar_Fastq_v1.1.txt	49
example/global_config/global_config_DnaCaptureVar_Bam_v1.1.txt	25
example/global_config/global_config_DnaCaptureVar_Fastq_v1.1.txt	36
example/global_config/global_config_DnaWgsVar_Fastq_v1.1.txt	33
example/global_config/global_config_HlaTyping_Fastq_v1.1.txt	28
example/global_config/global_config_RnaCaptureVar_Fastq_v1.1.txt	35
example/global_config/global_config_RnaExpression_Bam_v1.1.txt	27
example/global_config/global_config_RnaExpression_Fastq_v1.1.txt	37
example/global_config/global_config_RnaFusion_Fastq_v1.1.txt	31
example/global_config/global_config_TcrRepertoire_Fastq_v1.1.txt	35
example/global_config/global_config_scRnaExpression_Bam_v1.1.txt	25
example/global_config/global_config_scRnaExpression_CellRanger_Fastq_v1.1_human&mouse.txt	32
example/global_config/global_config_scRnaExpression_CellRanger_Fastq_v1.1_human.txt	33
example/global_config/global_config_scRnaExpression_CellRanger_Fastq_v1.1_mouse.txt	32
example/global_config/global_config_scRnaExpression_Fastq_v1.1.txt	36
example/sample_manifest/DnaCaptureVar_WES_SampleBamPaths.txt	7
example/sample_manifest/DnaCaptureVar_WES_SampleFastqPaths.txt	13
example/sample_manifest/HlaTyping_WES_SampleFastqPaths.txt	11
example/sample_manifest/RnaExpression_RNASeq_SampleFastqPaths.txt	9
example/sample_manifest/TcrRepertoire_WES_SampleFastqPaths.txt	11
example/sample_manifest/scRnaExpressionCellRanger_Fastq.txt	27
example/study_config/QC/config_RnaExpression_Fastq_PairEnd.txt	11
example/study_config/QC/config_RnaExpression_Fastq_SingleEnd.txt	11
example/study_config/config_Bam2Fastq_test.txt	10
example/study_config/config_DnaCaptureVar_Bam_test.txt	10
example/study_config/config_DnaCaptureVar_Fastq_test.txt	10
example/study_config/config_HlaTyping_Fastq_test.txt	10
example/study_config/config_RnaExpression_Bam_test.txt	10
example/study_config/config_RnaExpression_Fastq_test.txt	10
example/study_config/config_RnaFusion_Fastq_test.txt	10
example/study_config/config_TcrRepertoire_Fastq_test.txt	10
example/study_config/config_scRnaExpression_CellRanger_Fastq_test.txt	10
gradle.properties	16
src/integrationTest/resources/Bam2Fastq/gPairedNonPicard.txt	22
src/integrationTest/resources/Bam2Fastq/gPairedPicard.txt	22
src/integrationTest/resources/Bam2Fastq/gSinglePicard.txt	22
src/integrationTest/resources/Bam2Fastq/sPaired.txt	8
src/integrationTest/resources/Bam2Fastq/sSingle.txt	8
src/integrationTest/resources/Bam2Fastq/sSingleControlSample.txt	8
src/integrationTest/resources/Bam2Fastq/sSingleNotTumorOrCase.txt	8
src/integrationTest/resources/DnaAmpliconVarBam/gAllTasksSampleNotNA.txt	64
src/integrationTest/resources/DnaAmpliconVarBam/gSingleAllTasks.txt	60
src/integrationTest/resources/DnaAmpliconVarBam/gSingleSampleTasks.txt	60
src/integrationTest/resources/DnaAmpliconVarBam/sControlSampleNotNA.txt	9
src/integrationTest/resources/DnaAmpliconVarBam/sSingle.txt	9
src/integrationTest/resources/DnaAmpliconVarFastq/gAbraGatkPicardPaired.txt	59
src/integrationTest/resources/DnaAmpliconVarFastq/gAbraGatkPicardSingle.txt	59
src/integrationTest/resources/DnaAmpliconVarFastq/gPairedAllTasks.txt	65
src/integrationTest/resources/DnaAmpliconVarFastq/gPairedSeqpurgeBwaXenomeYes.txt	47
src/integrationTest/resources/DnaAmpliconVarFastq/gPairedSeqpurgeNovoalignXenomeYes.txt	47
src/integrationTest/resources/DnaAmpliconVarFastq/gPairedTrimmomaticBwaXenomeYes.txt	47
src/integrationTest/resources/DnaAmpliconVarFastq/gSingleAllTasks.txt	61
src/integrationTest/resources/DnaAmpliconVarFastq/gSingleTrimmomaticBwaYes.txt	47
src/integrationTest/resources/DnaAmpliconVarFastq/gSingleTrimmomaticNovoalignYes.txt	47
src/integrationTest/resources/DnaAmpliconVarFastq/sControlSampleNotNA.txt	9
src/integrationTest/resources/DnaAmpliconVarFastq/sControlSampleNotNaForPostAlignment.txt	9
src/integrationTest/resources/DnaAmpliconVarFastq/sPaired.txt	9
src/integrationTest/resources/DnaAmpliconVarFastq/sSingle.txt	9
src/integrationTest/resources/DnaAnalysis/gSingleDnaAmplicon.txt	61
src/integrationTest/resources/DnaAnalysis/gSingleDnaCapture.txt	61
src/integrationTest/resources/DnaAnalysis/sSingle.txt	9
src/integrationTest/resources/DnaCaptureVarBam/gAllTasksSampleNotNA.txt	64
src/integrationTest/resources/DnaCaptureVarBam/gSingleAllTasks.txt	60
src/integrationTest/resources/DnaCaptureVarBam/sControlSampleNotNA.txt	9
src/integrationTest/resources/DnaCaptureVarBam/sSingle.txt	9
src/integrationTest/resources/DnaCaptureVarBam/sSingleNotTumorOrCase.txt	7
src/integrationTest/resources/DnaCaptureVarFastq/gBwaPicardQcAbraGatkPaired.txt	59
src/integrationTest/resources/DnaCaptureVarFastq/gBwaPicardQcAbraGatkSingle.txt	59
src/integrationTest/resources/DnaCaptureVarFastq/gBwaPicardQcTargetSingle.txt	63
src/integrationTest/resources/DnaCaptureVarFastq/gBwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired.txt	59
src/integrationTest/resources/DnaCaptureVarFastq/gPairedAllTasks.txt	65
src/integrationTest/resources/DnaCaptureVarFastq/gSingleAllTasks.txt	59
src/integrationTest/resources/DnaCaptureVarFastq/gTrimmomaticNovoalignSingle.txt	63
src/integrationTest/resources/DnaCaptureVarFastq/gXenomeSeqpurgeBwaPaired.txt	63
src/integrationTest/resources/DnaCaptureVarFastq/sPaired.txt	9
src/integrationTest/resources/DnaCaptureVarFastq/sPairedCaseNA.txt	9
src/integrationTest/resources/DnaCaptureVarFastq/sPairedControlSampleNotNA.txt	9
src/integrationTest/resources/DnaCaptureVarFastq/sSingle.txt	9
src/integrationTest/resources/DnaCaptureVarFastq/sSingleNotTumorOrCase.txt	8
src/integrationTest/resources/DnaCaptureVarFastq/sSingleTarget.txt	9
src/integrationTest/resources/DnaWgsVarBam/gAllTasksSampleNA.txt	59
src/integrationTest/resources/DnaWgsVarBam/gAllTasksSampleNotNA.txt	61
src/integrationTest/resources/DnaWgsVarBam/sControlSampleNotNA.txt	9
src/integrationTest/resources/DnaWgsVarBam/sSingle.txt	9
src/integrationTest/resources/DnaWgsVarBam/sSingleNotTumorOrCase.txt	7
src/integrationTest/resources/DnaWgsVarFastq/global_config_DnaWgsVar_Fastq_v1.1.txt	40
src/integrationTest/resources/DnaWgsVarFastq/sscRnaExpressionCellRangerFastq.txt	9
src/integrationTest/resources/HlaTypingFastq/gPairedSeqpurgeOptiType.txt	24
src/integrationTest/resources/HlaTypingFastq/gPairedTrimmQcXenomeYes.txt	29
src/integrationTest/resources/HlaTypingFastq/sHlaTypingFastq.txt	10
src/integrationTest/resources/RnaCaptureVarFastq/gAllTasksWithoutTrimmomaticPaired.txt	66
src/integrationTest/resources/RnaCaptureVarFastq/gTrimmomaticStarPaired.txt.txt	65
src/integrationTest/resources/RnaCaptureVarFastq/sPaired.txt	9
src/integrationTest/resources/RnaExpressionBam/gFeatureCountRsemCufflinksStringtie.txt	36
src/integrationTest/resources/RnaExpressionBam/sRnaExpressionBam.txt	10
src/integrationTest/resources/RnaExpressionFastq/gCufflinks.txt	34
src/integrationTest/resources/RnaExpressionFastq/gFeatureCount.txt	34
src/integrationTest/resources/RnaExpressionFastq/gFlagXenomeYes.txt	36
src/integrationTest/resources/RnaExpressionFastq/gHisat2.txt	34
src/integrationTest/resources/RnaExpressionFastq/gNonFlagXenome.txt	34
src/integrationTest/resources/RnaExpressionFastq/gNonHisat2.txt	35
src/integrationTest/resources/RnaExpressionFastq/gNonSalmon.txt	35
src/integrationTest/resources/RnaExpressionFastq/gNonSeqpurge.txt	35
src/integrationTest/resources/RnaExpressionFastq/gNonStar.txt	35
src/integrationTest/resources/RnaExpressionFastq/gNonTrimmomatic.txt	34
src/integrationTest/resources/RnaExpressionFastq/gRsemWithoutHisat2.txt	34
src/integrationTest/resources/RnaExpressionFastq/gSalmon.txt	34
src/integrationTest/resources/RnaExpressionFastq/gSeqpurgeWithAdapters.txt	34
src/integrationTest/resources/RnaExpressionFastq/gSeqpurgeWithoutAdapters.txt	32
src/integrationTest/resources/RnaExpressionFastq/gStarWithRsem.txt	35
src/integrationTest/resources/RnaExpressionFastq/gStarWithoutRsem.txt	33
src/integrationTest/resources/RnaExpressionFastq/gStringtie.txt	35
src/integrationTest/resources/RnaExpressionFastq/gTrimmomaticWithAdapter.txt	35
src/integrationTest/resources/RnaExpressionFastq/gTrimmomaticWithoutAdapter.txt	32
src/integrationTest/resources/RnaExpressionFastq/sRnaExpressionFastq.txt	10
src/integrationTest/resources/RnaFusionFastq/gFlagXenomeYes.txt	36
src/integrationTest/resources/RnaFusionFastq/gNonFlagXenome.txt	34
src/integrationTest/resources/RnaFusionFastq/gNonFusionCatcher.txt	35
src/integrationTest/resources/RnaFusionFastq/gNonSeqpurge.txt	35
src/integrationTest/resources/RnaFusionFastq/gNonStarFusion.txt	35
src/integrationTest/resources/RnaFusionFastq/gNonTrimmomatic.txt	34
src/integrationTest/resources/RnaFusionFastq/gSeqpurgeWithAdapters.txt	34
src/integrationTest/resources/RnaFusionFastq/gSeqpurgeWithoutAdapters.txt	32
src/integrationTest/resources/RnaFusionFastq/gStarFusionAndFusionCatcher.txt	36
src/integrationTest/resources/RnaFusionFastq/gTrimmomaticWithAdapter.txt	35
src/integrationTest/resources/RnaFusionFastq/gTrimmomaticWithoutAdapter.txt	32
src/integrationTest/resources/RnaFusionFastq/sRnaFusionFastq.txt	9
src/integrationTest/resources/SCRnaExpressionBam/config_RnaExpression_Bam_test.txt	10
src/integrationTest/resources/SCRnaExpressionBam/global_config_scRnaExpression_Bam_v1.1.txt	29
src/integrationTest/resources/TcrRepertoireFast/config_TcrRepertoire_Fastq_test.txt	10
src/integrationTest/resources/TcrRepertoireFast/global_config_TcrRepertoire_Fastq_v1.1.txt	31
src/integrationTest/resources/scRnaExpressionCellRangerFastq/gCount.txt	45
src/integrationTest/resources/scRnaExpressionCellRangerFastq/gDoubletDetection.txt	45
src/integrationTest/resources/scRnaExpressionCellRangerFastq/gNonCount.txt	33
src/integrationTest/resources/scRnaExpressionCellRangerFastq/gScrublet.txt	45
src/integrationTest/resources/scRnaExpressionCellRangerFastq/sscRnaExpressionCellRangerFastq.txt	9
src/integrationTest/resources/scRnaExpressionFastq/gPairedNonFlagXenome.txt	36
src/integrationTest/resources/scRnaExpressionFastq/gRsemAndHisat2.txt	40
src/integrationTest/resources/scRnaExpressionFastq/gRsemWithoutHisat2.txt	35
src/integrationTest/resources/scRnaExpressionFastq/gStarAndRsem.txt	35
src/integrationTest/resources/scRnaExpressionFastq/gStarWithoutRsem.txt	36
src/integrationTest/resources/scRnaExpressionFastq/sPaired.txt	10
src/integrationTest/resources/sc_fastq_list.txt	27
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNAAllTasks/DnaAmpliconVar_Bam_freebayes_for_GA5_analysis.txt	37
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNAAllTasks/DnaAmpliconVar_Bam_gatkHaplotypeCaller_for_GA5_analysis.txt	37
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNAAllTasks/DnaAmpliconVar_Bam_lofreq_for_GA5_analysis.txt	37
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNAAllTasks/DnaAmpliconVar_Bam_mergeMutation_for_cohort_analysis.txt	134
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNAAllTasks/DnaAmpliconVar_Bam_mutect1_for_GA5_analysis.txt	37
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNAAllTasks/DnaAmpliconVar_Bam_scalpel_for_GA5_analysis.txt	38
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNAAllTasks/DnaAmpliconVar_Bam_strelka2_for_GA5_analysis.txt	39
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNAAllTasks/DnaAmpliconVar_Bam_vardict_for_GA5_analysis.txt	37
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNAAllTasks/DnaAmpliconVar_Bam_variantDetection_for_GA5_analysis.txt	92
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/DnaAmpliconVar_Bam_mergeMutation_for_cohort_analysis.txt	206
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA51/DnaAmpliconVar_Bam_contEst_for_GA51_analysis.txt	26
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA51/DnaAmpliconVar_Bam_exomecnv_for_GA51_analysis.txt	28
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA51/DnaAmpliconVar_Bam_lofreq_for_GA51_analysis.txt	40
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA51/DnaAmpliconVar_Bam_mutect2_for_GA51_analysis.txt	114
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA51/DnaAmpliconVar_Bam_scalpel_for_GA51_analysis.txt	38
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA51/DnaAmpliconVar_Bam_sequenza_for_GA51_analysis.txt	40
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA51/DnaAmpliconVar_Bam_strelka2_for_GA51_analysis.txt	43
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA51/DnaAmpliconVar_Bam_vardict_for_GA51_analysis.txt	37
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA51/DnaAmpliconVar_Bam_variantDetection_for_GA51_analysis.txt	103
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA52/DnaAmpliconVar_Bam_contEst_for_GA52_analysis.txt	26
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA52/DnaAmpliconVar_Bam_exomecnv_for_GA52_analysis.txt	28
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA52/DnaAmpliconVar_Bam_lofreq_for_GA52_analysis.txt	40
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA52/DnaAmpliconVar_Bam_mutect2_for_GA52_analysis.txt	114
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA52/DnaAmpliconVar_Bam_scalpel_for_GA52_analysis.txt	38
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA52/DnaAmpliconVar_Bam_sequenza_for_GA52_analysis.txt	40
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA52/DnaAmpliconVar_Bam_strelka2_for_GA52_analysis.txt	43
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA52/DnaAmpliconVar_Bam_vardict_for_GA52_analysis.txt	37
src/integrationTest/resources/templates/DnaAmpliconVarBam/ControlSampleNotNAAllTasks/ForGA52/DnaAmpliconVar_Bam_variantDetection_for_GA52_analysis.txt	103
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_gatkHaplotypeCaller_for_GA5_analysis_template.txt	37
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_lofreq_for_GA5_analysis_template.txt	37
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_mergeMutation_for_cohort_analysis_template.txt	152
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_mutect1_for_GA5_analysis_template.txt	37
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_postalignment_for_GA5_analysis_template.txt	164
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_scalpel_for_GA5_analysis_template.txt	38
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_strelka2_for_GA5_analysis_template.txt	39
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_vardict_for_GA5_analysis_template.txt	37
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_gatkHaplotypeCaller_for_GA5_analysis_template.txt	37
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_lofreq_for_GA5_analysis_template.txt	37
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_mergeMutation_for_cohort_analysis_template.txt	152
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_mutect1_for_GA5_analysis_template.txt	37
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_postalignment_for_GA5_analysis_template.txt	164
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_scalpel_for_GA5_analysis_template.txt	38
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_strelka2_for_GA5_analysis_template.txt	39
src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_vardict_for_GA5_analysis_template.txt	37
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNAAllTasks/DnaCaptureVar_Bam_freebayes_for_GA5_analysis_test.txt	37
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNAAllTasks/DnaCaptureVar_Bam_gatkHaplotypeCaller_for_GA5_analysis_test.txt	37
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNAAllTasks/DnaCaptureVar_Bam_lofreq_for_GA5_analysis_test.txt	37
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNAAllTasks/DnaCaptureVar_Bam_mutect1_for_GA5_analysis_test.txt	37
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNAAllTasks/DnaCaptureVar_Bam_scalpel_for_GA5_analysis_test.txt	38
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNAAllTasks/DnaCaptureVar_Bam_strelka2_for_GA5_analysis_test.txt	39
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNAAllTasks/DnaCaptureVar_Bam_vardict_for_GA5_analysis_test.txt	37
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNAAllTasks/DnaCaptureVar_Bam_variantDetection_for_GA5_analysis_test.txt	92
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNotNAAllTasks/DnaCaptureVar_Bam_contEst_for_GA51_analysis_test.txt	26
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNotNAAllTasks/DnaCaptureVar_Bam_exomecnv_for_GA51_analysis_test.txt	28
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNotNAAllTasks/DnaCaptureVar_Bam_lofreq_for_GA51_analysis_test.txt	40
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNotNAAllTasks/DnaCaptureVar_Bam_mutect2_for_GA51_analysis_test.txt	114
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNotNAAllTasks/DnaCaptureVar_Bam_scalpel_for_GA51_analysis_test.txt	38
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNotNAAllTasks/DnaCaptureVar_Bam_sequenza_for_GA51_analysis_test.txt	40
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNotNAAllTasks/DnaCaptureVar_Bam_strelka2_for_GA51_analysis_test.txt	43
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNotNAAllTasks/DnaCaptureVar_Bam_vardict_for_GA51_analysis_test.txt	37
src/integrationTest/resources/templates/DnaCaptureVarBam/testControlSampleNotNAAllTasks/DnaCaptureVar_Bam_variantDetection_for_GA51_analysis_test.txt	103
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_contEst_for_GA5_analysis_template.txt	26
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_exomecnv_for_GA5_analysis_template.txt	28
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_lofreq_for_GA5_analysis_template.txt	40
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_mergeMutation_for_cohort_analysis_template.txt	116
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_mutect2_for_GA5_analysis_template.txt	114
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_postalignment_for_GA5_analysis_template.txt	239
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_scalpel_for_GA5_analysis_template.txt	38
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_sequenza_for_GA5_analysis_template.txt	40
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_strelka2_for_GA5_analysis_template.txt	43
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_vardict_for_GA5_analysis_template.txt	37
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksSingle/dnaCaptureVar_Fastq_mergeMutation_for_cohort_analysis_template.txt	26
src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksSingle/dnaCaptureVar_Fastq_postalignment_for_GA5_analysis_template.txt	137
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkPaired/dnaCaptureVar_Fastq_postalignment_for_GA5_analysis_template.txt	183
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkPaired/dnaCaptureVar_Fastq_qcsummary_for_cohort_analysis_template.txt	46
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkSingle/dnaCaptureVar_Fastq_postalignment_for_GA5_analysis_template.txt	183
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkSingle/dnaCaptureVar_Fastq_qcsummary_for_cohort_analysis_template.txt	46
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcTargetSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcTargetSingle/dnaCaptureVar_Fastq_postalignment_for_GA5_analysis_template.txt	160
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcTargetSingle/dnaCaptureVar_Fastq_qcsummary_for_cohort_analysis_template.txt	46
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_alignment_for_smv1_1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_freebayes_for_smv1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_gatkHaplotypeCaller_for_smv1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_lofreq_for_smv1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_mergeMutation_for_cohort_analysis_template.txt	134
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_mutect1_for_smv1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_postalignment_for_smv1_analysis_template.txt	166
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_scalpel_for_smv1_analysis_template.txt	38
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_strelka2_for_smv1_analysis_template.txt	39
src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_vardict_for_smv1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaCaptureVarFastq/TrimmomaticNovoalignSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt	48
src/integrationTest/resources/templates/DnaCaptureVarFastq/TrimmomaticNovoalignSingle/dnaCaptureVar_Fastq_postalignment_for_GA5_analysis_template.txt	87
src/integrationTest/resources/templates/DnaCaptureVarFastq/XenomeSeqpurgeBwaPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt	63
src/integrationTest/resources/templates/DnaCaptureVarFastq/XenomeSeqpurgeBwaPaired/dnaCaptureVar_Fastq_postalignment_for_GA5_analysis_template.txt	87
src/integrationTest/resources/templates/DnaWgsVarBam/forGA5/DnaWgsVar_Bam_freebayes_for_GA5_analysis_template.txt	37
src/integrationTest/resources/templates/DnaWgsVarBam/forGA5/DnaWgsVar_Bam_gatkHaplotypeCaller_for_GA5_analysis_template.txt	37
src/integrationTest/resources/templates/DnaWgsVarBam/forGA5/DnaWgsVar_Bam_lofreq_for_GA5_analysis_template.txt	37
src/integrationTest/resources/templates/DnaWgsVarBam/forGA5/DnaWgsVar_Bam_strelka2_for_GA5_analysis_template.txt	39
src/integrationTest/resources/templates/DnaWgsVarBam/forGA5/DnaWgsVar_Bam_variantDetection_for_GA5_analysis_template.txt	59
src/integrationTest/resources/templates/DnaWgsVarBam/forGA51/DnaWgsVar_Bam_contEst_for_GA51_analysis_template.txt	26
src/integrationTest/resources/templates/DnaWgsVarBam/forGA51/DnaWgsVar_Bam_lofreq_for_GA51_analysis_template.txt	40
src/integrationTest/resources/templates/DnaWgsVarBam/forGA51/DnaWgsVar_Bam_mutect2_for_GA51_analysis_template.txt	114
src/integrationTest/resources/templates/DnaWgsVarBam/forGA51/DnaWgsVar_Bam_strelka2_for_GA51_analysis_template.txt	43
src/integrationTest/resources/templates/DnaWgsVarBam/forGA51/DnaWgsVar_Bam_variantDetection_for_GA51_analysis_template.txt	59
src/integrationTest/resources/templates/DnaWgsVarBam/forGA52/DnaWgsVar_Bam_contEst_for_GA52_analysis_template.txt	26
src/integrationTest/resources/templates/DnaWgsVarBam/forGA52/DnaWgsVar_Bam_lofreq_for_GA52_analysis_template.txt	40
src/integrationTest/resources/templates/DnaWgsVarBam/forGA52/DnaWgsVar_Bam_mutect2_for_GA52_analysis_template.txt	114
src/integrationTest/resources/templates/DnaWgsVarBam/forGA52/DnaWgsVar_Bam_strelka2_for_GA52_analysis_template.txt	43
src/integrationTest/resources/templates/DnaWgsVarBam/forGA52/DnaWgsVar_Bam_variantDetection_for_GA52_analysis_template.txt	59
src/integrationTest/resources/templates/DnaWgsVarFastq/DnaWgsVar_Fastq_alignment_for_GA5_1_analysis_template.txt	37
src/integrationTest/resources/templates/DnaWgsVarFastq/DnaWgsVar_Fastq_gatkHaplotypeCaller_for_GA5_analysis_template.txt	37
src/integrationTest/resources/templates/DnaWgsVarFastq/DnaWgsVar_Fastq_postalignment_for_GA5_analysis_template.txt	182
src/integrationTest/resources/templates/HlaTypingFastq/HlaTypingFastqPairedSeqpurgeOptiType/HlaTyping_Fastq_hlatyping_for_smv1_analysis.txt	63
src/integrationTest/resources/templates/HlaTypingFastq/HlaTypingFastqPairedSeqpurgeOptiType/HlaTyping_Fastq_hlatyping_for_smv2_analysis.txt	63
src/integrationTest/resources/templates/HlaTypingFastq/HlaTypingFastqPairedSeqpurgeOptiType/HlaTyping_Fastq_hlatyping_for_smv3_analysis.txt	63
src/integrationTest/resources/templates/HlaTypingFastq/HlaTypingFastqPairedSeqpurgeOptiType/HlaTyping_Fastq_hlatyping_for_smv5_analysis.txt	63
src/integrationTest/resources/templates/HlaTypingFastq/HlaTypingFastqPairedTrimmQcXenomeYes/HlaTyping_Fastq_hlatyping_for_smv1_analysis.txt	67
src/integrationTest/resources/templates/HlaTypingFastq/HlaTypingFastqPairedTrimmQcXenomeYes/HlaTyping_Fastq_hlatyping_for_smv2_analysis.txt	67
src/integrationTest/resources/templates/HlaTypingFastq/HlaTypingFastqPairedTrimmQcXenomeYes/HlaTyping_Fastq_hlatyping_for_smv3_analysis.txt	67
src/integrationTest/resources/templates/HlaTypingFastq/HlaTypingFastqPairedTrimmQcXenomeYes/HlaTyping_Fastq_hlatyping_for_smv5_analysis.txt	67
src/integrationTest/resources/templates/RnaCaptureVarFastq/AllTasksWithoutTrimmomaticPaired/rnaCaptureVar_Fastq_alignment_for_GA5_analysis_template.txt	228
src/integrationTest/resources/templates/RnaCaptureVarFastq/AllTasksWithoutTrimmomaticPaired/rnaCaptureVar_Fastq_gatkHaplotypeCaller_for_GA5_analysis_template.txt	48
src/integrationTest/resources/templates/RnaCaptureVarFastq/AllTasksWithoutTrimmomaticPaired/rnaCaptureVar_Fastq_mergeMutation_for_cohort_analysis_template.txt	44
src/integrationTest/resources/templates/RnaCaptureVarFastq/AllTasksWithoutTrimmomaticPaired/rnaCaptureVar_Fastq_qcsummary_for_cohort_analysis_template.txt	44
src/integrationTest/resources/templates/RnaCaptureVarFastq/TrimmomaticStarPaired/rnaCaptureVar_Fastq_alignment_for_GA5_analysis_template.txt	108
src/integrationTest/resources/templates/RnaExpressionBam/RnaExpression_Bam_ExpressionEstimation_for_GA5_analysis.txt	59
src/integrationTest/resources/templates/RnaExpressionBam/RnaExpression_Bam_cufflinks_for_GA5_analysis.txt	28
src/integrationTest/resources/templates/RnaExpressionBam/RnaExpression_Bam_featureCount_for_GA5_analysis.txt	26
src/integrationTest/resources/templates/RnaExpressionBam/RnaExpression_Bam_rsem_for_GA5_analysis.txt	40
src/integrationTest/resources/templates/RnaExpressionBam/RnaExpression_Bam_stringtie_for_GA5_analysis.txt	26
src/integrationTest/resources/templates/RnaExpressionFastq/RnaExpressionFastqCufflinks/RnaExpression_Fastq_cufflinks_for_smv1_analysis.txt	28
src/integrationTest/resources/templates/RnaExpressionFastq/RnaExpressionFastqFeatureCount/RnaExpression_Fastq_featureCount_for_smv1_analysis.txt	26
src/integrationTest/resources/templates/RnaExpressionFastq/RnaExpressionFastqRsemWithoutHisat2/RnaExpression_Fastq_alignment_for_smv1_analysis.txt	62
src/integrationTest/resources/templates/RnaExpressionFastq/RnaExpressionFastqRsemWithoutHisat2/RnaExpression_Fastq_qcsummary_for_cohort_analysis.txt	136
src/integrationTest/resources/templates/RnaExpressionFastq/RnaExpressionFastqRsemWithoutHisat2/RnaExpression_Fastq_rsem_for_smv1_analysis.txt	40
src/integrationTest/resources/templates/RnaExpressionFastq/RnaExpressionFastqStarWithRsem/RnaExpression_Fastq_alignment_for_smv1_analysis.txt	62
src/integrationTest/resources/templates/RnaExpressionFastq/RnaExpressionFastqStarWithRsem/RnaExpression_Fastq_qcsummary_for_cohort_analysis.txt	136
src/integrationTest/resources/templates/RnaExpressionFastq/RnaExpressionFastqStarWithRsem/RnaExpression_Fastq_rsem_for_smv1_analysis.txt	40
src/integrationTest/resources/templates/RnaExpressionFastq/RnaExpressionFastqStarWithoutRsem/RnaExpression_Fastq_alignment_for_smv1_analysis.txt	118
src/integrationTest/resources/templates/RnaExpressionFastq/RnaExpressionFastqStarWithoutRsem/RnaExpression_Fastq_qcsummary_for_cohort_analysis.txt	136
src/integrationTest/resources/templates/RnaExpressionFastq/RnaExpressionFastqStringtie/RnaExpression_Fastq_stringtie_for_smv1_analysis.txt	26
src/integrationTest/resources/templates/RnaExpressionFastq/rnaExpression_Fastq_Hisat2.txt	84
src/integrationTest/resources/templates/RnaExpressionFastq/rnaExpression_Fastq_Salmon.txt	57
src/integrationTest/resources/templates/RnaExpressionFastq/rnaExpression_Fastq_Seqpurge_with_Adapters.txt	51
src/integrationTest/resources/templates/RnaExpressionFastq/rnaExpression_Fastq_Seqpurge_without_Adapters.txt	51
src/integrationTest/resources/templates/RnaExpressionFastq/rnaExpression_Fastq_Trimmomatic_with_adapter.txt	53
src/integrationTest/resources/templates/RnaExpressionFastq/rnaExpression_Fastq_Trimmomatic_without_adapter.txt	40
src/integrationTest/resources/templates/RnaExpressionFastq/rnaExpression_Fastq_alignment_flag_Xenome_yes_template.txt	66
src/integrationTest/resources/templates/RnaExpressionFastq/rnaExpression_Fastq_non_Hisat2.txt	53
src/integrationTest/resources/templates/RnaExpressionFastq/rnaExpression_Fastq_non_Salmon.txt	53
src/integrationTest/resources/templates/RnaExpressionFastq/rnaExpression_Fastq_non_Seqpurge.txt	53
src/integrationTest/resources/templates/RnaExpressionFastq/rnaExpression_Fastq_non_Star.txt	53
src/integrationTest/resources/templates/RnaExpressionFastq/rnaExpression_Fastq_non_Trimmomatic.txt	51
src/integrationTest/resources/templates/RnaExpressionFastq/rnaExpression_Fastq_non_flag_Xenome.txt	51
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA5/scRnaExpression_Bam_ExpressionEstimation_for_GA5_analysis_template.txt	59
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA5/scRnaExpression_Bam_cufflinks_for_GA5_analysis_template.txt	28
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA5/scRnaExpression_Bam_featureCount_for_GA5_analysis_template.txt	26
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA5/scRnaExpression_Bam_rsem_for_GA5_analysis_template.txt	40
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA5/scRnaExpression_Bam_stringtie_for_GA5_analysis_template.txt	26
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA51/scRnaExpression_Bam_ExpressionEstimation_for_GA51_analysis_template.txt	59
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA51/scRnaExpression_Bam_cufflinks_for_GA51_analysis_template.txt	28
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA51/scRnaExpression_Bam_featureCount_for_GA51_analysis_template.txt	26
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA51/scRnaExpression_Bam_rsem_for_GA51_analysis_template.txt	40
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA51/scRnaExpression_Bam_stringtie_for_GA51_analysis_template.txt	26
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA52/scRnaExpression_Bam_ExpressionEstimation_for_GA52_analysis_template.txt	59
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA52/scRnaExpression_Bam_cufflinks_for_GA52_analysis_template.txt	28
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA52/scRnaExpression_Bam_featureCount_for_GA52_analysis_template.txt	26
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA52/scRnaExpression_Bam_rsem_for_GA52_analysis_template.txt	40
src/integrationTest/resources/templates/SCRnaExpressionBam/forGA52/scRnaExpression_Bam_stringtie_for_GA52_analysis_template.txt	26
src/integrationTest/resources/templates/SCRnaExpressionBam/scRnaExpression_Bam_cufflinks_for_cohort_analysis_template.txt	80
src/integrationTest/resources/templates/SCRnaExpressionBam/scRnaExpression_Bam_rsem_for_cohort_analysis_template.txt	80
src/integrationTest/resources/templates/SCRnaExpressionBam/scRnaExpression_Bam_stringtie_for_cohort_analysis_template.txt	80
src/integrationTest/resources/templates/TcrRepertoireFastq/TcrRepertoire_Fastq_TCR_detection_for_smv1_template.txt	64
src/integrationTest/resources/templates/TcrRepertoireFastq/TcrRepertoire_Fastq_TCR_detection_for_smv2_template.txt	64
src/integrationTest/resources/templates/TcrRepertoireFastq/TcrRepertoire_Fastq_TCR_detection_for_smv3_template.txt	64
src/integrationTest/resources/templates/TcrRepertoireFastq/TcrRepertoire_Fastq_TCR_detection_for_smv4_template.txt	64
src/integrationTest/resources/templates/TcrRepertoireFastq/TcrRepertoire_Fastq_TCR_detection_for_um_template.txt	64
src/integrationTest/resources/templates/bam2Fastq/testPairedPicard/Bam2Fastq_convert_for_GA52_analysis.txt	51
src/integrationTest/resources/templates/bam2Fastq/testPairedPicard/Bam2Fastq_convert_for_GA5_analysis.txt	51
src/integrationTest/resources/templates/bam2Fastq/testPairedPicard/Example_project-run1234-031814-FastqPaths.txt	4
src/integrationTest/resources/templates/bam2Fastq/testSinglePicard3Columns/Bam2Fastq_convert_for_GA5_analysis.txt	49
src/integrationTest/resources/templates/bam2Fastq/testSinglePicard3Columns/Example_project-run1234-031814-FastqPaths.txt	2
src/integrationTest/resources/templates/bam2Fastq/testSinglePicard5Columns/Bam2Fastq_convert_for_GA51_analysis.txt	49
src/integrationTest/resources/templates/bam2Fastq/testSinglePicard5Columns/Bam2Fastq_convert_for_GA52_analysis.txt	49
src/integrationTest/resources/templates/bam2Fastq/testSortPairedNonPicard/Bam2Fastq_convert_for_GA52_analysis.txt	37
src/integrationTest/resources/templates/bam2Fastq/testSortPairedNonPicard/Bam2Fastq_convert_for_GA5_analysis.txt	37
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt	37
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_freebayes_for_GA5_analysis.txt	37
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_gatkHaplotypeCaller_for_GA5_analysis.txt	37
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_lofreq_for_GA5_analysis.txt	37
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_mergeMutation_for_cohort_analysis.txt	134
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_mutect1_for_GA5_analysis.txt	37
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_postalignment_for_GA5_analysis.txt	210
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_scalpel_for_GA5_analysis.txt	38
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_strelka2_for_GA5_analysis.txt	39
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_vardict_for_GA5_analysis.txt	37
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt	37
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_contEst_for_GA5_analysis.txt	26
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_exomecnv_for_GA5_analysis.txt	28
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_lofreq_for_GA5_analysis.txt	40
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_mergeMutation_for_cohort_analysis.txt	116
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_mutect2_for_GA5_analysis.txt	37
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_postalignment_for_GA5_analysis.txt	164
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_scalpel_for_GA5_analysis.txt	38
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_sequenza_for_GA5_analysis.txt	40
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_strelka2_for_GA5_analysis.txt	43
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_vardict_for_GA5_analysis.txt	37
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedPicardAbraGatk/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt	37
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedPicardAbraGatk/DnaAmpliconVar_Fastq_postalignment_for_GA5_analysis.txt	161
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedPicardAbraGatk/DnaAmpliconVar_Fastq_qcsummary_for_cohort_analysis.txt	44
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt	63
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeBwa/DnaAmpliconVar_Fastq_postalignment_for_GA5_analysis.txt	87
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeBwa/DnaAmpliconVar_Fastq_qcsummary_for_cohort_analysis.txt	44
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeNovoalign/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt	63
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeNovoalign/DnaAmpliconVar_Fastq_postalignment_for_GA5_analysis.txt	87
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeNovoalign/DnaAmpliconVar_Fastq_qcsummary_for_cohort_analysis.txt	44
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt	65
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_postalignment_for_GA5_analysis.txt	87
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_qcsummary_for_cohort_analysis.txt	44
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSinglePicardAbraGatk/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt	37
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSinglePicardAbraGatk/DnaAmpliconVar_Fastq_postalignment_for_GA5_analysis.txt	161
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSinglePicardAbraGatk/DnaAmpliconVar_Fastq_qcsummary_for_cohort_analysis.txt	44
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt	61
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_postalignment_for_GA5_analysis.txt	87
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_qcsummary_for_cohort_analysis.txt	44
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticNovoalign/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt	61
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticNovoalign/DnaAmpliconVar_Fastq_postalignment_for_GA5_analysis.txt	87
src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticNovoalign/DnaAmpliconVar_Fastq_qcsummary_for_cohort_analysis.txt	44
src/integrationTest/resources/templates/master_template_test.txt	92
src/integrationTest/resources/templates/rnaFusionFastq_templates/rnaFusionFastq_Flag_Xenome_Yes_template.txt	65
src/integrationTest/resources/templates/rnaFusionFastq_templates/rnaFusionFastq_Non_Flag_Xenome_template.txt	50
src/integrationTest/resources/templates/rnaFusionFastq_templates/rnaFusionFastq_Non_Fusion_Catcher.txt	52
src/integrationTest/resources/templates/rnaFusionFastq_templates/rnaFusionFastq_Non_Trimmomatic_template.txt	50
src/integrationTest/resources/templates/rnaFusionFastq_templates/rnaFusionFastq_Seqpurge_With_Adapters_template.txt	50
src/integrationTest/resources/templates/rnaFusionFastq_templates/rnaFusionFastq_Seqpurge_Without_Adapters_template.txt	50
src/integrationTest/resources/templates/rnaFusionFastq_templates/rnaFusionFastq_StarFusion_And_FusionCatcher_template.txt	96
src/integrationTest/resources/templates/rnaFusionFastq_templates/rnaFusionFastq_Trimmomatic_With_Adapter_template.txt	52
src/integrationTest/resources/templates/rnaFusionFastq_templates/rnaFusionFastq_Trimmomatic_Without_Adapter_template.txt	40
src/integrationTest/resources/templates/scRnaExpressionCellRangerFastq/scRnaExpressionCellRangerFast_CountQC_template.txt	54
src/integrationTest/resources/templates/scRnaExpressionCellRangerFastq/scRnaExpressionCellRangerFast_CountScrubletQC_template.txt	65
src/integrationTest/resources/templates/scRnaExpressionCellRangerFastq/scRnaExpressionCellRangerFastq_CountDoubletDetectionQC_template.txt	65
src/integrationTest/resources/templates/scRnaExpressionFastq/RsemWithoutHisat2/scRnaExpression_Fastq_alignment_for_pbmc4k_analysis.txt	50
src/integrationTest/resources/templates/scRnaExpressionFastq/RsemWithoutHisat2/scRnaExpression_Fastq_rsem_for_pbmc4k_analysis.txt	40
src/integrationTest/resources/templates/scRnaExpressionFastq/StarAndRsem/scRnaExpression_Fastq_alignment_for_pbmc4k_analysis.txt	61
src/integrationTest/resources/templates/scRnaExpressionFastq/StarAndRsem/scRnaExpression_Fastq_rsem_for_pbmc4k_analysis.txt	40
src/integrationTest/resources/templates/scRnaExpressionFastq/StarWithoutRsem/scRnaExpression_Fastq_alignment_for_pbmc4k_analysis.txt	144
src/integrationTest/resources/templates/scRnaExpressionFastq/StarWithoutRsem/scRnaExpression_Fastq_qcsummary_for_cohort_analysis.txt	44
src/integrationTest/resources/templates/scRnaExpressionFastq/featureCountCufflinksConversion/scRnaExpression_Fastq_alignment_for_pbmc4k_analysis.txt	177
src/integrationTest/resources/templates/scRnaExpressionFastq/featureCountCufflinksConversion/scRnaExpression_Fastq_cufflinks_for_cohort_analysis.txt	44
src/integrationTest/resources/templates/scRnaExpressionFastq/featureCountCufflinksConversion/scRnaExpression_Fastq_cufflinks_for_pbmc4k_analysis.txt	28
src/integrationTest/resources/templates/scRnaExpressionFastq/featureCountCufflinksConversion/scRnaExpression_Fastq_featureCount_for_pbmc4k_analysis.txt	26
src/main/java/com/epam/fonda/samples/Sample.java	3
src/main/java/com/epam/fonda/samples/SampleBuilder.java	186
src/main/java/com/epam/fonda/samples/SampleType.java	12
src/main/java/com/epam/fonda/samples/bam/BamFileSample.java	27
src/main/java/com/epam/fonda/samples/fastq/FastqFileSample.java	112
src/main/java/com/epam/fonda/samples/fastq/FastqReadType.java	20
src/main/java/com/epam/fonda/samples/fastq/LibraryCsv.java	12
src/main/java/com/epam/fonda/samples/parameters/Parameters.java	52
src/main/resources/application.properties	4
src/main/resources/fonda_details.txt	20
src/main/resources/templates/RNASeQC_tool_template.txt	23
src/main/resources/templates/abra_realign_tool_template.txt	12
src/main/resources/templates/add_task_template.txt	11
src/main/resources/templates/amplicon_gatk_haplotype_tool_template.txt	11
src/main/resources/templates/amplicon_gatk_realign_tool_template.txt	12
src/main/resources/templates/amplicon_gatk_recalibrate_tool_template.txt	12
src/main/resources/templates/analysis_logFile_template.txt	18
src/main/resources/templates/bwaSortFields_tool_template.txt	22
src/main/resources/templates/calculate_contamination_template.txt	11
src/main/resources/templates/clean_up_tmpDir_template.txt	12
src/main/resources/templates/contest_tool_template.txt	11
src/main/resources/templates/cufflinks_tool_template.txt	13
src/main/resources/templates/dna_amplicon_picard_qc_tool_template.txt	28
src/main/resources/templates/dna_capture_picard_qc_tool_template.txt	29
src/main/resources/templates/dna_picard_qc_tool_template.txt	28
src/main/resources/templates/dna_wgs_picard_qc_tool_template.txt	28
src/main/resources/templates/doublet_detection_template.txt	11
src/main/resources/templates/exomecnv_template.txt	13
src/main/resources/templates/fastq_list_analysis_template.txt	5
src/main/resources/templates/featurecount_tool_template.txt	11
src/main/resources/templates/filter_alignment_artifacts_tool_template.txt	11
src/main/resources/templates/filter_mutect_calls_tool_template.txt	11
src/main/resources/templates/freebayes_template.txt	11
src/main/resources/templates/fusionCatcher_tool_template.txt	12
src/main/resources/templates/gatk_haplotype_caller_rna_filter_tool_template.txt	11
src/main/resources/templates/gatk_haplotype_rna_tool_template.txt	11
src/main/resources/templates/gatk_sort_bam_template.txt	22
src/main/resources/templates/gatk_split_reads_tool_template.txt	11
src/main/resources/templates/hisat2_tool_template.txt	22
src/main/resources/templates/learnReadOrientationModel_tool_template.txt	11
src/main/resources/templates/library_csv_template.txt	3
src/main/resources/templates/lofreq_template.txt	14
src/main/resources/templates/logfile_scanning_shell_script_template.txt	38
src/main/resources/templates/master_template.txt	98
src/main/resources/templates/merge_fastq_template.txt	14
src/main/resources/templates/mixcr_tool_template.txt	17
src/main/resources/templates/mutation_analysis_template.txt	11
src/main/resources/templates/mutect1_template.txt	11
src/main/resources/templates/mutect2_template.txt	11
src/main/resources/templates/novoalign_sort_tool_template.txt	22
src/main/resources/templates/optiType_tool_template.txt	14
src/main/resources/templates/periodic_index_check_for_fastqs.txt	3
src/main/resources/templates/picard_mark_duplicates_tool_template.txt	22
src/main/resources/templates/picard_merge_dna_bam_tool_template.txt	22
src/main/resources/templates/picard_remove_duplicate_tool_template.txt	22
src/main/resources/templates/pileup_summaries_template.txt	11
src/main/resources/templates/pileup_tool_template.txt	12
src/main/resources/templates/qc_summary_analysis_template.txt	11
src/main/resources/templates/qc_summary_status_check_template.txt	18
src/main/resources/templates/rna_analysis_data_analysis_template.txt	11
src/main/resources/templates/rsem_annotation_template.txt	12
src/main/resources/templates/rsem_expression_template.txt	13
src/main/resources/templates/salmon_tool_template.txt	17
src/main/resources/templates/sam_to_fastq_tool_template.txt	14
src/main/resources/templates/scRna_analysis_count_tool_template.txt	11
src/main/resources/templates/scalpel_template.txt	12
src/main/resources/templates/scrublet_detection_template.txt	11
src/main/resources/templates/seqpurge_tool_template.txt	11
src/main/resources/templates/sequenza_template.txt	13
src/main/resources/templates/sort_bam_by_read_name_template.txt	22
src/main/resources/templates/star_fusion_tool_template.txt	45
src/main/resources/templates/static_shell_template.txt	19
src/main/resources/templates/strelka2_template.txt	17
src/main/resources/templates/stringtie_tool_template.txt	11
src/main/resources/templates/trimmomatic_tool_template.txt	14
src/main/resources/templates/vardict_template.txt	11
src/main/resources/templates/vcf_snpeff_annotation_tool_template.txt	11
src/main/resources/templates/vdj_tool_template.txt	12
src/main/resources/templates/xenome_tool_template.txt	15
src/main/scripts/config_templates/global_config/DnaCaptureVar_Fastq_tool_human_sure_select_v4.json	46
src/main/scripts/config_templates/global_config/DnaCaptureVar_Fastq_tool_human_sure_select_v5.json	46
src/main/scripts/config_templates/global_config/DnaCaptureVar_Fastq_tool_human_sure_select_v6.json	46
src/main/scripts/config_templates/global_config/DnaCaptureVar_Fastq_tool_mouse_exome_v1.json	45
src/main/scripts/config_templates/global_config/RnaExpression_tool_human.json	27
src/main/scripts/config_templates/global_config/RnaExpression_tool_mouse.json	27
src/main/scripts/config_templates/global_config/ScRnaExpression_CellRanger_Fastq_tool_human_toolchain1.json	11
src/main/scripts/config_templates/global_config/ScRnaExpression_CellRanger_Fastq_tool_human_toolchain2.json	11
src/main/scripts/config_templates/global_config/ScRnaExpression_CellRanger_Fastq_tool_mouse_toolchain1.json	11
src/main/scripts/config_templates/global_config/ScRnaExpression_CellRanger_Fastq_tool_mouse_toolchain2.json	11
src/main/scripts/config_templates/templates/global_template_DnaCaptureVar_Fastq.txt	58
src/main/scripts/config_templates/templates/global_template_RnaExpressionFastq.txt	39
src/main/scripts/config_templates/templates/global_template_scRnaExpression_CellRanger_Fastq.txt	33
src/main/scripts/config_templates/templates/sample_manifest_paired_template.txt	4
src/main/scripts/config_templates/templates/sample_manifest_single_template.txt	4
src/main/scripts/config_templates/templates/study_template.txt	10
src/main/scripts/requirements.txt	1
src/test/java/com/epam/fonda/samples/SampleBuilderTest.java	130
src/test/java/com/epam/fonda/samples/parameters/ParametersTest.java	104
src/test/resources/global_config/global_config_DnaCaptureVar_Fastq_v1.1.txt	37
src/test/resources/global_config/global_config_with_all_possible_fields.txt	74
src/test/resources/global_config/global_config_with_one_wrong_field.txt	5
src/test/resources/study_config/DnaCaptureVar_WES_SampleBamPaths.txt	7
src/test/resources/study_config/DnaCaptureVar_WES_SampleBamPathsOnlyNA.txt	3
src/test/resources/study_config/RnaExpression_RNASeq_SampleFastqPaths.txt	9
src/test/resources/study_config/RnaExpression_RNASeq_SampleFastqPathsIncorrect.txt	5
src/test/resources/study_config/RnaExpression_RNASeq_SampleFastqPathsSingle.txt	9
src/test/resources/study_config/RnaExpression_RNASeq_SampleFastqPaths_ONE_SAMPLE.txt	2
src/test/resources/study_config/ScRnaExpression_SampleFastqPaths.txt	27
src/test/resources/study_config/config_DnaCaptureVar_Fastq_test.txt	10
src/test/resources/study_config/study_config_with_all_possible_fields.txt	11
src/test/resources/study_config/study_config_with_one_wrong_field.txt	11
src/test/resources/templates/RNASeQC_tool_test_output_data.txt	23
src/test/resources/templates/RNASeQC_tool_test_output_data_with_bwa.txt	23
src/test/resources/templates/RNASeQC_tool_test_output_data_without_RNABED.txt	23
src/test/resources/templates/RnaPicardQc_tool_test_output_data.txt	28
src/test/resources/templates/add_task_test_output_data.txt	11
src/test/resources/templates/ampliconBwaSortTest_tool_test_input_data_with_fastq1.txt	22
src/test/resources/templates/ampliconBwaSortTest_tool_test_input_data_with_fastq1_and_fastq2.txt	22
src/test/resources/templates/amplicon_abra_realign_tool_test_output_data.txt	12
src/test/resources/templates/amplicon_gatk_realign_tool_test_output_data.txt	12
src/test/resources/templates/amplicon_gatk_recalibrate_tool_test_output_data.txt	12
src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1.txt	22
src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2.txt	22
src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2_with_tune.txt	22
src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_with_tune.txt	22
src/test/resources/templates/calculate_contamination_template_test.txt	11
src/test/resources/templates/captureBwaSortTest_tool_test_input_data_with_fastq1.txt	22
src/test/resources/templates/captureBwaSortTest_tool_test_input_data_with_fastq1_and_fastq2.txt	22
src/test/resources/templates/capture_novoalign_sort_test_tool_test_input_data_with_fastq1.txt	22
src/test/resources/templates/capture_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2.txt	22
src/test/resources/templates/clean_up_tmpdir_test_output_data.txt	12
src/test/resources/templates/contest_tool_test_output_data.txt	11
src/test/resources/templates/count_template_exp_cells_test_output.txt	39
src/test/resources/templates/count_template_output.txt	39
src/test/resources/templates/cufflinks_tool_test_input_data.txt	13
src/test/resources/templates/dnaAmpliconPicardQc_tool_test_output_data.txt	28
src/test/resources/templates/dnaCapturePicardQc_tool_test_output_data.txt	29
src/test/resources/templates/dnaPicardQc_tool_test_output_data.txt	28
src/test/resources/templates/dna_analysis_test_output_data.txt	44
src/test/resources/templates/doublet_detection_test_output.txt	11
src/test/resources/templates/exomecnv_template_test.txt	13
src/test/resources/templates/fastq_list_analysis_tool_test_output_data_with_paired_read_type.txt	3
src/test/resources/templates/fastq_list_analysis_tool_test_output_data_with_single_read_type.txt	3
src/test/resources/templates/featurecount_tool_test_output_data.txt	11
src/test/resources/templates/filter_alignment_artifacts_tool_template_test.txt	11
src/test/resources/templates/filter_mutect_calls_human_tool_template_test.txt	11
src/test/resources/templates/filter_mutect_calls_mouse_tool_template_test.txt	11
src/test/resources/templates/freebayes_test.txt	11
src/test/resources/templates/fusion_catcher_tool_test_output_data.txt	12
src/test/resources/templates/gatk_haplotype_caller_dna_tool_test_output_data.txt	11
src/test/resources/templates/gatk_haplotype_caller_rna_filter_tool_test_output_data.txt	11
src/test/resources/templates/gatk_haplotype_caller_rna_tool_test_output_data.txt	11
src/test/resources/templates/gatk_sort_bam_template_test.txt	22
src/test/resources/templates/gatk_split_reads_tool_test_output_data.txt	11
src/test/resources/templates/hisat2_tool_with_qc_test_output_data.txt	67
src/test/resources/templates/hisat2_tool_with_rmdup_test_output_data.txt	66
src/test/resources/templates/learnReadOrientationModel_tool_template_test.txt	11
src/test/resources/templates/library_csv_template_output.txt	3
src/test/resources/templates/lofreq_paired_test.txt	14
src/test/resources/templates/lofreq_unpaired_test.txt	11
src/test/resources/templates/logfile_scanning_shell_script_output_data.txt	38
src/test/resources/templates/merge_fastq_with_fastq2_test_output_data.txt	12
src/test/resources/templates/mixcr_tool_test_human_dna_paired_output_data.txt	13
src/test/resources/templates/mixcr_tool_test_human_dna_single_output_data.txt	13
src/test/resources/templates/mixcr_tool_test_human_rna_paired_output_data.txt	14
src/test/resources/templates/mixcr_tool_test_human_rna_single_output_data.txt	14
src/test/resources/templates/mixcr_tool_test_mouse_dna_paired_output_data.txt	13
src/test/resources/templates/mixcr_tool_test_mouse_dna_single_output_data.txt	13
src/test/resources/templates/mixcr_tool_test_mouse_rna_paired_output_data.txt	14
src/test/resources/templates/mixcr_tool_test_mouse_rna_single_output_data.txt	14
src/test/resources/templates/mutect1_template_test.txt	11
src/test/resources/templates/mutect2_template_test.txt	11
src/test/resources/templates/mutect2_tumor_only_template_test.txt	11
src/test/resources/templates/mutect2_without_bed_template_test.txt	11
src/test/resources/templates/optiType_tool_with_dna_lt_test_output_data.txt	13
src/test/resources/templates/optiType_tool_with_no_lt_test_output_data.txt	1
src/test/resources/templates/optiType_tool_with_rna_lt_test_output_data.txt	13
src/test/resources/templates/picard_mark_duplicate_tool_test_output_data.txt	22
src/test/resources/templates/picard_merge_dna_bam_tool_test_output_data.txt	22
src/test/resources/templates/picard_remove_duplicate_test_output_data.txt	22
src/test/resources/templates/pileup_summaries_template_test.txt	11
src/test/resources/templates/pileup_tool_test_output_data.txt	12
src/test/resources/templates/rna_analysis_data_analysis_test_output.txt	11
src/test/resources/templates/rna_analysis_logFile_test_output.txt	18
src/test/resources/templates/rsem_annotation_test_input_data.txt	12
src/test/resources/templates/rsem_expression_test_input_data.txt	13
src/test/resources/templates/salmon_tool_test_output_data.txt	17
src/test/resources/templates/sam_to_fastq_tool_test_output_data_with_paired_type_read.txt	14
src/test/resources/templates/sam_to_fastq_tool_test_output_data_with_single_type_read.txt	12
src/test/resources/templates/scRna_analysis_count_tool_test_output.txt	11
src/test/resources/templates/scalpel_paired_test.txt	12
src/test/resources/templates/scalpel_unpaired_test.txt	12
src/test/resources/templates/scrna_analysis_logFile_test_output.txt	18
src/test/resources/templates/scrublet_detection_test_output.txt	11
src/test/resources/templates/seqpurge_tool_test_output_data.txt	11
src/test/resources/templates/sequenza_template_test.txt	13
src/test/resources/templates/sort_bam_by_read_name_tool_test_output_data.txt	22
src/test/resources/templates/star_fusion_tool_test_output_data.txt	45
src/test/resources/templates/star_tool_with_load_and_remove_genome_load.txt	33
src/test/resources/templates/star_tool_with_qc_test_output_data.txt	78
src/test/resources/templates/star_tool_with_rmdup_test_output_data.txt	77
src/test/resources/templates/strelka2_paired_test.txt	17
src/test/resources/templates/strelka2_unpaired_test.txt	13
src/test/resources/templates/stringtie_tool_test_input_data.txt	11
src/test/resources/templates/trimmomatic_tool_test_output_data.txt	13
src/test/resources/templates/vardict_paired_test.txt	11
src/test/resources/templates/vardict_unpaired_test.txt	11
src/test/resources/templates/vcf_snpeff_annotation_tool_test_output_data.txt	11
src/test/resources/templates/vdj_tool_test_output_data.txt	12
src/test/resources/templates/wgs_abra_realign_tool_test_output_data.txt	12
src/test/resources/templates/xenome_tool_test_output_data.txt	15
src/test/resources/templates/xenome_tool_test_output_data_index.txt	15
src/test/resources/templates/xenome_tool_test_single_output_data.txt	13