src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java [330:347]:
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                                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),
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src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java [371:388]:
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
                                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),
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