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Support BCL Convert 4.2.7 #124

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merged 8 commits into from
Sep 3, 2024
Merged

Support BCL Convert 4.2.7 #124

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5334e0a
bclconvert reports: handle missing files
pdiakumis Aug 27, 2024
869db2c
alignqc: remove aws-vault
pdiakumis Aug 28, 2024
1f1040d
bclconvert reports: add Adapter_Cycle_Metrics.csv
pdiakumis Aug 30, 2024
b14f713
refactor bclc reports parsers
pdiakumis Aug 30, 2024
51bcd05
refactor bclc reports parsers
pdiakumis Aug 31, 2024
aec1156
bclc reports: support demultiplextilestats, qualitymetrics, qualityti…
pdiakumis Sep 1, 2024
9b18a99
keep support for bclconvert 3.7.5
pdiakumis Sep 3, 2024
6381b93
bclc: fix old parsers
pdiakumis Sep 3, 2024
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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
# R specific hooks: https://github.com/lorenzwalthert/precommit
repos:
- repo: https://github.com/lorenzwalthert/precommit
rev: v0.4.2
rev: v0.4.3
hooks:
- id: style-files
args: [--style_pkg=styler, --style_fun=tidyverse_style]
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2 changes: 1 addition & 1 deletion NAMESPACE
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Expand Up @@ -3,6 +3,7 @@
S3method(read,File)
export(BcftoolsStatsFile)
export(BclconvertReports)
export(BclconvertReports375)
export(FastqcMetricsFile)
export(File)
export(FragmentLengthHistFile)
Expand Down Expand Up @@ -33,7 +34,6 @@ export(UmQcSumFile)
export(UmSigsSnvFile)
export(VCMetricsFile)
export(Wf)
export(Wf_bcl_convert)
export(Wf_tso_ctdna_tumor_only)
export(WgsContigMeanCovFile)
export(WgsCoverageMetricsFile)
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