private static Stream initParameters()

in src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java [243:294]
52 lines of code
6 McCabe index (conditional complexity)

    private static Stream<Arguments> initParameters() {
        return Stream.of(
                Arguments.of(
                        format("%s/gXenomeSeqpurgeBwaPaired.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/%s", DNA_CAPTURE_VAR_FASTQ_DIR, STUDY_CONFIG_PAIRED),
                        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, XENOME_SEQPURGE_BWA_PAIRED_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/gXenomeSeqpurgeBwaPaired.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/%s", DNA_CAPTURE_VAR_FASTQ_DIR, STUDY_CONFIG_PAIRED),
                        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, XENOME_SEQPURGE_BWA_PAIRED_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/gBwaPicardQcAbraGatkPaired.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/%s", DNA_CAPTURE_VAR_FASTQ_DIR, STUDY_CONFIG_PAIRED),
                        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_PAIRED_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/gBwaPicardQcAbraGatkPaired.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/%s", DNA_CAPTURE_VAR_FASTQ_DIR, STUDY_CONFIG_PAIRED),
                        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_PAIRED_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/gBwaPicardQcAbraGatkPaired.txt", DNA_CAPTURE_VAR_FASTQ_DIR),
                        format("%s/%s", DNA_CAPTURE_VAR_FASTQ_DIR, STUDY_CONFIG_PAIRED),
                        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_PAIRED_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)))
        );
    }