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DRAGEN: new module ROH Metrics #1912

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DRAGEN: new module ROH Metrics #1912

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1283c1d
Update search_patterns.yaml
Just-Roma Apr 25, 2023
93c72c3
Update dragen.py
Just-Roma Apr 25, 2023
594148d
Update utils.py
Just-Roma Apr 25, 2023
e67a38d
Add files via upload
Just-Roma Apr 25, 2023
5ca08d5
Update roh_metrics.py
Just-Roma Apr 25, 2023
af337c8
Update roh_metrics.py
Just-Roma Apr 25, 2023
0618f9c
Merge branch 'master' into DRAGEN-New-Module-ROH-Metrics
Just-Roma May 31, 2023
d828eac
Update roh_metrics.py
Just-Roma Jun 3, 2023
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5 changes: 5 additions & 0 deletions multiqc/modules/dragen/dragen.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
from .ploidy_estimation_metrics import DragenPloidyEstimationMetrics
from .rna_quant_metrics import DragenRnaQuantMetrics
from .rna_transcript_cov import DragenRnaTranscriptCoverage
from .roh_metrics import DragenROHMetrics
from .sc_atac_metrics import DragenScAtacMetrics
from .sc_rna_metrics import DragenScRnaMetrics
from .time_metrics import DragenTimeMetrics
Expand All @@ -20,6 +21,7 @@


class MultiqcModule(
DragenROHMetrics,
DragenMappingMetics,
DragenFragmentLength,
DragenPloidyEstimationMetrics,
Expand Down Expand Up @@ -73,6 +75,9 @@ def __init__(self):
samples_found |= self.add_ploidy_estimation_metrics()
# <output prefix>.ploidy_estimation_metrics.csv - add just Ploidy estimation into gen stats

samples_found |= self.add_roh_metrics()
# <output-file-prefix>.roh_metrics.csv

self.collect_overall_mean_cov_data()
# <output prefix>.<coverage region prefix>_overall_mean_cov<arbitrary suffix>.csv
# This data will be used by in the DragenCoverageMetrics.
Expand Down