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rnafusion HK tags as constants #2759

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merged 5 commits into from
Dec 13, 2023
Merged

rnafusion HK tags as constants #2759

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4f404f0
rnafusion delivery tags as constants
fevac Dec 11, 2023
d4479a0
add missing import
fevac Dec 11, 2023
9d8139b
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fevac Dec 11, 2023
8ef93d8
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fevac Dec 13, 2023
0272172
Merge branch 'master' into delivery_constants
fevac Dec 13, 2023
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53 changes: 27 additions & 26 deletions cg/constants/delivery.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
"""Constants for delivery."""

from cg.constants.constants import Pipeline
from cg.constants.housekeeper_tags import AlignmentFileTag, AnalysisTag, HK_DELIVERY_REPORT_TAG

ONLY_ONE_CASE_PER_TICKET: list[Pipeline] = [
Pipeline.FASTQ,
Expand Down Expand Up @@ -37,8 +38,8 @@
]

BALSAMIC_ANALYSIS_SAMPLE_TAGS: list[set[str]] = [
{"cram"},
{"cram-index"},
{AlignmentFileTag.CRAM},
{AlignmentFileTag.CRAM_INDEX},
]

BALSAMIC_QC_ANALYSIS_CASE_TAGS: list[set[str]] = [
Expand Down Expand Up @@ -95,10 +96,10 @@
]

MIP_DNA_ANALYSIS_SAMPLE_TAGS: list[set[str]] = [
{"bam"},
{"bam-index"},
{"cram"},
{"cram-index"},
{AlignmentFileTag.BAM},
{AlignmentFileTag.BAM_BAI},
{AlignmentFileTag.CRAM},
{AlignmentFileTag.CRAM_INDEX},
]

MIP_RNA_ANALYSIS_CASE_TAGS: list[set[str]] = [
Expand All @@ -114,12 +115,12 @@
]

MIP_RNA_ANALYSIS_SAMPLE_TAGS: list[set[str]] = [
{"fusion", "star-fusion"},
{"fusion", "arriba"},
{"cram"},
{"cram-index"},
{"fusion", "vcf"},
{"fusion", "vcf-index"},
{AnalysisTag.FUSION, AnalysisTag.STARFUSION},
{AnalysisTag.FUSION, AnalysisTag.ARRIBA},
{AlignmentFileTag.CRAM},
{AlignmentFileTag.CRAM_INDEX},
{AnalysisTag.FUSION, "vcf"},
{AnalysisTag.FUSION, "vcf-index"},
{"salmon-quant"},
]

Expand Down Expand Up @@ -150,23 +151,23 @@
]

RNAFUSION_ANALYSIS_CASE_TAGS: list[set[str]] = [
{"fusion", "arriba"},
{"fusion", "star-fusion"},
{"fusion", "fusioncatcher"},
{"fusioncatcher-summary"},
{"fusioninspector"},
{"fusionreport", "research"},
{"fusioninspector-html", "research"},
{"arriba-visualisation", "research"},
{"multiqc-html", "rna"},
{"delivery-report"},
{"vcf-fusion"},
{"gene-counts"},
{AnalysisTag.FUSION, AnalysisTag.ARRIBA},
{AnalysisTag.FUSION, AnalysisTag.STARFUSION},
{AnalysisTag.FUSION, AnalysisTag.FUSIONCATCHER},
{AnalysisTag.FUSIONCATCHER_SUMMARY},
{AnalysisTag.FUSIONINSPECTOR},
{AnalysisTag.FUSIONREPORT, AnalysisTag.RESEARCH},
{AnalysisTag.FUSIONINSPECTOR_HTML, AnalysisTag.RESEARCH},
{AnalysisTag.ARRIBA_VISUALIZATION, AnalysisTag.RESEARCH},
{AnalysisTag.MULTIQC_HTML, AnalysisTag.RNA},
{HK_DELIVERY_REPORT_TAG},
{AnalysisTag.VCF_FUSION},
{AnalysisTag.GENE_COUNTS},
]

RNAFUSION_ANALYSIS_SAMPLE_TAGS: list[set[str]] = [
{"cram"},
{"cram-index"},
{AlignmentFileTag.CRAM},
{AlignmentFileTag.CRAM_INDEX},
]


Expand Down
19 changes: 19 additions & 0 deletions cg/constants/housekeeper_tags.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,25 @@ class SequencingFileTag(StrEnum):
HK_DELIVERY_REPORT_TAG = "delivery-report"


class AnalysisTag(StrEnum):
"""Tags for analysis files."""

ARRIBA: str = "arriba"
ARRIBA_VISUALIZATION: str = "arriba-visualisation"
FUSION: str = "fusion"
FUSIONCATCHER: str = "fusioncatcher"
FUSIONCATCHER_SUMMARY: str = "fusioncatcher-summary"
FUSIONINSPECTOR: str = "fusioninspector"
FUSIONINSPECTOR_HTML: str = "fusioninspector-html"
FUSIONREPORT: str = "fusionreport"
GENE_COUNTS: str = "gene-counts"
MULTIQC_HTML: str = "multiqc-html"
RESEARCH: str = "research"
RNA: str = "rna"
STARFUSION: str = "star-fusion"
VCF_FUSION: str = "vcf-fusion"


class HkMipAnalysisTag:
CONFIG: list[str] = ["mip-config"]
QC_METRICS: list[str] = ["qc-metrics", "deliverable"]
Expand Down
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