private static Stream initParametersSingle()

in src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java [129:240]
112 lines of code
12 McCabe index (conditional complexity)

    private static Stream<Arguments> initParametersSingle() {
        return Stream.of(
                Arguments.of(
                        format("%s/gTrimmomaticNovoalignSingle.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/%s", DNA_CAPTURE_VAR_FASTQ_DIR, STUDY_CONFIG_SINGLE),
                        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, TRIMMOMATIC_NOVOALIGN_SINGLE_TEMPLATES),
                        new String[] { format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1) },
                        new String[] { format("%s%s%s &\n     ", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
                        null),
                Arguments.of(
                        format("%s/gTrimmomaticNovoalignSingle.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/%s", DNA_CAPTURE_VAR_FASTQ_DIR, STUDY_CONFIG_SINGLE),
                        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, TRIMMOMATIC_NOVOALIGN_SINGLE_TEMPLATES),
                        new String[] { format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1) },
                        new String[] { format("%s%s%s &\n     ", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
                        null),
                Arguments.of(
                        format("%s/gBwaPicardQcAbraGatkSingle.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/%s", DNA_CAPTURE_VAR_FASTQ_DIR, STUDY_CONFIG_SINGLE),
                        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, BWA_PICARD_QC_ABRA_GATK_SINGLE_TEMPLATES),
                        new String[] { format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1) },
                        new String[] { format("%s%s%s &\n     ", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
                        Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, QCSUMMARY,
                                FOR_COHORT_ANALYSIS))),
                Arguments.of(
                        format("%s/gBwaPicardQcAbraGatkSingle.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/%s", DNA_CAPTURE_VAR_FASTQ_DIR, STUDY_CONFIG_SINGLE),
                        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, BWA_PICARD_QC_ABRA_GATK_SINGLE_TEMPLATES),
                        new String[] { format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1) },
                        new String[] { format("%s%s%s &\n     ", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
                        Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, QCSUMMARY,
                                FOR_COHORT_ANALYSIS))),
                Arguments.of(
                        format("%s/gBwaPicardQcAbraGatkSingle.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/%s", DNA_CAPTURE_VAR_FASTQ_DIR, STUDY_CONFIG_SINGLE),
                        format("%s/DnaCaptureVar_Fastq_qcsummary_for_cohort_analysis.sh", OUTPUT_SH_FILES_DIR),
                        format("%s/%s/dnaCaptureVar_Fastq_qcsummary_for_cohort_analysis_template",
                                DNA_CAPTURE_VAR_FASTQ_DIR, BWA_PICARD_QC_ABRA_GATK_SINGLE_TEMPLATES),
                        new String[] { format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1) },
                        new String[] { format("%s%s%s &\n     ", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
                        Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, QCSUMMARY,
                                FOR_COHORT_ANALYSIS))),
                Arguments.of(
                        format("%s/gSingleAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/sSingleNotTumorOrCase.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_SINGLE_TEMPLATES),
                        new String[] { format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1) },
                        new String[] { format("%s%s%s &\n     ", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
                        Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
                                FOR_COHORT_ANALYSIS))),
                Arguments.of(
                        format("%s/gSingleAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/sSingleNotTumorOrCase.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_SINGLE_TEMPLATES),
                        new String[] { format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1) },
                        new String[] { format("%s%s%s &\n     ", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
                        Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
                                FOR_COHORT_ANALYSIS))),
                Arguments.of(
                        format("%s/gSingleAllTasks.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/sSingleNotTumorOrCase.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_SINGLE_TEMPLATES),
                        new String[] { format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1) },
                        new String[] { format("%s%s%s &\n     ", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
                        Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, MERGE_MUTATION,
                                FOR_COHORT_ANALYSIS))),
                Arguments.of(
                        format("%s/gBwaPicardQcTargetSingle.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/sSingleTarget.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, BWA_PICARD_QC_TARGET_SINGLE),
                        new String[] { format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1) },
                        new String[] { format("%s%s%s &\n     ", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
                        Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, QCSUMMARY,
                                FOR_COHORT_ANALYSIS))),
                Arguments.of(
                        format("%s/gBwaPicardQcTargetSingle.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/sSingleTarget.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, BWA_PICARD_QC_TARGET_SINGLE),
                        new String[] { format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1) },
                        new String[] { format("%s%s%s &\n     ", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
                        Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, QCSUMMARY,
                                FOR_COHORT_ANALYSIS))),
                Arguments.of(
                        format("%s/gBwaPicardQcTargetSingle.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/sSingleTarget.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/DnaCaptureVar_Fastq_qcsummary_for_cohort_analysis.sh", OUTPUT_SH_FILES_DIR),
                        format("%s/%s/dnaCaptureVar_Fastq_qcsummary_for_cohort_analysis_template",
                                DNA_CAPTURE_VAR_FASTQ_DIR, BWA_PICARD_QC_TARGET_SINGLE),
                        new String[] { format("%s%s%s && \\", EXPECTED_SCRIPT_START, ALIGNMENT, FOR_GA5_1) },
                        new String[] { format("%s%s%s &\n     ", EXPECTED_SCRIPT_START, POSTALIGNMENT, FOR_GA5) },
                        Collections.singletonList(format("%s%s%s &", EXPECTED_SCRIPT_START, QCSUMMARY,
                                FOR_COHORT_ANALYSIS)))
        );
    }