run all tests

all pass
roblanf · Jun 25, 2018 · fa93f92 · fa93f92
1 parent 8bea45e
commit fa93f92
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Showing 102 changed files with 28 additions and 10 deletions.
diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,21 @@ testfiles/1D2_summary/sequencing_summary.txt
 testfiles/1D2a/sequencing_summary.txt
 
 testfiles/2D/sequencing_summary.txt
+
+testfiles/short_run/flowcell_overview.png
+
+testfiles/1D2/channel_summary.png
+
+testfiles/1D2/channel_summary.png
+
+testfiles/1D2/length_histogram.png
+
+testfiles/1D2/q_histogram.png
+
+testfiles/1D2/yield_by_length.png
+
+testfiles/directRNA/channel_summary.png
+
+testfiles/1D2/yield_by_length.png
+
+testfiles/1D2/channel_summary.png
diff --git a/testfiles/1D2/channel_summary.png b/testfiles/1D2/channel_summary.png
diff --git a/testfiles/1D2/flowcell_overview.png b/testfiles/1D2/flowcell_overview.png
diff --git a/testfiles/1D2/length_by_hour.png b/testfiles/1D2/length_by_hour.png
diff --git a/testfiles/1D2/length_histogram.png b/testfiles/1D2/length_histogram.png
diff --git a/testfiles/1D2/length_vs_q.png b/testfiles/1D2/length_vs_q.png
diff --git a/testfiles/1D2/q_by_hour.png b/testfiles/1D2/q_by_hour.png
diff --git a/testfiles/1D2/q_histogram.png b/testfiles/1D2/q_histogram.png
diff --git a/testfiles/1D2/reads_per_hour.png b/testfiles/1D2/reads_per_hour.png
diff --git a/testfiles/1D2/summary.yaml b/testfiles/1D2/summary.yaml
@@ -1,6 +1,6 @@
 input file: ~/Documents/github/minion_qc/testfiles/1D2/sequencing_summary.txt
 All reads:
-  total.gigabases: 0.9302495
+  total.gigabases: 0.930249
   total.reads: 159799
   N50.length: 7937.0
   mean.length: 5821.4
@@ -27,7 +27,7 @@ All reads:
     '>1m': 0.0e+00
     ultralong: 0.0e+00
 Q>=7:
-  total.gigabases: 0.9301052
+  total.gigabases: 0.930105
   total.reads: 158952
   N50.length: 7937.0
   mean.length: 5851.5
@@ -45,8 +45,8 @@ Q>=7:
     '>1m': 0
     ultralong: 0.0e+00
   gigabases:
-    '>10kb': 0.2497112
-    '>20kb': 0.0069372
+    '>10kb': 0.249711
+    '>20kb': 0.006937
     '>50kb': 5.4577e-05
     '>100kb': 0.0e+00
     '>200kb': 0.0e+00

diff --git a/testfiles/1D2/yield_by_length.png b/testfiles/1D2/yield_by_length.png
diff --git a/testfiles/1D2/yield_over_time.png b/testfiles/1D2/yield_over_time.png
diff --git a/testfiles/directRNA/channel_summary.png b/testfiles/directRNA/channel_summary.png
diff --git a/testfiles/directRNA/flowcell_overview.png b/testfiles/directRNA/flowcell_overview.png
diff --git a/testfiles/directRNA/length_by_hour.png b/testfiles/directRNA/length_by_hour.png
diff --git a/testfiles/directRNA/length_histogram.png b/testfiles/directRNA/length_histogram.png
diff --git a/testfiles/directRNA/length_vs_q.png b/testfiles/directRNA/length_vs_q.png
diff --git a/testfiles/directRNA/q_by_hour.png b/testfiles/directRNA/q_by_hour.png
diff --git a/testfiles/directRNA/q_histogram.png b/testfiles/directRNA/q_histogram.png
diff --git a/testfiles/directRNA/reads_per_hour.png b/testfiles/directRNA/reads_per_hour.png
diff --git a/testfiles/directRNA/yield_by_length.png b/testfiles/directRNA/yield_by_length.png
diff --git a/testfiles/directRNA/yield_over_time.png b/testfiles/directRNA/yield_over_time.png
diff --git a/testfiles/nested_multiple/combinedQC/combined_length_histogram.png b/testfiles/nested_multiple/combinedQC/combined_length_histogram.png
diff --git a/testfiles/nested_multiple/combinedQC/combined_q_histogram.png b/testfiles/nested_multiple/combinedQC/combined_q_histogram.png
diff --git a/testfiles/nested_multiple/combinedQC/combined_yield_by_length.png b/testfiles/nested_multiple/combinedQC/combined_yield_by_length.png
diff --git a/testfiles/nested_multiple/combinedQC/length_by_hour.png b/testfiles/nested_multiple/combinedQC/length_by_hour.png
diff --git a/testfiles/nested_multiple/combinedQC/length_distributions.png b/testfiles/nested_multiple/combinedQC/length_distributions.png
diff --git a/testfiles/nested_multiple/combinedQC/q_by_hour.png b/testfiles/nested_multiple/combinedQC/q_by_hour.png
diff --git a/testfiles/nested_multiple/combinedQC/q_distributions.png b/testfiles/nested_multiple/combinedQC/q_distributions.png
diff --git a/testfiles/nested_multiple/combinedQC/yield_by_length.png b/testfiles/nested_multiple/combinedQC/yield_by_length.png
diff --git a/testfiles/nested_multiple/combinedQC/yield_over_time.png b/testfiles/nested_multiple/combinedQC/yield_over_time.png
diff --git a/testfiles/nested_multiple/secondA/thirdA/channel_summary.png b/testfiles/nested_multiple/secondA/thirdA/channel_summary.png
diff --git a/testfiles/nested_multiple/secondA/thirdA/flowcell_overview.png b/testfiles/nested_multiple/secondA/thirdA/flowcell_overview.png
diff --git a/testfiles/nested_multiple/secondA/thirdA/length_by_hour.png b/testfiles/nested_multiple/secondA/thirdA/length_by_hour.png
diff --git a/testfiles/nested_multiple/secondA/thirdA/length_histogram.png b/testfiles/nested_multiple/secondA/thirdA/length_histogram.png
diff --git a/testfiles/nested_multiple/secondA/thirdA/length_vs_q.png b/testfiles/nested_multiple/secondA/thirdA/length_vs_q.png
diff --git a/testfiles/nested_multiple/secondA/thirdA/q_by_hour.png b/testfiles/nested_multiple/secondA/thirdA/q_by_hour.png
diff --git a/testfiles/nested_multiple/secondA/thirdA/q_histogram.png b/testfiles/nested_multiple/secondA/thirdA/q_histogram.png
diff --git a/testfiles/nested_multiple/secondA/thirdA/reads_per_hour.png b/testfiles/nested_multiple/secondA/thirdA/reads_per_hour.png
diff --git a/testfiles/nested_multiple/secondA/thirdA/yield_by_length.png b/testfiles/nested_multiple/secondA/thirdA/yield_by_length.png
diff --git a/testfiles/nested_multiple/secondA/thirdA/yield_over_time.png b/testfiles/nested_multiple/secondA/thirdA/yield_over_time.png
diff --git a/testfiles/nested_multiple/secondB/channel_summary.png b/testfiles/nested_multiple/secondB/channel_summary.png
diff --git a/testfiles/nested_multiple/secondB/flowcell_overview.png b/testfiles/nested_multiple/secondB/flowcell_overview.png
diff --git a/testfiles/nested_multiple/secondB/length_by_hour.png b/testfiles/nested_multiple/secondB/length_by_hour.png
diff --git a/testfiles/nested_multiple/secondB/length_histogram.png b/testfiles/nested_multiple/secondB/length_histogram.png
diff --git a/testfiles/nested_multiple/secondB/length_vs_q.png b/testfiles/nested_multiple/secondB/length_vs_q.png
diff --git a/testfiles/nested_multiple/secondB/q_by_hour.png b/testfiles/nested_multiple/secondB/q_by_hour.png
diff --git a/testfiles/nested_multiple/secondB/q_histogram.png b/testfiles/nested_multiple/secondB/q_histogram.png
diff --git a/testfiles/nested_multiple/secondB/reads_per_hour.png b/testfiles/nested_multiple/secondB/reads_per_hour.png
diff --git a/testfiles/nested_multiple/secondB/yield_by_length.png b/testfiles/nested_multiple/secondB/yield_by_length.png
diff --git a/testfiles/nested_multiple/secondB/yield_over_time.png b/testfiles/nested_multiple/secondB/yield_over_time.png
diff --git a/testfiles/nested_multiple/secondC/thirdC/channel_summary.png b/testfiles/nested_multiple/secondC/thirdC/channel_summary.png
diff --git a/testfiles/nested_multiple/secondC/thirdC/flowcell_overview.png b/testfiles/nested_multiple/secondC/thirdC/flowcell_overview.png
diff --git a/testfiles/nested_multiple/secondC/thirdC/length_by_hour.png b/testfiles/nested_multiple/secondC/thirdC/length_by_hour.png
diff --git a/testfiles/nested_multiple/secondC/thirdC/length_histogram.png b/testfiles/nested_multiple/secondC/thirdC/length_histogram.png
diff --git a/testfiles/nested_multiple/secondC/thirdC/length_vs_q.png b/testfiles/nested_multiple/secondC/thirdC/length_vs_q.png
diff --git a/testfiles/nested_multiple/secondC/thirdC/q_by_hour.png b/testfiles/nested_multiple/secondC/thirdC/q_by_hour.png
diff --git a/testfiles/nested_multiple/secondC/thirdC/q_histogram.png b/testfiles/nested_multiple/secondC/thirdC/q_histogram.png
diff --git a/testfiles/nested_multiple/secondC/thirdC/reads_per_hour.png b/testfiles/nested_multiple/secondC/thirdC/reads_per_hour.png
diff --git a/testfiles/nested_multiple/secondC/thirdC/yield_by_length.png b/testfiles/nested_multiple/secondC/thirdC/yield_by_length.png
diff --git a/testfiles/nested_multiple/secondC/thirdC/yield_over_time.png b/testfiles/nested_multiple/secondC/thirdC/yield_over_time.png
diff --git a/testfiles/nested_multiple_testoutput/thirdA/channel_summary.png b/testfiles/nested_multiple_testoutput/thirdA/channel_summary.png
diff --git a/testfiles/nested_multiple_testoutput/thirdA/flowcell_overview.png b/testfiles/nested_multiple_testoutput/thirdA/flowcell_overview.png
diff --git a/testfiles/nested_multiple_testoutput/thirdA/length_by_hour.png b/testfiles/nested_multiple_testoutput/thirdA/length_by_hour.png
diff --git a/testfiles/nested_multiple_testoutput/thirdA/length_histogram.png b/testfiles/nested_multiple_testoutput/thirdA/length_histogram.png
diff --git a/testfiles/nested_multiple_testoutput/thirdA/length_vs_q.png b/testfiles/nested_multiple_testoutput/thirdA/length_vs_q.png
diff --git a/testfiles/nested_multiple_testoutput/thirdA/q_by_hour.png b/testfiles/nested_multiple_testoutput/thirdA/q_by_hour.png
diff --git a/testfiles/nested_multiple_testoutput/thirdA/q_histogram.png b/testfiles/nested_multiple_testoutput/thirdA/q_histogram.png
diff --git a/testfiles/nested_multiple_testoutput/thirdA/reads_per_hour.png b/testfiles/nested_multiple_testoutput/thirdA/reads_per_hour.png
diff --git a/testfiles/nested_multiple_testoutput/thirdA/yield_by_length.png b/testfiles/nested_multiple_testoutput/thirdA/yield_by_length.png
diff --git a/testfiles/nested_multiple_testoutput/thirdA/yield_over_time.png b/testfiles/nested_multiple_testoutput/thirdA/yield_over_time.png
diff --git a/testfiles/nested_single/secondA/thirdA/channel_summary.png b/testfiles/nested_single/secondA/thirdA/channel_summary.png
diff --git a/testfiles/nested_single/secondA/thirdA/flowcell_overview.png b/testfiles/nested_single/secondA/thirdA/flowcell_overview.png
diff --git a/testfiles/nested_single/secondA/thirdA/length_by_hour.png b/testfiles/nested_single/secondA/thirdA/length_by_hour.png
diff --git a/testfiles/nested_single/secondA/thirdA/length_histogram.png b/testfiles/nested_single/secondA/thirdA/length_histogram.png
diff --git a/testfiles/nested_single/secondA/thirdA/length_vs_q.png b/testfiles/nested_single/secondA/thirdA/length_vs_q.png
diff --git a/testfiles/nested_single/secondA/thirdA/q_by_hour.png b/testfiles/nested_single/secondA/thirdA/q_by_hour.png
diff --git a/testfiles/nested_single/secondA/thirdA/q_histogram.png b/testfiles/nested_single/secondA/thirdA/q_histogram.png
diff --git a/testfiles/nested_single/secondA/thirdA/reads_per_hour.png b/testfiles/nested_single/secondA/thirdA/reads_per_hour.png
diff --git a/testfiles/nested_single/secondA/thirdA/yield_by_length.png b/testfiles/nested_single/secondA/thirdA/yield_by_length.png
diff --git a/testfiles/nested_single/secondA/thirdA/yield_over_time.png b/testfiles/nested_single/secondA/thirdA/yield_over_time.png
diff --git a/testfiles/nested_single_testoutput/thirdA/channel_summary.png b/testfiles/nested_single_testoutput/thirdA/channel_summary.png
diff --git a/testfiles/nested_single_testoutput/thirdA/flowcell_overview.png b/testfiles/nested_single_testoutput/thirdA/flowcell_overview.png
diff --git a/testfiles/nested_single_testoutput/thirdA/length_by_hour.png b/testfiles/nested_single_testoutput/thirdA/length_by_hour.png
diff --git a/testfiles/nested_single_testoutput/thirdA/length_histogram.png b/testfiles/nested_single_testoutput/thirdA/length_histogram.png
diff --git a/testfiles/nested_single_testoutput/thirdA/length_vs_q.png b/testfiles/nested_single_testoutput/thirdA/length_vs_q.png
diff --git a/testfiles/nested_single_testoutput/thirdA/q_by_hour.png b/testfiles/nested_single_testoutput/thirdA/q_by_hour.png
diff --git a/testfiles/nested_single_testoutput/thirdA/q_histogram.png b/testfiles/nested_single_testoutput/thirdA/q_histogram.png
diff --git a/testfiles/nested_single_testoutput/thirdA/reads_per_hour.png b/testfiles/nested_single_testoutput/thirdA/reads_per_hour.png
diff --git a/testfiles/nested_single_testoutput/thirdA/yield_by_length.png b/testfiles/nested_single_testoutput/thirdA/yield_by_length.png
diff --git a/testfiles/nested_single_testoutput/thirdA/yield_over_time.png b/testfiles/nested_single_testoutput/thirdA/yield_over_time.png
diff --git a/testfiles/short_run/channel_summary.png b/testfiles/short_run/channel_summary.png
diff --git a/testfiles/short_run/flowcell_overview.png b/testfiles/short_run/flowcell_overview.png
diff --git a/testfiles/short_run/length_by_hour.png b/testfiles/short_run/length_by_hour.png
diff --git a/testfiles/short_run/length_histogram.png b/testfiles/short_run/length_histogram.png
diff --git a/testfiles/short_run/length_vs_q.png b/testfiles/short_run/length_vs_q.png
diff --git a/testfiles/short_run/q_by_hour.png b/testfiles/short_run/q_by_hour.png
diff --git a/testfiles/short_run/q_histogram.png b/testfiles/short_run/q_histogram.png
diff --git a/testfiles/short_run/reads_per_hour.png b/testfiles/short_run/reads_per_hour.png
diff --git a/testfiles/short_run/summary.yaml b/testfiles/short_run/summary.yaml
@@ -1,6 +1,6 @@
 input file: ~/Documents/github/minion_qc/testfiles/short_run/sequencing_summary.txt
 All reads:
-  total.gigabases: 0.0010896
+  total.gigabases: 0.00109
   total.reads: 99
   N50.length: 18145.0
   mean.length: 11006.4
@@ -18,16 +18,16 @@ All reads:
     '>1m': 0
     ultralong: 0.0e+00
   gigabases:
-    '>10kb': 0.0008817
-    '>20kb': 0.0004697
+    '>10kb': 0.000882
+    '>20kb': 0.00047
     '>50kb': 0.0e+00
     '>100kb': 0.0e+00
     '>200kb': 0.0e+00
     '>500kb': 0.0e+00
     '>1m': 0.0e+00
     ultralong: 0.0e+00
 Q>=7:
-  total.gigabases: 0.0009699
+  total.gigabases: 0.00097
   total.reads: 76
   N50.length: 18946.0
   mean.length: 12761.6
@@ -45,8 +45,8 @@ Q>=7:
     '>1m': 0
     ultralong: 0.0e+00
   gigabases:
-    '>10kb': 0.0007927
-    '>20kb': 0.0004439
+    '>10kb': 0.000793
+    '>20kb': 0.000444
     '>50kb': 0.0e+00
     '>100kb': 0.0e+00
     '>200kb': 0.0e+00

diff --git a/testfiles/short_run/yield_by_length.png b/testfiles/short_run/yield_by_length.png
diff --git a/testfiles/short_run/yield_over_time.png b/testfiles/short_run/yield_over_time.png