Add delivery report to Balsamic-QC workflow (#2689)

### Added: - Delivery report to Balsamic-QC workflow
Clinical-Genomics · Nov 21, 2023 · aa5e12e · aa5e12e
1 parent 72e7fec
commit aa5e12e
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Showing 11 changed files with 153 additions and 115 deletions.
diff --git a/cg/cli/generate/report/utils.py b/cg/cli/generate/report/utils.py
@@ -11,11 +11,13 @@
     Pipeline,
 )
 from cg.meta.report.balsamic import BalsamicReportAPI
+from cg.meta.report.balsamic_qc import BalsamicQCReportAPI
 from cg.meta.report.balsamic_umi import BalsamicUmiReportAPI
 from cg.meta.report.mip_dna import MipDNAReportAPI
 from cg.meta.report.report_api import ReportAPI
 from cg.meta.report.rnafusion import RnafusionReportAPI
 from cg.meta.workflow.balsamic import BalsamicAnalysisAPI
+from cg.meta.workflow.balsamic_qc import BalsamicQCAnalysisAPI
 from cg.meta.workflow.balsamic_umi import BalsamicUmiAnalysisAPI
 from cg.meta.workflow.mip_dna import MipDNAAnalysisAPI
 from cg.meta.workflow.rnafusion import RnafusionAnalysisAPI
@@ -85,6 +87,9 @@ def get_report_api_pipeline(context: click.Context, pipeline: Pipeline) -> Repor
         Pipeline.BALSAMIC_UMI: BalsamicUmiReportAPI(
             config=context.obj, analysis_api=BalsamicUmiAnalysisAPI(config=context.obj)
         ),
+        Pipeline.BALSAMIC_QC: BalsamicQCReportAPI(
+            config=context.obj, analysis_api=BalsamicQCAnalysisAPI(config=context.obj)
+        ),
         Pipeline.MIP_DNA: MipDNAReportAPI(
             config=context.obj, analysis_api=MipDNAAnalysisAPI(config=context.obj)
         ),

diff --git a/cg/constants/delivery.py b/cg/constants/delivery.py
@@ -2,19 +2,19 @@
 
 from cg.constants.constants import Pipeline
 
-ONLY_ONE_CASE_PER_TICKET = [
+ONLY_ONE_CASE_PER_TICKET: list[Pipeline] = [
     Pipeline.FASTQ,
     Pipeline.MICROSALT,
     Pipeline.SARS_COV_2,
 ]
 
-SKIP_MISSING = [
+SKIP_MISSING: list[Pipeline] = [
     Pipeline.FASTQ,
     Pipeline.MICROSALT,
     Pipeline.SARS_COV_2,
 ]
 
-BALSAMIC_ANALYSIS_CASE_TAGS = [
+BALSAMIC_ANALYSIS_CASE_TAGS: list[set[str]] = [
     {"delivery-report"},
     {"multiqc-html"},
     {"metrics"},
@@ -36,21 +36,22 @@
     {"vcf2cytosure"},
 ]
 
-BALSAMIC_ANALYSIS_SAMPLE_TAGS = [
+BALSAMIC_ANALYSIS_SAMPLE_TAGS: list[set[str]] = [
     {"cram"},
     {"cram-index"},
 ]
 
-BALSAMIC_QC_ANALYSIS_CASE_TAGS = [
+BALSAMIC_QC_ANALYSIS_CASE_TAGS: list[set[str]] = [
+    {"delivery-report"},
     {"multiqc-html"},
 ]
 
-BALSAMIC_QC_ANALYSIS_SAMPLE_TAGS = [
+BALSAMIC_QC_ANALYSIS_SAMPLE_TAGS: list[set[str]] = [
     {"qc-cram"},
     {"qc-cram-index"},
 ]
 
-BALSAMIC_UMI_ANALYSIS_CASE_TAGS = [
+BALSAMIC_UMI_ANALYSIS_CASE_TAGS: list[set[str]] = [
     {"vcf-umi-snv"},
     {"vcf-umi-snv-index"},
     {"vcf-umi-snv-research"},
@@ -61,15 +62,15 @@
 
 BALSAMIC_UMI_ANALYSIS_CASE_TAGS.extend(BALSAMIC_ANALYSIS_CASE_TAGS)
 
-BALSAMIC_UMI_ANALYSIS_SAMPLE_TAGS = [
+BALSAMIC_UMI_ANALYSIS_SAMPLE_TAGS: list[set[str]] = [
     {"umi-cram"},
     {"umi-cram-index"},
 ]
 
 BALSAMIC_UMI_ANALYSIS_SAMPLE_TAGS.extend(BALSAMIC_ANALYSIS_SAMPLE_TAGS)
 
 
-MIP_DNA_ANALYSIS_CASE_TAGS = [
+MIP_DNA_ANALYSIS_CASE_TAGS: list[set[str]] = [
     {"delivery-report"},
     {"vcf-clinical-sv-bin"},
     {"vcf-clinical-sv-bin-index"},
@@ -93,9 +94,14 @@
     {"vcf-sv-research-index"},
 ]
 
-MIP_DNA_ANALYSIS_SAMPLE_TAGS = [{"bam"}, {"bam-index"}, {"cram"}, {"cram-index"}]
+MIP_DNA_ANALYSIS_SAMPLE_TAGS: list[set[str]] = [
+    {"bam"},
+    {"bam-index"},
+    {"cram"},
+    {"cram-index"},
+]
 
-MIP_RNA_ANALYSIS_CASE_TAGS = [
+MIP_RNA_ANALYSIS_CASE_TAGS: list[set[str]] = [
     {"fusion", "clinical", "pdf"},
     {"fusion", "research", "pdf"},
     {"fusion", "vcf"},
@@ -107,7 +113,7 @@
     {"multiqc-html"},
 ]
 
-MIP_RNA_ANALYSIS_SAMPLE_TAGS = [
+MIP_RNA_ANALYSIS_SAMPLE_TAGS: list[set[str]] = [
     {"fusion", "star-fusion"},
     {"fusion", "arriba"},
     {"cram"},
@@ -117,7 +123,7 @@
     {"salmon-quant"},
 ]
 
-MICROSALT_ANALYSIS_CASE_TAGS = [
+MICROSALT_ANALYSIS_CASE_TAGS: list[set[str]] = [
     {"microsalt-qc"},
     {"microsalt-type"},
     {"assembly"},
@@ -126,24 +132,24 @@
     {"reference-alignment-deduplicated"},
 ]
 
-MICROSALT_ANALYSIS_SAMPLE_TAGS = []
+MICROSALT_ANALYSIS_SAMPLE_TAGS: list[set[str]] = []
 
-FASTQ_ANALYSIS_CASE_TAGS = []
+FASTQ_ANALYSIS_CASE_TAGS: list[set[str]] = []
 
-FASTQ_ANALYSIS_SAMPLE_TAGS = [
+FASTQ_ANALYSIS_SAMPLE_TAGS: list[set[str]] = [
     {"fastq"},
 ]
 
-SARSCOV2_ANALYSIS_CASE_TAGS = [
+SARSCOV2_ANALYSIS_CASE_TAGS: list[set[str]] = [
     {"pangolin"},
     {"ks-delivery"},
 ]
 
-SARSCOV2_ANALYSIS_SAMPLE_TAGS = [
+SARSCOV2_ANALYSIS_SAMPLE_TAGS: list[set[str]] = [
     {"fastq"},
 ]
 
-RNAFUSION_ANALYSIS_CASE_TAGS = [
+RNAFUSION_ANALYSIS_CASE_TAGS: list[set[str]] = [
     {"fusion", "arriba"},
     {"fusion", "star-fusion"},
     {"fusion", "fusioncatcher"},
@@ -160,10 +166,10 @@
     {"delivery-report"},
 ]
 
-RNAFUSION_ANALYSIS_SAMPLE_TAGS = []
+RNAFUSION_ANALYSIS_SAMPLE_TAGS: list[set[str]] = []
 
 
-PIPELINE_ANALYSIS_TAG_MAP = {
+PIPELINE_ANALYSIS_TAG_MAP: dict[Pipeline, dict] = {
     Pipeline.BALSAMIC: {
         "case_tags": BALSAMIC_ANALYSIS_CASE_TAGS,
         "sample_tags": BALSAMIC_ANALYSIS_SAMPLE_TAGS,
@@ -204,5 +210,5 @@
 
 PIPELINE_ANALYSIS_OPTIONS = PIPELINE_ANALYSIS_TAG_MAP.keys()
 
-INBOX_NAME = "inbox"
-OUTBOX_NAME = "outbox"
+INBOX_NAME: str = "inbox"
+OUTBOX_NAME: str = "outbox"
diff --git a/cg/constants/report.py b/cg/constants/report.py
@@ -1,18 +1,18 @@
-# Delivery report constants
-
+"""Delivery report constants."""
 from cg.constants import DataDelivery
 from cg.constants.constants import Pipeline
 
-BALSAMIC_REPORT_ACCREDITED_PANELS = ["gmsmyeloid"]
+BALSAMIC_REPORT_ACCREDITED_PANELS: list[str] = ["gmsmyeloid"]
 
-REPORT_SUPPORTED_PIPELINES = (
+REPORT_SUPPORTED_PIPELINES: tuple[Pipeline, ...] = (
     Pipeline.BALSAMIC,
     Pipeline.BALSAMIC_UMI,
+    Pipeline.BALSAMIC_QC,
     Pipeline.MIP_DNA,
     Pipeline.RNAFUSION,
 )
 
-REPORT_SUPPORTED_DATA_DELIVERY = (
+REPORT_SUPPORTED_DATA_DELIVERY: tuple[DataDelivery, ...] = (
     DataDelivery.ANALYSIS_FILES,
     DataDelivery.ANALYSIS_SCOUT,
     DataDelivery.FASTQ_ANALYSIS,
@@ -22,41 +22,41 @@
     DataDelivery.SCOUT,
 )
 
-NA_FIELD = "N/A"
-YES_FIELD = "Ja"
-NO_FIELD = "Nej"
-PRECISION = 2
+NA_FIELD: str = "N/A"
+YES_FIELD: str = "Ja"
+NO_FIELD: str = "Nej"
+PRECISION: int = 2
 
-REPORT_GENDER = {
+REPORT_GENDER: dict[str, str] = {
     "unknown": "Okänd",
     "female": "Kvinna",
     "male": "Man",
 }
 
-BALSAMIC_ANALYSIS_TYPE = {
+BALSAMIC_ANALYSIS_TYPE: dict[str, str] = {
     "tumor_wgs": "Tumör-endast (helgenomsekvensering)",
     "tumor_normal_wgs": "Tumör/normal (helgenomsekvensering)",
     "tumor_panel": "Tumör-endast (panelsekvensering)",
     "tumor_normal_panel": "Tumör/normal (panelsekvensering)",
 }
 
 # Report required fields (OPTIONAL: "version")
-REQUIRED_REPORT_FIELDS = [
+REQUIRED_REPORT_FIELDS: list[str] = [
     "customer",
     "date",
     "case",
     "accredited",
 ]
 
 # Customer required fields (OPTIONAL: "id")
-REQUIRED_CUSTOMER_FIELDS = [
+REQUIRED_CUSTOMER_FIELDS: list[str] = [
     "name",
     "invoice_address",
     "scout_access",
 ]
 
 # Case required fields
-REQUIRED_CASE_FIELDS = [
+REQUIRED_CASE_FIELDS: list[str] = [
     "name",
     "id",
     "samples",
@@ -65,32 +65,32 @@
 ]
 
 # Application required fields (OPTIONAL: "version", "prep_category", "description", "limitations", "external")
-REQUIRED_APPLICATION_FIELDS = [
+REQUIRED_APPLICATION_FIELDS: list[str] = [
     "tag",
     "accredited",
 ]
 
 # Data analysis required fields
-_REQUIRED_DATA_ANALYSIS_FIELDS = [
+REQUIRED_DATA_ANALYSIS_FIELDS: list[str] = [
     "customer_pipeline",
     "pipeline",
     "pipeline_version",
     "genome_build",
 ]
 
-REQUIRED_DATA_ANALYSIS_MIP_DNA_FIELDS = _REQUIRED_DATA_ANALYSIS_FIELDS + [
+REQUIRED_DATA_ANALYSIS_MIP_DNA_FIELDS: list[str] = REQUIRED_DATA_ANALYSIS_FIELDS + [
     "panels",
 ]
 
-REQUIRED_DATA_ANALYSIS_BALSAMIC_FIELDS = _REQUIRED_DATA_ANALYSIS_FIELDS + [
+REQUIRED_DATA_ANALYSIS_BALSAMIC_FIELDS: list[str] = REQUIRED_DATA_ANALYSIS_FIELDS + [
     "type",
     "variant_callers",
 ]
 
-REQUIRED_DATA_ANALYSIS_RNAFUSION_FIELDS = _REQUIRED_DATA_ANALYSIS_FIELDS
+REQUIRED_DATA_ANALYSIS_RNAFUSION_FIELDS: list[str] = REQUIRED_DATA_ANALYSIS_FIELDS
 
 # Sample required fields
-_REQUIRED_SAMPLE_FIELDS = [
+_REQUIRED_SAMPLE_FIELDS: list[str] = [
     "name",
     "id",
     "ticket",
@@ -102,48 +102,50 @@
     "timestamps",
 ]
 
-REQUIRED_SAMPLE_MIP_DNA_FIELDS = _REQUIRED_SAMPLE_FIELDS + [
+REQUIRED_SAMPLE_MIP_DNA_FIELDS: list[str] = _REQUIRED_SAMPLE_FIELDS + [
     "status",
 ]
 
-REQUIRED_SAMPLE_BALSAMIC_FIELDS = _REQUIRED_SAMPLE_FIELDS + [
+REQUIRED_SAMPLE_BALSAMIC_FIELDS: list[str] = _REQUIRED_SAMPLE_FIELDS + [
     "tumour",
 ]
 
-REQUIRED_SAMPLE_RNAFUSION_FIELDS = REQUIRED_SAMPLE_BALSAMIC_FIELDS
+REQUIRED_SAMPLE_RNAFUSION_FIELDS: list[str] = REQUIRED_SAMPLE_BALSAMIC_FIELDS
 
 # Methods required fields (OPTIONAL: "library_prep", "sequencing")
-REQUIRED_SAMPLE_METHODS_FIELDS = []
+REQUIRED_SAMPLE_METHODS_FIELDS: list[str] = []
 
 # Timestamp required fields (OPTIONAL: "prepared_at", "reads_updated_at")
-REQUIRED_SAMPLE_TIMESTAMP_FIELDS = [
+REQUIRED_SAMPLE_TIMESTAMP_FIELDS: list[str] = [
     "ordered_at",
     "received_at",  # Optional for external samples
 ]
 
 # Metadata required fields
-_REQUIRED_SAMPLE_METADATA_FIELDS = [
+_REQUIRED_SAMPLE_METADATA_FIELDS: list[str] = [
     "million_read_pairs",
     "duplicates",
 ]
 
-REQUIRED_SAMPLE_METADATA_MIP_DNA_WGS_FIELDS = _REQUIRED_SAMPLE_METADATA_FIELDS + [
+REQUIRED_SAMPLE_METADATA_MIP_DNA_WGS_FIELDS: list[str] = _REQUIRED_SAMPLE_METADATA_FIELDS + [
     "gender",
     "mapped_reads",
     "mean_target_coverage",
     "pct_10x",
 ]
 
-REQUIRED_SAMPLE_METADATA_MIP_DNA_FIELDS = REQUIRED_SAMPLE_METADATA_MIP_DNA_WGS_FIELDS + [
+REQUIRED_SAMPLE_METADATA_MIP_DNA_FIELDS: list[str] = REQUIRED_SAMPLE_METADATA_MIP_DNA_WGS_FIELDS + [
     "bait_set",
 ]
 
-_REQUIRED_SAMPLE_METADATA_BALSAMIC_FIELDS = _REQUIRED_SAMPLE_METADATA_FIELDS + [
+_REQUIRED_SAMPLE_METADATA_BALSAMIC_FIELDS: list[str] = _REQUIRED_SAMPLE_METADATA_FIELDS + [
     "mean_insert_size",
     "fold_80",
 ]
 
-REQUIRED_SAMPLE_METADATA_BALSAMIC_TARGETED_FIELDS = _REQUIRED_SAMPLE_METADATA_BALSAMIC_FIELDS + [
+REQUIRED_SAMPLE_METADATA_BALSAMIC_TARGETED_FIELDS: list[
+    str
+] = _REQUIRED_SAMPLE_METADATA_BALSAMIC_FIELDS + [
     "bait_set",
     "bait_set_version",
     "median_target_coverage",
@@ -152,20 +154,21 @@
     "gc_dropout",
 ]
 
-REQUIRED_SAMPLE_METADATA_BALSAMIC_TO_WGS_FIELDS = _REQUIRED_SAMPLE_METADATA_BALSAMIC_FIELDS + [
+REQUIRED_SAMPLE_METADATA_BALSAMIC_TO_WGS_FIELDS: list[
+    str
+] = _REQUIRED_SAMPLE_METADATA_BALSAMIC_FIELDS + [
     "median_coverage",
     "pct_60x",
     "pct_reads_improper_pairs",
 ]
 
-REQUIRED_SAMPLE_METADATA_BALSAMIC_TN_WGS_FIELDS = (
-    REQUIRED_SAMPLE_METADATA_BALSAMIC_TO_WGS_FIELDS
-    + [
-        "pct_15x",
-    ]
-)
+REQUIRED_SAMPLE_METADATA_BALSAMIC_TN_WGS_FIELDS: list[
+    str
+] = REQUIRED_SAMPLE_METADATA_BALSAMIC_TO_WGS_FIELDS + [
+    "pct_15x",
+]
 
-REQUIRED_SAMPLE_METADATA_RNAFUSION_FIELDS = _REQUIRED_SAMPLE_METADATA_FIELDS + [
+REQUIRED_SAMPLE_METADATA_RNAFUSION_FIELDS: list[str] = _REQUIRED_SAMPLE_METADATA_FIELDS + [
     "bias_5_3",
     "gc_content",
     "input_amount",