add(rnafusion support)

janus/constants/FileTag.py

@@ -12,3 +12,6 @@ class FileTag(StrEnum):
     FASTP: str = "fastp"
     SOMALIER: str = "somalier"
     SAMTOOLS_STATS: str = "samtools-stats"
+    GENERAL_STATS: str = "general-stats"
+    STAR: str = "star"
+    RNA_SEQ_METRICS: str = "picard-rnaseq"

janus/dto/collect_qc_response.py

@@ -1,10 +1,10 @@
-from pydantic import BaseModel
-
 from janus.models.workflow.balsamic import Balsamic
+from janus.models.workflow.rnafusion import RNAFusion
+from pydantic import BaseModel
 
 
 class CollectQCResponse(BaseModel):
     """Collect QC response model."""
 
     case_id: str
-    case_info: Balsamic
+    case_info: Balsamic | RNAFusion

janus/mappers/tag_to_models.py

@@ -1,25 +1,26 @@
-from enum import Enum
-
 from janus.constants.FileTag import FileTag
 from janus.models.multiqc.models import (
-    PicardHsMetrics,
-    PicardWGSMetrics,
+    Fastp,
+    PicardAlignmentSummary,
     PicardDuplicates,
+    PicardHsMetrics,
     PicardInsertSize,
-    PicardAlignmentSummary,
-    Fastp,
-    Somalier,
+    PicardRNASeqMetrics,
+    PicardWGSMetrics,
+    RNAFusionGeneralStats,
     SamtoolsStats,
+    Somalier,
 )
 
-
 tag_to_model = {
-    FileTag.HS_METRICS: PicardHsMetrics,
-    FileTag.WGS_METRICS: PicardWGSMetrics,
+    FileTag.ALIGNMENT_SUMMARY_METRICS: PicardAlignmentSummary,
     FileTag.DUPLICATES: PicardDuplicates,
-    FileTag.INSERT_SIZE: PicardInsertSize,
     FileTag.FASTP: Fastp,
-    FileTag.ALIGNMENT_SUMMARY_METRICS: PicardAlignmentSummary,
-    FileTag.SOMALIER: Somalier,
+    FileTag.GENERAL_STATS: RNAFusionGeneralStats,
+    FileTag.HS_METRICS: PicardHsMetrics,
+    FileTag.INSERT_SIZE: PicardInsertSize,
+    FileTag.RNA_SEQ_METRICS: PicardRNASeqMetrics,
     FileTag.SAMTOOLS_STATS: SamtoolsStats,
+    FileTag.SOMALIER: Somalier,
+    FileTag.WGS_METRICS: PicardWGSMetrics,
 }

janus/mappers/tag_to_parse_function.py

@@ -1,14 +1,21 @@
 from janus.constants.FileTag import FileTag
-from janus.services.parser import parse_sample_metrics, parse_fastp, parse_somalier
-
+from janus.services.parser import (
+    parse_fastp,
+    parse_general_stats,
+    parse_sample_metrics,
+    parse_somalier,
+)
 
 tag_to_parse_function: dict = {
-    FileTag.HS_METRICS: parse_sample_metrics,
-    FileTag.WGS_METRICS: parse_sample_metrics,
-    FileTag.DUPLICATES: parse_sample_metrics,
-    FileTag.INSERT_SIZE: parse_sample_metrics,
     FileTag.ALIGNMENT_SUMMARY_METRICS: parse_sample_metrics,
+    FileTag.DUPLICATES: parse_sample_metrics,
     FileTag.FASTP: parse_fastp,
-    FileTag.SOMALIER: parse_somalier,
+    FileTag.GENERAL_STATS: parse_general_stats,
+    FileTag.HS_METRICS: parse_sample_metrics,
+    FileTag.INSERT_SIZE: parse_sample_metrics,
+    FileTag.RNA_SEQ_METRICS: parse_sample_metrics,
     FileTag.SAMTOOLS_STATS: parse_sample_metrics,
+    FileTag.SOMALIER: parse_somalier,
+    FileTag.STAR: parse_sample_metrics,
+    FileTag.WGS_METRICS: parse_sample_metrics,
 }

janus/models/multiqc/models.py

@@ -13,11 +13,15 @@ def validate_float(value):
 class PicardDuplicates(BaseModel):
     unpaired_reads_examined: float = Field(..., alias="UNPAIRED_READS_EXAMINED")
     read_pairs_examined: float = Field(..., alias="READ_PAIRS_EXAMINED")
-    secondary_or_supplementary_reads: float = Field(..., alias="SECONDARY_OR_SUPPLEMENTARY_RDS")
+    secondary_or_supplementary_reads: float = Field(
+        ..., alias="SECONDARY_OR_SUPPLEMENTARY_RDS"
+    )
     unmapped_reads: float = Field(..., alias="UNMAPPED_READS")
     unpaired_read_duplicates: float = Field(..., alias="UNPAIRED_READ_DUPLICATES")
     read_pair_duplicates: float = Field(..., alias="READ_PAIR_DUPLICATES")
-    read_pair_optical_duplicates: float = Field(..., alias="READ_PAIR_OPTICAL_DUPLICATES")
+    read_pair_optical_duplicates: float = Field(
+        ..., alias="READ_PAIR_OPTICAL_DUPLICATES"
+    )
     percent_duplication: float = Field(..., alias="PERCENT_DUPLICATION")
     estimated_library_size: float = Field(..., alias="ESTIMATED_LIBRARY_SIZE")
 
@@ -193,7 +197,9 @@ class PicardHsMetrics(BaseModel):
     het_snp_sensitivity: float = Field(..., alias="HET_SNP_SENSITIVITY")
     het_snp_q: float = Field(..., alias="HET_SNP_Q")
 
-    validate_float = validator("fold_80_base_penalty", pre=True, always=True)(validate_float)
+    validate_float = validator("fold_80_base_penalty", pre=True, always=True)(
+        validate_float
+    )
 
 
 class PicardAlignmentSummary(BaseModel):
@@ -228,7 +234,9 @@ class PicardAlignmentSummary(BaseModel):
     pct_adapter: float = Field(..., alias="PCT_ADAPTER")
     pct_softclip: float = Field(..., alias="PCT_SOFTCLIP")
     pct_hardclip: float = Field(..., alias="PCT_HARDCLIP")
-    avg_pos_3prime_softclip_length: float = Field(..., alias="AVG_POS_3PRIME_SOFTCLIP_LENGTH")
+    avg_pos_3prime_softclip_length: float = Field(
+        ..., alias="AVG_POS_3PRIME_SOFTCLIP_LENGTH"
+    )
 
 
 class SomalierIndividual(BaseModel):
@@ -368,11 +376,19 @@ class PicardRNASeqMetrics(BaseModel):
     ignored_reads: float = Field(..., alias="IGNORED_READS")
     correct_strand_reads: float = Field(..., alias="CORRECT_STRAND_READS")
     incorrect_strand_reads: float = Field(..., alias="INCORRECT_STRAND_READS")
-    num_r1_transcript_strand_reads: float = Field(..., alias="NUM_R1_TRANSCRIPT_STRAND_READS")
-    num_r2_transcript_strand_reads: float = Field(..., alias="NUM_R2_TRANSCRIPT_STRAND_READS")
+    num_r1_transcript_strand_reads: float = Field(
+        ..., alias="NUM_R1_TRANSCRIPT_STRAND_READS"
+    )
+    num_r2_transcript_strand_reads: float = Field(
+        ..., alias="NUM_R2_TRANSCRIPT_STRAND_READS"
+    )
     num_unexplained_reads: float = Field(..., alias="NUM_UNEXPLAINED_READS")
-    pct_r1_transcript_strand_reads: float = Field(..., alias="PCT_R1_TRANSCRIPT_STRAND_READS")
-    pct_r2_transcript_strand_reads: float = Field(..., alias="PCT_R2_TRANSCRIPT_STRAND_READS")
+    pct_r1_transcript_strand_reads: float = Field(
+        ..., alias="PCT_R1_TRANSCRIPT_STRAND_READS"
+    )
+    pct_r2_transcript_strand_reads: float = Field(
+        ..., alias="PCT_R2_TRANSCRIPT_STRAND_READS"
+    )
     pct_ribosomal_bases: float = Field(..., alias="PCT_RIBOSOMAL_BASES")
     pct_coding_bases: float = Field(..., alias="PCT_CODING_BASES")
     pct_utr_bases: float = Field(..., alias="PCT_UTR_BASES")
@@ -384,7 +400,9 @@ class PicardRNASeqMetrics(BaseModel):
     median_cv_coverage: float = Field(..., alias="MEDIAN_CV_COVERAGE")
     median_5prime_bias: float = Field(..., alias="MEDIAN_5PRIME_BIAS")
     median_3prime_bias: float = Field(..., alias="MEDIAN_3PRIME_BIAS")
-    median_5prime_to_3prime_bias: float = Field(..., alias="MEDIAN_5PRIME_TO_3PRIME_BIAS")
+    median_5prime_to_3prime_bias: float = Field(
+        ..., alias="MEDIAN_5PRIME_TO_3PRIME_BIAS"
+    )
     library: str = Field(..., alias="LIBRARY")
     read_group: str = Field(..., alias="READ_GROUP")
     pf_not_aligned_bases: float = Field(..., alias="PF_NOT_ALIGNED_BASES")
@@ -419,7 +437,7 @@ class STARAlignment(BaseModel):
     unmapped_other: float
 
 
-class RNAfusionGeneralStats(BaseModel):
+class RNAFusionGeneralStatsSummary(BaseModel):
     insert_size_sum_median: float = Field(
         ...,
         alias="Picard_InsertSizeMetrics_mqc_generalstats_picard_insertsizemetrics_summed_median",
@@ -428,7 +446,7 @@ class RNAfusionGeneralStats(BaseModel):
         ...,
         alias="Picard_InsertSizeMetrics_mqc_generalstats_picard_insertsizemetrics_summed_mean",
     )
-    percent_duplication: float = Field(
+    percent_duplication_picard: float = Field(
         ...,
         alias="Picard_MarkDuplicates_mqc_generalstats_picard_mark_duplicates_PERCENT_DUPLICATION",
     )
@@ -443,7 +461,12 @@ class RNAfusionGeneralStats(BaseModel):
     percent_uniquely_mapped: float = Field(
         ..., alias="STAR_mqc_generalstats_star_uniquely_mapped_percent"
     )
-    uniquely_mapped: float = Field(..., alias="STAR_mqc_generalstats_star_uniquely_mapped")
+    uniquely_mapped: float = Field(
+        ..., alias="STAR_mqc_generalstats_star_uniquely_mapped"
+    )
+    percent_duplication_fastq: float = Field(
+        ..., alias="fastp_mqc-generalstats-fastp-pct_duplication"
+    )
     after_filtering_q30_rate: float = Field(
         ..., alias="fastp_mqc_generalstats_fastp_after_filtering_q30_rate"
     )
@@ -456,5 +479,75 @@ class RNAfusionGeneralStats(BaseModel):
     after_filtering_gc_content: float = Field(
         ..., alias="fastp_mqc_generalstats_fastp_after_filtering_gc_content"
     )
-    pct_surviving: float = Field(..., alias="fastp_mqc_generalstats_fastp_pct_surviving")
+    pct_surviving: float = Field(
+        ..., alias="fastp_mqc_generalstats_fastp_pct_surviving"
+    )
     pct_adapter: float = Field(..., alias="fastp_mqc_generalstats_fastp_pct_adapter")
+
+
+class RNAFusionGeneralStatsRead(BaseModel):
+    percent_duplicates: float = Field(
+        alias="FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates"
+    )
+    percent_gc: float = Field(
+        alias="FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc"
+    )
+    avg_sequence_length: float = Field(
+        alias="FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length"
+    )
+    median_sequence_length: int = Field(
+        alias="FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length"
+    )
+    percent_fails: float = Field(
+        alias="FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails"
+    )
+    total_sequences: float = Field(
+        alias="FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences"
+    )
+
+
+class RNAFusionGeneralStatsTrimmedRead(BaseModel):
+    raw_percent_duplicates: float = Field(
+        alias="FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates"
+    )
+    raw_percent_gc: float = Field(
+        alias="FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc"
+    )
+    raw_avg_sequence_length: float = Field(
+        alias="FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length"
+    )
+    raw_median_sequence_length: int = Field(
+        alias="FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length"
+    )
+    raw_percent_fails: float = Field(
+        alias="FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails"
+    )
+    raw_total_sequences: float = Field(
+        alias="FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences"
+    )
+    trimmed_percent_duplicates: float = Field(
+        alias="FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates"
+    )
+    trimmed_percent_gc: float = Field(
+        alias="FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc"
+    )
+    trimmed_avg_sequence_length: float = Field(
+        alias="FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length"
+    )
+    trimmed_median_sequence_length: int = Field(
+        alias="FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length"
+    )
+    trimmed_percent_fails: float = Field(
+        alias="FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails"
+    )
+    trimmed_total_sequences: float = Field(
+        alias="FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences"
+    )
+
+
+class RNAFusionGeneralStats(BaseModel):
+    summary: RNAFusionGeneralStatsSummary
+    read_1: RNAFusionGeneralStatsRead
+    read_1_trimmed: RNAFusionGeneralStatsTrimmedRead
+    read_2: RNAFusionGeneralStatsRead
+    read_2_trimmed: RNAFusionGeneralStatsTrimmedRead

janus/models/workflow/rnafusion.py

@@ -0,0 +1,28 @@
+"""Module for the RNAfusion workflow model."""
+
+from pydantic import BaseModel, Field
+
+from janus.constants.FileTag import FileTag
+from janus.dto.collect_qc_request import WorkflowInfo
+from janus.models.multiqc.models import (
+    PicardDuplicates,
+    PicardInsertSize,
+    Fastp,
+    STARAlignment,
+    PicardRNASeqMetrics,
+    RNAFusionGeneralStats,
+)
+
+
+class RNAFusionSample(BaseModel):
+    duplicates: PicardDuplicates = Field(..., alias=FileTag.DUPLICATES)
+    rna_seq_metrics: PicardRNASeqMetrics
+    insert_size: PicardInsertSize = Field(..., alias=FileTag.INSERT_SIZE)
+    star_alignment: STARAlignment
+    fastp: Fastp = Field(..., alias=FileTag.FASTP)
+    general_stats: RNAFusionGeneralStats
+
+
+class RNAFusion(BaseModel):
+    samples: list[RNAFusionSample]
+    workflow: WorkflowInfo

janus/server/api.py

@@ -19,11 +19,20 @@
     response_model_by_alias=False,
     response_model_exclude_none=True,
 )
-def collect_qc(collect_request: CollectQCRequest = Body(...)) -> CollectQCResponse | JSONResponse:
+def collect_qc(
+    collect_request: CollectQCRequest = Body(...),
+) -> CollectQCResponse | JSONResponse:
     """Collect qc metrics for the external request."""
     service = CollectQCService(collect_request)
     try:
-        collected_qc_metrics: CollectQCResponse = service.collect_qc_metrics_for_request()
+        collected_qc_metrics: CollectQCResponse = (
+            service.collect_qc_metrics_for_request()
+        )
         return collected_qc_metrics
-    except (ValueError, FileNotFoundError, ValidationError, WorkflowNotSupportedError) as error:
+    except (
+        ValueError,
+        FileNotFoundError,
+        ValidationError,
+        WorkflowNotSupportedError,
+    ) as error:
         return JSONResponse(content=repr(error), status_code=HTTPStatus.BAD_REQUEST)

janus/services/collect_qc_service.py

@@ -104,5 +104,7 @@ def collect_qc_metrics_for_request(self) -> CollectQCResponse:
                 f"Janus does not support parsing of qc metrics for {self.request.workflow_info.workflow})"
             )
         case_info: callable = self.get_case_info_for_workflow()
-        qc_metrics = CollectQCResponse(case_id=self.request.case_id, case_info=case_info)
+        qc_metrics = CollectQCResponse(
+            case_id=self.request.case_id, case_info=case_info
+        )
         return qc_metrics