Merge pull request #77 from ShawHahnLab/release-0.0.2

Version 0.0.2
ShawHahnLab · Aug 4, 2020 · df6ca03 · df6ca03
2 parents bd7a97c + ba09978
commit df6ca03
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,35 @@
+# Changelog
+
+## 0.0.2 - 2020-08-04
+
+### Added
+
+ * Support for custom task classes ([#56])
+ * Timeout feature for manual and geneious tasks ([#66])
+ * Flow cell ID property for Illumina run objects ([#75])
+
+### Changed
+
+ * Append flow cell ID from each run to project workdir names ([#76])
+ * Ignore empty rows and columns when parsing metadata.csv files ([#73])
+ * Use chunked Box.com uploader for more reliable uploads of large files ([#69])
+ * Handle missing Experiment Name in sample sheets ([#59])
+
+### Fixed
+
+ * Catch and log errors parsing metadata.csv files during project setup ([#74])
+ * Handle missing FASTQ file case during project setup ([#63])
+
+[#76]: https://github.com/ShawHahnLab/umbra/pull/76
+[#75]: https://github.com/ShawHahnLab/umbra/pull/75
+[#74]: https://github.com/ShawHahnLab/umbra/pull/74
+[#73]: https://github.com/ShawHahnLab/umbra/pull/73
+[#69]: https://github.com/ShawHahnLab/umbra/pull/69
+[#66]: https://github.com/ShawHahnLab/umbra/pull/66
+[#63]: https://github.com/ShawHahnLab/umbra/pull/63
+[#59]: https://github.com/ShawHahnLab/umbra/pull/59
+[#56]: https://github.com/ShawHahnLab/umbra/pull/56
+
+## 0.0.1 - 2019-06-03
+
+First named release
diff --git a/demo/demo_2.sh b/demo/demo_2.sh
@@ -15,7 +15,7 @@ function run_demo_2 {
 
 # Check that we get exactly the expected files.
 function test_files {
-	local dir_work=$SEQROOT/processed/2018-01-01-STR-Jesse
+	local dir_work=$SEQROOT/processed/2018-01-01-STR-Jesse-XXXXX
 	diff <((
 	for task in trim metadata package upload email; do
 		echo "$dir_work/RunDiagnostics/Logs/log_${task}.txt"

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="umbra",
-    version="0.0.1",
+    version="0.0.2",
     description="A package and executable for handling Illumina sequencing runs",
     long_description=long_description,
     long_description_content_type="text/markdown",

diff --git a/test_umbra/data/experiments/Partials_1_1_18/metadata_emptycols.csv b/test_umbra/data/experiments/Partials_1_1_18/metadata_emptycols.csv
@@ -0,0 +1,5 @@
+Sample_Name,Project,Contacts,Tasks,,
+1086S1_01,STR,Jesse <[email protected]>,trim,,
+1086S1_02,STR,Jesse <[email protected]>,trim,,
+1086S1_03,Something Else,Someone <[email protected]>,,,
+1086S1_04,Something Else,"Someone <[email protected]>, Jesse Connell <[email protected]>",,,
diff --git a/test_umbra/data/experiments/Partials_1_1_18/metadata_emptyrows.csv b/test_umbra/data/experiments/Partials_1_1_18/metadata_emptyrows.csv
@@ -0,0 +1,7 @@
+Sample_Name,Project,Contacts,Tasks
+1086S1_01,STR,Jesse <[email protected]>,trim
+1086S1_02,STR,Jesse <[email protected]>,trim
+,,,
+,,,
+1086S1_03,Something Else,Someone <[email protected]>,
+1086S1_04,Something Else,"Someone <[email protected]>, Jesse Connell <[email protected]>",
diff --git a/test_umbra/data/other/tasks/task_extra.py b/test_umbra/data/other/tasks/task_extra.py
@@ -0,0 +1,9 @@
+"Example of an extra Task."
+
+from umbra import task
+
+class TaskExtra(task.Task):
+    "Only override the run method, all else is defaults."
+
+    def run(self):
+        "Do nothing."
diff --git a/test_umbra/data/other/tasks/task_other.py b/test_umbra/data/other/tasks/task_other.py
@@ -0,0 +1,9 @@
+"Example of an extra Task."
+
+from umbra import task
+
+class TaskOther(task.Task):
+    "Only override the run method, all else is defaults."
+
+    def run(self):
+        "Do nothing."
diff --git a/test_umbra/data/runs/180110_M00000_0000_000000000-XXXXX/CompletedJobInfo.xml b/test_umbra/data/runs/180110_M00000_0000_000000000-XXXXX/CompletedJobInfo.xml
@@ -0,0 +1,80 @@
+<?xml version="1.0"?>
+<AnalysisJobInfo xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Version="0">
+  <AlignmentFolder>D:\Illumina\MiSeqAnalysis\180110_M00000_0000_000000000-XXXXX\Data\Intensities\BaseCalls\Alignment</AlignmentFolder>
+  <CompletionTime>2018-01-02T06:48:32.608024-04:00</CompletionTime>
+  <RTARunInfo Version="2">
+    <Run Id="180110_M00000_0000_000000000-XXXXX" Number="000">
+      <Flowcell>000000000-XXXXX</Flowcell>
+      <Instrument>M00000</Instrument>
+      <Date>180110</Date>
+      <Reads>
+        <Read NumCycles="151" StartFromCycle="1" EndWithCycle="151" IsIndexedRead="N" />
+        <Read NumCycles="8" StartFromCycle="1" EndWithCycle="8" IsIndexedRead="Y" />
+        <Read NumCycles="8" StartFromCycle="1" EndWithCycle="8" IsIndexedRead="Y" />
+        <Read NumCycles="151" StartFromCycle="1" EndWithCycle="151" IsIndexedRead="N" />
+      </Reads>
+      <FlowcellLayout LaneCount="1" SurfaceCount="1" SwathCount="1" TileCount="2" />
+      <AlignToPhiX />
+    </Run>
+  </RTARunInfo>
+  <RunFolder>D:\Illumina\MiSeqAnalysis\180110_M00000_0000_000000000-XXXXX</RunFolder>
+  <Sheet>
+    <Type>MiSeq</Type>
+    <WorkflowType>GenerateFASTQ</WorkflowType>
+    <Header>
+      <Chemistry>Amplicon</Chemistry>
+      <Date>1_1_18</Date>
+    </Header>
+  </Sheet>
+  <StartTime>2018-01-02T06:48:22.0480092-04:00</StartTime>
+  <Workflow>
+    <WorkflowSettings>
+      <AdapterSequences />
+      <AdapterSequences2 />
+      <TrimFastq>false</TrimFastq>
+      <FastQInput>false</FastQInput>
+      <StitchReads>false</StitchReads>
+      <MaximumThreadCount>0</MaximumThreadCount>
+      <ReadTrimQualityScoreLevel>0</ReadTrimQualityScoreLevel>
+      <ReverseComplement>false</ReverseComplement>
+      <VarCallerSettings>
+        <Filters>
+          <FilterOutSingleProbePoolVariants>false</FilterOutSingleProbePoolVariants>
+          <FilterOutSingleStrandVariants>false</FilterOutSingleStrandVariants>
+          <IndelRepeatFilterCutoff>8</IndelRepeatFilterCutoff>
+          <MinQScore>0</MinQScore>
+          <MinimumCoverageDepthEmitCutoff>-1</MinimumCoverageDepthEmitCutoff>
+          <MinimumDepthCutoff>-1</MinimumDepthCutoff>
+          <MinimumGQCutoff>0</MinimumGQCutoff>
+          <MinimumGQXCutoff>0</MinimumGQXCutoff>
+          <MinimumMQCutoff>-1</MinimumMQCutoff>
+          <MinimumQDCutoff>0</MinimumQDCutoff>
+          <MinimumQualCutoff>-1</MinimumQualCutoff>
+          <MinimumQualityEmitCutoff>-1</MinimumQualityEmitCutoff>
+          <OnlyCallInROI>false</OnlyCallInROI>
+          <OnlyUseProperPairs>false</OnlyUseProperPairs>
+          <CallPhasedSNVs>false</CallPhasedSNVs>
+          <StrandBiasFilterCutoff>0</StrandBiasFilterCutoff>
+          <MaxSizePhasedSNV>100</MaxSizePhasedSNV>
+          <QualityModel>Poisson</QualityModel>
+          <VariantFrequencyEmitCutoff>0.1</VariantFrequencyEmitCutoff>
+          <VariantFrequencyFilterCutoff>0.2</VariantFrequencyFilterCutoff>
+          <FilterOffTargetVariants>false</FilterOffTargetVariants>
+        </Filters>
+        <Annotation>MARS</Annotation>
+        <SVAnnotation>None</SVAnnotation>
+        <AnnotationSource>refseq</AnnotationSource>
+        <AnnotateHGMD>false</AnnotateHGMD>
+        <OutputGenomeVcf>false</OutputGenomeVcf>
+        <GVcfBlockCompression>true</GVcfBlockCompression>
+      </VarCallerSettings>
+      <VariantCaller>None</VariantCaller>
+      <ComputePerTileStats>true</ComputePerTileStats>
+      <CompressBam>false</CompressBam>
+    </WorkflowSettings>
+    <Analysis>GenerateFASTQ</Analysis>
+    <WorkflowVersion>0.0.0.0</WorkflowVersion>
+  </Workflow>
+  <AnalysisSoftwareVersion>2.6.2.3</AnalysisSoftwareVersion>
+  <RTAOutputFolder>\\192.168.1.1\sequencing-incoming\180110_M00000_0000_000000000-XXXXX</RTAOutputFolder>
+</AnalysisJobInfo>
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diff --git a/...M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/1176-4-04_S26_L001_R1_001.fastq.gz b/...M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/1176-4-04_S26_L001_R1_001.fastq.gz
diff --git a/...M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/1176-4-04_S26_L001_R2_001.fastq.gz b/...M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/1176-4-04_S26_L001_R2_001.fastq.gz
diff --git a/..._M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/256-puri_S27_L001_R1_001.fastq.gz b/..._M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/256-puri_S27_L001_R1_001.fastq.gz
diff --git a/..._M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/256-puri_S27_L001_R2_001.fastq.gz b/..._M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/256-puri_S27_L001_R2_001.fastq.gz
diff --git a/..._M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/848-puri_S28_L001_R1_001.fastq.gz b/..._M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/848-puri_S28_L001_R1_001.fastq.gz
diff --git a/..._M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/848-puri_S28_L001_R2_001.fastq.gz b/..._M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/848-puri_S28_L001_R2_001.fastq.gz
diff --git a/...ns/180110_M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Alignment/Checkpoint.txt b/...ns/180110_M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Alignment/Checkpoint.txt
@@ -0,0 +1,2 @@
+3
+
diff --git a/...110_M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Alignment/CompletedJobInfo.xml b/...110_M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Alignment/CompletedJobInfo.xml
@@ -0,0 +1,80 @@
+<?xml version="1.0"?>
+<AnalysisJobInfo xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Version="0">
+  <AlignmentFolder>D:\Illumina\MiSeqAnalysis\180110_M00000_0000_000000000-XXXXX\Data\Intensities\BaseCalls\Alignment</AlignmentFolder>
+  <CompletionTime>2018-01-02T06:48:32.608024-04:00</CompletionTime>
+  <RTARunInfo Version="2">
+    <Run Id="180110_M00000_0000_000000000-XXXXX" Number="000">
+      <Flowcell>000000000-XXXXX</Flowcell>
+      <Instrument>M00000</Instrument>
+      <Date>180110</Date>
+      <Reads>
+        <Read NumCycles="151" StartFromCycle="1" EndWithCycle="151" IsIndexedRead="N" />
+        <Read NumCycles="8" StartFromCycle="1" EndWithCycle="8" IsIndexedRead="Y" />
+        <Read NumCycles="8" StartFromCycle="1" EndWithCycle="8" IsIndexedRead="Y" />
+        <Read NumCycles="151" StartFromCycle="1" EndWithCycle="151" IsIndexedRead="N" />
+      </Reads>
+      <FlowcellLayout LaneCount="1" SurfaceCount="1" SwathCount="1" TileCount="2" />
+      <AlignToPhiX />
+    </Run>
+  </RTARunInfo>
+  <RunFolder>D:\Illumina\MiSeqAnalysis\180110_M00000_0000_000000000-XXXXX</RunFolder>
+  <Sheet>
+    <Type>MiSeq</Type>
+    <WorkflowType>GenerateFASTQ</WorkflowType>
+    <Header>
+      <Chemistry>Amplicon</Chemistry>
+      <Date>1_1_18</Date>
+    </Header>
+  </Sheet>
+  <StartTime>2018-01-02T06:48:22.0480092-04:00</StartTime>
+  <Workflow>
+    <WorkflowSettings>
+      <AdapterSequences />
+      <AdapterSequences2 />
+      <TrimFastq>false</TrimFastq>
+      <FastQInput>false</FastQInput>
+      <StitchReads>false</StitchReads>
+      <MaximumThreadCount>0</MaximumThreadCount>
+      <ReadTrimQualityScoreLevel>0</ReadTrimQualityScoreLevel>
+      <ReverseComplement>false</ReverseComplement>
+      <VarCallerSettings>
+        <Filters>
+          <FilterOutSingleProbePoolVariants>false</FilterOutSingleProbePoolVariants>
+          <FilterOutSingleStrandVariants>false</FilterOutSingleStrandVariants>
+          <IndelRepeatFilterCutoff>8</IndelRepeatFilterCutoff>
+          <MinQScore>0</MinQScore>
+          <MinimumCoverageDepthEmitCutoff>-1</MinimumCoverageDepthEmitCutoff>
+          <MinimumDepthCutoff>-1</MinimumDepthCutoff>
+          <MinimumGQCutoff>0</MinimumGQCutoff>
+          <MinimumGQXCutoff>0</MinimumGQXCutoff>
+          <MinimumMQCutoff>-1</MinimumMQCutoff>
+          <MinimumQDCutoff>0</MinimumQDCutoff>
+          <MinimumQualCutoff>-1</MinimumQualCutoff>
+          <MinimumQualityEmitCutoff>-1</MinimumQualityEmitCutoff>
+          <OnlyCallInROI>false</OnlyCallInROI>
+          <OnlyUseProperPairs>false</OnlyUseProperPairs>
+          <CallPhasedSNVs>false</CallPhasedSNVs>
+          <StrandBiasFilterCutoff>0</StrandBiasFilterCutoff>
+          <MaxSizePhasedSNV>100</MaxSizePhasedSNV>
+          <QualityModel>Poisson</QualityModel>
+          <VariantFrequencyEmitCutoff>0.1</VariantFrequencyEmitCutoff>
+          <VariantFrequencyFilterCutoff>0.2</VariantFrequencyFilterCutoff>
+          <FilterOffTargetVariants>false</FilterOffTargetVariants>
+        </Filters>
+        <Annotation>MARS</Annotation>
+        <SVAnnotation>None</SVAnnotation>
+        <AnnotationSource>refseq</AnnotationSource>
+        <AnnotateHGMD>false</AnnotateHGMD>
+        <OutputGenomeVcf>false</OutputGenomeVcf>
+        <GVcfBlockCompression>true</GVcfBlockCompression>
+      </VarCallerSettings>
+      <VariantCaller>None</VariantCaller>
+      <ComputePerTileStats>true</ComputePerTileStats>
+      <CompressBam>false</CompressBam>
+    </WorkflowSettings>
+    <Analysis>GenerateFASTQ</Analysis>
+    <WorkflowVersion>0.0.0.0</WorkflowVersion>
+  </Workflow>
+  <AnalysisSoftwareVersion>2.6.2.3</AnalysisSoftwareVersion>
+  <RTAOutputFolder>\\192.168.1.1\sequencing-incoming\180110_M00000_0000_000000000-XXXXX</RTAOutputFolder>
+</AnalysisJobInfo>
diff --git a/...0110_M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Alignment/SampleSheetUsed.csv b/...0110_M00000_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Alignment/SampleSheetUsed.csv
@@ -0,0 +1,98 @@
+[Header],,,,,,,,,
+IEMFileVersion,4,,,,,,,,
+Investigator_Name,Partials,,,,,,,,
+Date,1_10_18,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,
+Application,FASTQ_Only,,,,,,,,
+Assay,Nextera,,,,,,_,,
+Description,,,,,,,,,
+Chemistry,Amplicon,,,,,,,,
+,,,,,,,,,
+[Reads],,,,,,,,,
+151,,,,,,,,,
+151,,,,,,,,,
+,,,,,,,,,
+[Settings],,,,,,,,,
+,,,,,,,,,
+[Data],,,,,,,,,
+Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
+1,1086S1_01,Shuyi,A01,N701,TAAGGCGA,N502,CTCTCTAT,,
+2,1086S1_02,,A02,N702,CGTACTAG,N502,CTCTCTAT,,
+3,1086S1_03,,A03,N703,AGGCAGAA,N502,CTCTCTAT,,
+4,1086S1_04,,A04,N704,TCCTGAGC,N502,CTCTCTAT,,
+5,1086S1_05,,A05,N705,GGACTCCT,N502,CTCTCTAT,,
+6,1086S2_01,,A06,N706,TAGGCATG,N502,CTCTCTAT,,
+7,1086S2_02,,A07,N707,CTCTCTAC,N502,CTCTCTAT,,
+8,1086S2_03,,A08,N708,CAGAGAGG,N502,CTCTCTAT,,
+9,1086S2_04,,A09,N709,GCTACGCT,N502,CTCTCTAT,,
+10,1086S2_05,,A10,N710,CGAGGCTG,N502,CTCTCTAT,,
+11,1086S2_06,,A11,N711,AAGAGGCA,N502,CTCTCTAT,,
+12,1086S2_07,,A12,N712,GTAGAGGA,N502,CTCTCTAT,,
+13,1086S3_01,,B01,N701,TAAGGCGA,N503,TATCCTCT,,
+14,1086S3_02,,B02,N702,CGTACTAG,N503,TATCCTCT,,
+15,1086S3_03,,B03,N703,AGGCAGAA,N503,TATCCTCT,,
+16,1086S3_04,,B04,N704,TCCTGAGC,N503,TATCCTCT,,
+17,1086S4_01,,B05,N705,GGACTCCT,N503,TATCCTCT,,
+18,1086S4_02,,B06,N706,TAGGCATG,N503,TATCCTCT,,
+19,1086S4_03,,B07,N707,CTCTCTAC,N503,TATCCTCT,,
+20,1086S4_04,,B08,N708,CAGAGAGG,N503,TATCCTCT,,
+21,1086S4_05,,B09,N709,GCTACGCT,N503,TATCCTCT,,
+22,1086S4_06,,B10,N710,CGAGGCTG,N503,TATCCTCT,,
+23,1176_4_01,,B11,N711,AAGAGGCA,N503,TATCCTCT,,
+24,1176_4_02,,B12,N712,GTAGAGGA,N503,TATCCTCT,,
+25,1176_4_03,,C01,N701,TAAGGCGA,N504,AGAGTAGA,,
+26,1176_4_04,,C02,N702,CGTACTAG,N504,AGAGTAGA,,
+27,256_puri,,C03,N703,AGGCAGAA,N504,AGAGTAGA,,
+28,848_puri,,C04,N704,TCCTGAGC,N504,AGAGTAGA,,
+29,Miniprep_mut1,Chengyan,C05,N705,GGACTCCT,N504,AGAGTAGA,,
+30,Miniprep_mut2,,C06,N706,TAGGCATG,N504,AGAGTAGA,,
+31,Miniprep_mut4,,C07,N707,CTCTCTAC,N504,AGAGTAGA,,
+32,Miniprep_mut5,,C08,N708,CAGAGAGG,N504,AGAGTAGA,,
+33,Miniprep_mut8,,C09,N709,GCTACGCT,N504,AGAGTAGA,,
+34,Miniprep_mut12,,C10,N710,CGAGGCTG,N504,AGAGTAGA,,
+35,env_BG505_N88Q,,C11,N711,AAGAGGCA,N504,AGAGTAGA,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
+,,,,,,,,,
diff --git a/...0_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut12_S34_L001_R1_001.fastq.gz b/...0_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut12_S34_L001_R1_001.fastq.gz
diff --git a/...0_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut12_S34_L001_R2_001.fastq.gz b/...0_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut12_S34_L001_R2_001.fastq.gz
diff --git a/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut1_S29_L001_R1_001.fastq.gz b/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut1_S29_L001_R1_001.fastq.gz
diff --git a/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut1_S29_L001_R2_001.fastq.gz b/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut1_S29_L001_R2_001.fastq.gz
diff --git a/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut2_S30_L001_R1_001.fastq.gz b/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut2_S30_L001_R1_001.fastq.gz
diff --git a/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut2_S30_L001_R2_001.fastq.gz b/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut2_S30_L001_R2_001.fastq.gz
diff --git a/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut4_S31_L001_R1_001.fastq.gz b/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut4_S31_L001_R1_001.fastq.gz
diff --git a/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut4_S31_L001_R2_001.fastq.gz b/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut4_S31_L001_R2_001.fastq.gz
diff --git a/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut5_S32_L001_R1_001.fastq.gz b/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut5_S32_L001_R1_001.fastq.gz
diff --git a/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut5_S32_L001_R2_001.fastq.gz b/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut5_S32_L001_R2_001.fastq.gz
diff --git a/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut8_S33_L001_R1_001.fastq.gz b/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut8_S33_L001_R1_001.fastq.gz
diff --git a/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut8_S33_L001_R2_001.fastq.gz b/...00_0000_000000000-XXXXX/Data/Intensities/BaseCalls/Miniprep-mut8_S33_L001_R2_001.fastq.gz
diff --git a/...0_0000_000000000-XXXXX/Data/Intensities/BaseCalls/env-BG505-N88Q_S35_L001_R1_001.fastq.gz b/...0_0000_000000000-XXXXX/Data/Intensities/BaseCalls/env-BG505-N88Q_S35_L001_R1_001.fastq.gz
diff --git a/...0_0000_000000000-XXXXX/Data/Intensities/BaseCalls/env-BG505-N88Q_S35_L001_R2_001.fastq.gz b/...0_0000_000000000-XXXXX/Data/Intensities/BaseCalls/env-BG505-N88Q_S35_L001_R2_001.fastq.gz
diff --git a/test_umbra/data/runs/180110_M00000_0000_000000000-XXXXX/RTAComplete.txt b/test_umbra/data/runs/180110_M00000_0000_000000000-XXXXX/RTAComplete.txt
@@ -0,0 +1 @@
+1/1/2018,06:21:31.705,Illumina RTA 1.18.54
diff --git a/test_umbra/data/runs/180110_M00000_0000_000000000-XXXXX/RunInfo.xml b/test_umbra/data/runs/180110_M00000_0000_000000000-XXXXX/RunInfo.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<RunInfo xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Version="2">
+  <Run Id="180110_M00000_0000_000000000-XXXXX" Number="000">
+    <Flowcell>000000000-XXXXX</Flowcell>
+    <Instrument>M00000</Instrument>
+    <Date>180110</Date>
+    <Reads>
+      <Read NumCycles="151" Number="1" IsIndexedRead="N" />
+      <Read NumCycles="8" Number="2" IsIndexedRead="Y" />
+      <Read NumCycles="8" Number="3" IsIndexedRead="Y" />
+      <Read NumCycles="151" Number="4" IsIndexedRead="N" />
+    </Reads>
+    <FlowcellLayout LaneCount="1" SurfaceCount="2" SwathCount="1" TileCount="4" />
+  </Run>
+</RunInfo>
diff --git a/test_umbra/data/runs/README.md b/test_umbra/data/runs/README.md
@@ -7,7 +7,4 @@ Where present, FASTQ files are all gzipped zero-length files.
  * Second MiSeq Run:`180102_M00000_0000_000000000-XXXXX`
  * Basic MiniSeq Run: `180103_M000000_0000_0000000000`
  * Single-ended MiSeq: `180105_M00000_0000_000000000-XXXXX`
- * MiSeq run, renamed directory: `run-files-custom-name` (same run 180102)
-
-
-single-ended: 170816_M00281_0262_000000000-D2WH5
+ * MiSeq Run, missing experiment row: `180110_M00000_0000_000000000-XXXXX`