in src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java [206:420]
private static Stream<Arguments> initParameters() {
return Stream.of(
Arguments.of(
RNA_EXPRESSION_FASTQ_G_FLAG_XENOME_YES,
OUTPUT_SH_FILE,
RNA_EXPRESSION_FASTQ_ALIGNMENT_FOR_SMV1_ANALYSIS_TEMPLATE_PATH,
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_SEQPURGE_WITH_ADAPTERS,
OUTPUT_SH_FILE,
RNA_EXPRESSION_FASTQ_SEQPURGE_WITH_ADAPTERS_TEMPLATE,
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_SEQPURGE_WITHOUT_ADAPTERS,
OUTPUT_SH_FILE,
RNA_EXPRESSION_FASTQ_SEQPURGE_WITHOUT_ADAPTERS_TEMPLATE,
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_TRIMMOMATIC_WITH_ADAPTER,
OUTPUT_SH_FILE,
RNA_EXPRESSION_FASTQ_TRIMMOMATIC_WITH_ADAPTER_TEMPLATE,
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_TRIMMOMATIC_WITHOUT_ADAPTER,
OUTPUT_SH_FILE,
RNA_EXPRESSION_FASTQ_TRIMMOMATIC_WITHOUT_ADAPTER_TEMPLATE,
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_STAR_WITH_RSEM,
OUTPUT_SH_FILE,
format("%sRnaExpression_Fastq_alignment_for_smv1_analysis",
RNA_EXPRESSION_FASTQ_STAR_WITH_RSEM_SUFFIX),
format("%1$s_alignment_for_smv%2$s_analysis.sh && \\", EXPECTED_SCRIPT_START, "%d"),
format("%1$s_rsem_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
NUMBER_OF_SCRIPTS,
Arrays.asList(POST_PROCESS_SCRIPT, POST_PROCESS_SCRIPT_RSEM)),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_STAR_WITH_RSEM,
format("%sRnaExpression_Fastq_qcsummary_for_cohort_analysis.sh",
OUTPUT_SH_FILES_SUFFIX),
format("%sRnaExpression_Fastq_qcsummary_for_cohort_analysis",
RNA_EXPRESSION_FASTQ_STAR_WITH_RSEM_SUFFIX),
format("%1$s_alignment_for_smv%2$s_analysis.sh && \\", EXPECTED_SCRIPT_START, "%d"),
format("%1$s_rsem_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
NUMBER_OF_SCRIPTS,
Arrays.asList(POST_PROCESS_SCRIPT, POST_PROCESS_SCRIPT_RSEM)),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_STAR_WITH_RSEM,
format("%sRnaExpression_Fastq_rsem_for_smv1_analysis.sh",
OUTPUT_SH_FILES_SUFFIX),
format("%sRnaExpression_Fastq_rsem_for_smv1_analysis",
RNA_EXPRESSION_FASTQ_STAR_WITH_RSEM_SUFFIX),
format("%1$s_alignment_for_smv%2$s_analysis.sh && \\", EXPECTED_SCRIPT_START, "%d"),
format("%1$s_rsem_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
NUMBER_OF_SCRIPTS,
Arrays.asList(POST_PROCESS_SCRIPT, POST_PROCESS_SCRIPT_RSEM)),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_STAR_WITHOUT_RSEM,
OUTPUT_SH_FILE,
format("%sRnaExpression_Fastq_alignment_for_smv1_analysis",
RNA_EXPRESSION_FASTQ_STAR_WITHOUT_RSEM_SUFFIX),
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
Collections.singletonList(POST_PROCESS_SCRIPT)),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_STAR_WITHOUT_RSEM,
format("%sRnaExpression_Fastq_qcsummary_for_cohort_analysis.sh",
OUTPUT_SH_FILES_SUFFIX),
format("%sRnaExpression_Fastq_qcsummary_for_cohort_analysis",
RNA_EXPRESSION_FASTQ_STAR_WITHOUT_RSEM_SUFFIX),
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
Collections.singletonList(POST_PROCESS_SCRIPT)),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_HISAT2,
OUTPUT_SH_FILE,
RNA_EXPRESSION_FASTQ_HISAT2_TEMPLATE,
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_SALMON,
OUTPUT_SH_FILE,
RNA_EXPRESSION_FASTQ_SALMON_TEMPLATE,
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_FEATURE_COUNT,
format("%sRnaExpression_Fastq_featureCount_for_smv1_analysis.sh",
OUTPUT_SH_FILES_SUFFIX),
format("%sRnaExpression_Fastq_featureCount_for_smv1_analysis",
RNA_EXPRESSION_FASTQ_FEATURE_COUNT_SUFFIX),
format("%1$s_alignment_for_smv%2$s_analysis.sh && \\", EXPECTED_SCRIPT_START, "%d"),
format("%1$s_featureCount_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_CUFFLINKS,
format("%sRnaExpression_Fastq_cufflinks_for_smv1_analysis.sh",
OUTPUT_SH_FILES_SUFFIX),
RNA_EXPRESSION_FASTQ_CUFFLINKS_SUFFIX +
"RnaExpression_Fastq_cufflinks_for_smv1_analysis",
format("%1$s_alignment_for_smv%2$s_analysis.sh && \\", EXPECTED_SCRIPT_START, "%d"),
format("%1$s_cufflinks_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_STRINGTIE,
format("%sRnaExpression_Fastq_stringtie_for_smv1_analysis.sh",
OUTPUT_SH_FILES_SUFFIX),
format("%sRnaExpression_Fastq_stringtie_for_smv1_analysis",
RNA_EXPRESSION_FASTQ_STRINGTIE_SUFFIX),
format("%1$s_alignment_for_smv%2$s_analysis.sh && \\", EXPECTED_SCRIPT_START, "%d"),
format("%1$s_stringtie_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_RSEM_WITHOUT_HISAT2,
format("%sRnaExpression_Fastq_rsem_for_smv1_analysis.sh",
OUTPUT_SH_FILES_SUFFIX),
format("%sRnaExpression_Fastq_rsem_for_smv1_analysis",
RNA_EXPRESSION_FASTQ_RSEM_WITHOUT_HISAT2_SUFFIX),
format("%1$s_alignment_for_smv%2$s_analysis.sh && \\", EXPECTED_SCRIPT_START, "%d"),
format("%1$s_rsem_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
NUMBER_OF_SCRIPTS,
Collections.singletonList(POST_PROCESS_SCRIPT)),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_RSEM_WITHOUT_HISAT2,
OUTPUT_SH_FILE,
format("%sRnaExpression_Fastq_alignment_for_smv1_analysis",
RNA_EXPRESSION_FASTQ_RSEM_WITHOUT_HISAT2_SUFFIX),
format("%1$s_alignment_for_smv%2$s_analysis.sh && \\", EXPECTED_SCRIPT_START, "%d"),
format("%1$s_rsem_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
NUMBER_OF_SCRIPTS,
Collections.singletonList(POST_PROCESS_SCRIPT)),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_RSEM_WITHOUT_HISAT2,
format("%sRnaExpression_Fastq_qcsummary_for_cohort_analysis.sh",
OUTPUT_SH_FILES_SUFFIX),
format("%sRnaExpression_Fastq_qcsummary_for_cohort_analysis",
RNA_EXPRESSION_FASTQ_RSEM_WITHOUT_HISAT2_SUFFIX),
format("%1$s_alignment_for_smv%2$s_analysis.sh && \\", EXPECTED_SCRIPT_START, "%d"),
format("%1$s_rsem_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
NUMBER_OF_SCRIPTS,
Collections.singletonList(POST_PROCESS_SCRIPT)),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_NON_FLAG_XENOME,
OUTPUT_SH_FILE,
RNA_EXPRESSION_FASTQ_NON_FLAG_XENOME_TEMPLATE,
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_NON_SEQPURGE,
OUTPUT_SH_FILE,
RNA_EXPRESSION_FASTQ_NON_SEQPURGE_TEMPLATE,
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_NON_TRIMMOMATIC,
OUTPUT_SH_FILE,
RNA_EXPRESSION_FASTQ_NON_TRIMMOMATIC_TEMPLATE,
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_NON_STAR,
OUTPUT_SH_FILE,
RNA_EXPRESSION_FASTQ_NON_STAR_TEMPLATE,
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_NON_HISAT2,
OUTPUT_SH_FILE,
RNA_EXPRESSION_FASTQ_NON_HISAT2_TEMPLATE,
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
null),
Arguments.of(
RNA_EXPRESSION_FASTQ_G_NON_SALMON,
OUTPUT_SH_FILE,
RNA_EXPRESSION_FASTQ_NON_SALMON_TEMPLATE,
format("%1$s_alignment_for_smv%2$s_analysis.sh &", EXPECTED_SCRIPT_START, "%d"),
"",
NUMBER_OF_SCRIPTS,
null)
);
}