in src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java [297:732]
private static Stream<Arguments> initParametersPaired() {
return Stream.of(
Arguments.of(
format("%s/gBwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired.txt",
DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedCaseNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_alignment_for_smv1_1_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_alignment_for_smv1_1_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR,
BWA_VARDICT_MUTECT1_STRELKA2_GATK_HAPOTYPECALLER_SCALPEL_LOFREQ_FREEBAYES_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_SMV1_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_SMV1)
},
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, GATK_HAPLOTYPE_CALLER, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT1, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, FREEBAYES, FOR_SMV1)
},
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gBwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired.txt",
DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedCaseNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_freebayes_for_smv1_analysis.sh",
OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_freebayes_for_smv1_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR,
BWA_VARDICT_MUTECT1_STRELKA2_GATK_HAPOTYPECALLER_SCALPEL_LOFREQ_FREEBAYES_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_SMV1_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_SMV1) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, GATK_HAPLOTYPE_CALLER, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT1, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, FREEBAYES, FOR_SMV1) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gBwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired.txt",
DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedCaseNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_gatkHaplotypeCaller_for_smv1_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_gatkHaplotypeCaller_for_smv1_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR,
BWA_VARDICT_MUTECT1_STRELKA2_GATK_HAPOTYPECALLER_SCALPEL_LOFREQ_FREEBAYES_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_SMV1_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_SMV1) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, GATK_HAPLOTYPE_CALLER, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT1, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, FREEBAYES, FOR_SMV1) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gBwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired.txt",
DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedCaseNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_lofreq_for_smv1_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_lofreq_for_smv1_analysis_template", DNA_CAPTURE_VAR_FASTQ_DIR,
BWA_VARDICT_MUTECT1_STRELKA2_GATK_HAPOTYPECALLER_SCALPEL_LOFREQ_FREEBAYES_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_SMV1_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_SMV1) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, GATK_HAPLOTYPE_CALLER, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT1, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, FREEBAYES, FOR_SMV1) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gBwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired.txt",
DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedCaseNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_mergeMutation_for_cohort_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_mergeMutation_for_cohort_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR,
BWA_VARDICT_MUTECT1_STRELKA2_GATK_HAPOTYPECALLER_SCALPEL_LOFREQ_FREEBAYES_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_SMV1_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_SMV1) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, GATK_HAPLOTYPE_CALLER, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT1, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, FREEBAYES, FOR_SMV1) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gBwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired.txt",
DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedCaseNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_mutect1_for_smv1_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_mutect1_for_smv1_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR,
BWA_VARDICT_MUTECT1_STRELKA2_GATK_HAPOTYPECALLER_SCALPEL_LOFREQ_FREEBAYES_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_SMV1_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_SMV1) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, GATK_HAPLOTYPE_CALLER, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT1, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, FREEBAYES, FOR_SMV1) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gBwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired.txt",
DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedCaseNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_postalignment_for_smv1_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_postalignment_for_smv1_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR,
BWA_VARDICT_MUTECT1_STRELKA2_GATK_HAPOTYPECALLER_SCALPEL_LOFREQ_FREEBAYES_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_SMV1_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_SMV1) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, GATK_HAPLOTYPE_CALLER, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT1, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, FREEBAYES, FOR_SMV1) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gBwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired.txt",
DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedCaseNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_scalpel_for_smv1_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_scalpel_for_smv1_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR,
BWA_VARDICT_MUTECT1_STRELKA2_GATK_HAPOTYPECALLER_SCALPEL_LOFREQ_FREEBAYES_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_SMV1_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_SMV1) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, GATK_HAPLOTYPE_CALLER, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT1, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, FREEBAYES, FOR_SMV1) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gBwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired.txt",
DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedCaseNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_strelka2_for_smv1_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_strelka2_for_smv1_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR,
BWA_VARDICT_MUTECT1_STRELKA2_GATK_HAPOTYPECALLER_SCALPEL_LOFREQ_FREEBAYES_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_SMV1_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_SMV1) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, GATK_HAPLOTYPE_CALLER, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT1, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, FREEBAYES, FOR_SMV1) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gBwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired.txt",
DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedCaseNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_vardict_for_smv1_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_vardict_for_smv1_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR,
BWA_VARDICT_MUTECT1_STRELKA2_GATK_HAPOTYPECALLER_SCALPEL_LOFREQ_FREEBAYES_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_SMV1_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_SMV1) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, GATK_HAPLOTYPE_CALLER, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT1, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_SMV1),
format("%s%s%s &", EXPECTED_SCRIPT_START, FREEBAYES, FOR_SMV1) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gPairedAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedControlSampleNotNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_alignment_for_GA5_1_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR, ALL_TASKS_PAIRED_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, CONT_EST, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SEQUENZA, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, EXOMECNV, FOR_GA5) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gPairedAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedControlSampleNotNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_contEst_for_GA5_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_contEst_for_GA5_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR, ALL_TASKS_PAIRED_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, CONT_EST, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SEQUENZA, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, EXOMECNV, FOR_GA5) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gPairedAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedControlSampleNotNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_exomecnv_for_GA5_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_exomecnv_for_GA5_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR, ALL_TASKS_PAIRED_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, CONT_EST, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SEQUENZA, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, EXOMECNV, FOR_GA5) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gPairedAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedControlSampleNotNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_lofreq_for_GA5_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_lofreq_for_GA5_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR, ALL_TASKS_PAIRED_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, CONT_EST, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SEQUENZA, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, EXOMECNV, FOR_GA5) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gPairedAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedControlSampleNotNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_mergeMutation_for_cohort_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_mergeMutation_for_cohort_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR, ALL_TASKS_PAIRED_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, CONT_EST, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SEQUENZA, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, EXOMECNV, FOR_GA5) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gPairedAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedControlSampleNotNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_mutect2_for_GA5_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_mutect2_for_GA5_analysis_template", DNA_CAPTURE_VAR_FASTQ_DIR,
ALL_TASKS_PAIRED_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, CONT_EST, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SEQUENZA, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, EXOMECNV, FOR_GA5) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gPairedAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedControlSampleNotNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_postalignment_for_GA5_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_postalignment_for_GA5_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR, ALL_TASKS_PAIRED_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, CONT_EST, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SEQUENZA, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, EXOMECNV, FOR_GA5) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gPairedAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedControlSampleNotNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_scalpel_for_GA5_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_scalpel_for_GA5_analysis_template", DNA_CAPTURE_VAR_FASTQ_DIR,
ALL_TASKS_PAIRED_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, CONT_EST, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SEQUENZA, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, EXOMECNV, FOR_GA5) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gPairedAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedControlSampleNotNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_sequenza_for_GA5_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_sequenza_for_GA5_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR, ALL_TASKS_PAIRED_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, CONT_EST, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SEQUENZA, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, EXOMECNV, FOR_GA5) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gPairedAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedControlSampleNotNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_strelka2_for_GA5_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_strelka2_for_GA5_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR, ALL_TASKS_PAIRED_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, CONT_EST, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SEQUENZA, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, EXOMECNV, FOR_GA5) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS))),
Arguments.of(
format("%s/gPairedAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/sPairedControlSampleNotNA.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
format("%s/DnaCaptureVar_Fastq_vardict_for_GA5_analysis.sh", OUTPUT_SH_FILES_DIR),
format("%s/%s/dnaCaptureVar_Fastq_vardict_for_GA5_analysis_template",
DNA_CAPTURE_VAR_FASTQ_DIR, ALL_TASKS_PAIRED_TEMPLATES),
new String[] {
format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1),
format("%s%s%s && \\", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
new String[] {
format("%s%s%s &", EXPECTED_SCRIPT_START, VARDICT, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, CONT_EST, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, STRELKA2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, MUTECT2, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SCALPEL, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, LOFREQ, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, SEQUENZA, FOR_GA5),
format("%s%s%s &", EXPECTED_SCRIPT_START, EXOMECNV, FOR_GA5) },
Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
FOR_COHORT_ANALYSIS)))
);
}