in src/integrationTest/java/com/epam/fonda/DnaAmpliconVarBamIntegrationTest.java [164:281]
private static Stream<Arguments> initParametersNotNAAll() {
return Stream.of(
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_CONTEST, FOR_GA_51_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA51_SUFFIX, DNA_AMPLICON_VAR_BAM_CONTEST,
FOR_GA_51_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_EXOMECNV, FOR_GA_51_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA51_SUFFIX, DNA_AMPLICON_VAR_BAM_EXOMECNV,
FOR_GA_51_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_LOFREQ, FOR_GA_51_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA51_SUFFIX, DNA_AMPLICON_VAR_BAM_LOFREQ,
FOR_GA_51_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_MUTECT_2, FOR_GA_51_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA51_SUFFIX, DNA_AMPLICON_VAR_BAM_MUTECT_2,
FOR_GA_51_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_SCALPEL, FOR_GA_51_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA51_SUFFIX, DNA_AMPLICON_VAR_BAM_SCALPEL,
FOR_GA_51_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_SEQUENZA, FOR_GA_51_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA51_SUFFIX, DNA_AMPLICON_VAR_BAM_SEQUENZA,
FOR_GA_51_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_STRELKA_2, FOR_GA_51_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA51_SUFFIX, DNA_AMPLICON_VAR_BAM_STRELKA_2,
FOR_GA_51_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_VARDICT, FOR_GA_51_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA51_SUFFIX, DNA_AMPLICON_VAR_BAM_VARDICT,
FOR_GA_51_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_VARIANT_DETECTION, FOR_GA_51_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA51_SUFFIX, DNA_AMPLICON_VAR_BAM_VARIANT_DETECTION,
FOR_GA_51_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_CONTEST, FOR_GA_52_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA52_SUFFIX, DNA_AMPLICON_VAR_BAM_CONTEST,
FOR_GA_52_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_EXOMECNV, FOR_GA_52_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA52_SUFFIX, DNA_AMPLICON_VAR_BAM_EXOMECNV,
FOR_GA_52_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_LOFREQ, FOR_GA_52_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA52_SUFFIX, DNA_AMPLICON_VAR_BAM_LOFREQ,
FOR_GA_52_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_MUTECT_2, FOR_GA_52_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA52_SUFFIX, DNA_AMPLICON_VAR_BAM_MUTECT_2,
FOR_GA_52_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_SCALPEL, FOR_GA_52_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA52_SUFFIX, DNA_AMPLICON_VAR_BAM_SCALPEL,
FOR_GA_52_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_SEQUENZA, FOR_GA_52_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA52_SUFFIX, DNA_AMPLICON_VAR_BAM_SEQUENZA,
FOR_GA_52_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_STRELKA_2, FOR_GA_52_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA52_SUFFIX, DNA_AMPLICON_VAR_BAM_STRELKA_2,
FOR_GA_52_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_VARDICT, FOR_GA_52_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA52_SUFFIX, DNA_AMPLICON_VAR_BAM_VARDICT,
FOR_GA_52_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_VARIANT_DETECTION, FOR_GA_52_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_FOR_GA52_SUFFIX, DNA_AMPLICON_VAR_BAM_VARIANT_DETECTION,
FOR_GA_52_TEMPLATE_SUFFIX)),
of(DNA_AMPLICON_VAR_BAM_G_ALL_TASKS_NOT_NA, DNA_AMPLICON_VAR_BAM_S_CONTROL_NOT_NA,
format("%s%s%s",
OUTPUT_SH_SUFFIX, DNA_AMPLICON_VAR_BAM_MERGE_MUTATION, FOR_COHORT_ANALYSIS_SH_SUFFIX),
format("%s%s%s",
CONTROL_SAMPLE_NOT_NAALL_TASKS_SUFFIX, DNA_AMPLICON_VAR_BAM_MERGE_MUTATION,
FOR_COHORT_ANALYSIS_TEMPLATE_SUFFIX))
);
}