DEV-2532 Fix tests and issue with persisted output naming

hartwigmedical · Feb 22, 2022 · 2def489 · 2def489
1 parent 1d78058
commit 2def489
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Showing 2 changed files with 20 additions and 18 deletions.
diff --git a/cluster/src/main/java/com/hartwig/pipeline/calling/structural/gripss/GripssSomatic.java b/cluster/src/main/java/com/hartwig/pipeline/calling/structural/gripss/GripssSomatic.java
@@ -137,21 +137,11 @@ public GripssSomaticOutput persistedOutput(final SomaticRunMetadata metadata) {
         GoogleStorageLocation somaticFilteredLocation =
                 persistedDataset.path(metadata.tumor().sampleName(), DataType.SOMATIC_STRUCTURAL_VARIANTS_GRIPSS)
                         .orElse(GoogleStorageLocation.of(metadata.bucket(),
-                                PersistedLocations.blobForSet(metadata.set(),
-                                        namespace(),
-                                        format("%s.%s.%s",
-                                                metadata.tumor().sampleName(),
-                                                GripssSomatic.GRIPSS_SOMATIC_FILTERED,
-                                                FileTypes.GZIPPED_VCF))));
+                                PersistedLocations.blobForSet(metadata.set(), namespace(), filteredVcf(metadata.tumor().sampleName()))));
         GoogleStorageLocation somaticLocation =
                 persistedDataset.path(metadata.tumor().sampleName(), DataType.SOMATIC_STRUCTURAL_VARIANTS_GRIPSS_RECOVERY)
                         .orElse(GoogleStorageLocation.of(metadata.bucket(),
-                                PersistedLocations.blobForSet(metadata.set(),
-                                        namespace(),
-                                        format("%s.%s.%s",
-                                                metadata.tumor().sampleName(),
-                                                GripssSomatic.GRIPSS_SOMATIC_UNFILTERED,
-                                                FileTypes.GZIPPED_VCF))));
+                                PersistedLocations.blobForSet(metadata.set(), namespace(), unfilteredVcf(metadata.tumor().sampleName()))));
 
         return GripssSomaticOutput.builder()
                 .status(PipelineStatus.PERSISTED)

diff --git a/cluster/src/test/resources/smoke_test/expected_output_files b/cluster/src/test/resources/smoke_test/expected_output_files
@@ -96,6 +96,12 @@ linx/CPCT12345678T.linx.vis_protein_domain.tsv
 linx/CPCT12345678T.linx.vis_segments.tsv
 linx/CPCT12345678T.linx.vis_sv_data.tsv
 linx/linx.version
+linx_germline/CPCT12345678T.linx.clusters.tsv
+linx_germline/CPCT12345678T.linx.germline.disruption.tsv
+linx_germline/CPCT12345678T.linx.germline.driver.catalog.tsv
+linx_germline/CPCT12345678T.linx.svs.tsv
+linx_germline/linx.version
+linx_germline/run.log
 metadata.json
 orange/CPCT12345678T.orange.json
 orange/CPCT12345678T.orange.pdf
@@ -211,12 +217,18 @@ gridss/CPCT12345678T.bam.gridss.working/CPCT12345678T.bam.sv.bam.csi
 gridss/CPCT12345678T.bam.gridss.working/CPCT12345678T.bam.tag_metrics
 gridss/run.log
 gridss/run.sh
-gripss/CPCT12345678T.gripss.somatic.vcf.gz
-gripss/CPCT12345678T.gripss.somatic.vcf.gz.tbi
-gripss/CPCT12345678T.gripss.filtered.somatic.vcf.gz
-gripss/CPCT12345678T.gripss.filtered.somatic.vcf.gz.tbi
-gripss/run.log
-gripss/run.sh
+gripss_germline/CPCT12345678R.gripss.filtered.germline.vcf.gz
+gripss_germline/CPCT12345678R.gripss.filtered.germline.vcf.gz.tbi
+gripss_germline/CPCT12345678R.gripss.germline.vcf.gz
+gripss_germline/CPCT12345678R.gripss.germline.vcf.gz.tbi
+gripss_germline/run.log
+gripss_germline/run.sh
+gripss_somatic/CPCT12345678T.gripss.filtered.somatic.vcf.gz
+gripss_somatic/CPCT12345678T.gripss.filtered.somatic.vcf.gz.tbi
+gripss_somatic/CPCT12345678T.gripss.somatic.vcf.gz
+gripss_somatic/CPCT12345678T.gripss.somatic.vcf.gz.tbi
+gripss_somatic/run.log
+gripss_somatic/run.sh
 virusbreakend/CPCT12345678T.virus.annotated.tsv
 virusbreakend/CPCT12345678T.virusbreakend.vcf
 virusbreakend/CPCT12345678T.virusbreakend.vcf.summary.tsv