Merge branch 'issue168' into 'develop'

Shiva report messages

Add messsages for Shiva report

See #168

See merge request !183

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp

@@ -25,7 +25,15 @@
     <div class="col-md-1"></div>
     <div class="col-md-6">
         <p>
-            Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+        #if (sampleId.isDefined && libId.isDefined)
+            Here we show basic <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Alignment">alignment</a> statistics for this run for sample ${sampleId} with library ${libId}. Total number of reads, number of alignments reads and number of duplicate reads are given, and the percentages thereof as a percentage of total.
+        #elseif(sampleId.isDefined && showPlot)
+            The following plot shows basic <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Alignment">alignment</a> statistics for this run for sample ${sampleId}. Every library is represented by a multi-color bar. Red represents the total number of properly mapped reads for this sample. Green represents the total number of duplicates reads, which is usually caused by <a href="http://www.cureffi.org/2012/12/11/how-pcr-duplicates-arise-in-next-generation-sequencing/">PCR duplicates</a>. Blue denotes the number of unmapped reads, and purple denotes reads flagged <em>secondary</em> (this is dependent on the aligner used). A table showing similar statistics, including values represented as percent of total, can be downloaded as a tab-delimited file.
+        #elseif(sampleId.isDefined && !showPlot)
+            Here we show basic <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Alignment">alignment</a> statistics for this run for every library of sample ${sampleId}. Total number of reads, number of alignments reads and number of duplicate reads are given, and the percentages thereof as a percentage of total.
+        #else
+            The following plot shows basic <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Alignment">alignment</a> statistics for this run. Every sample is represented by a multi-color bar. Red represents the total number of properly mapped reads for this sample. Green represents the total number of duplicates reads, which is usually caused by <a href="http://www.cureffi.org/2012/12/11/how-pcr-duplicates-arise-in-next-generation-sequencing/">PCR duplicates</a>. Blue denotes the number of unmapped reads, and purple denotes reads flagged <em>secondary</em> (this is dependent on the aligner used). A table showing similar statistics, including values represented as percent of total, can be downloaded as a tab-delimited file.
+        #end
         </p>
     </div>
     </div>

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp

@@ -29,7 +29,13 @@
     <div class="col-md-1"></div>
     <div class="col-md-6">
         <p>
-            Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+        #if (sampleId.isDefined && libId.isDefined)
+            something
+        #elseif(sampleId.isDefined)
+            This plot shows the insert size distribution for the libraries of sample ${sampleId}. <a href="http://thegenomefactory.blogspot.nl/2013/08/paired-end-read-confusion-library.html">Insert size</a> denotes the size of the so-called <em>insert</em> between two read pairs in a paired-end sequencing run. This should correspond to the length of the sequence between the sequencing adaptors. The provided table shows mean and median insert size for each sample, together with the standard deviation.
+        #else
+            This plot shows the insert size distribution for each of the ${samples.size} samples. <a href="http://thegenomefactory.blogspot.nl/2013/08/paired-end-read-confusion-library.html">Insert size</a> denotes the size of the so-called <em>insert</em> between two read pairs in a paired-end sequencing run. This should correspond to the length of the sequence between the sequencing adaptors. The provided table shows mean and median insert size for each sample, together with the standard deviation.
+        #end
         </p>
     </div>
     </div>

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp

@@ -29,7 +29,7 @@
     <div class="col-md-1"></div>
     <div class="col-md-6">
         <p>
-            Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+            Here we show the total number of positions in the reference that are covered with a given coverage. This plot is whole-genome based, and will therefore be highly skewed in the case of an exome or targeted approach.
         </p>
     </div>
     </div>

public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp

@@ -15,6 +15,9 @@
         case Some(sample) => List(sample.toString)
         case _ => summary.samples.toList
     }
+    val trimCount = summary.getLibraryValues("flexiprep", "settings", "skip_trim").count(_._2 == Some(false))
+    val clipCount = summary.getLibraryValues("flexiprep", "settings", "skip_clip").count(_._2 == Some(false))
+    val librariesCount = summary.samples.foldLeft(0)(_ + summary.libraries(_).size)
 }#
 #if (showIntro)
     <br/>
@@ -22,7 +25,30 @@
     <div class="col-md-1"></div>
     <div class="col-md-6">
         <p>
-            Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+            #if (trimCount == librariesCount && clipCount == librariesCount)
+                You have selected both <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Alternative_clipping_strategies_.28Adaptor_clipping.29">adaptor clipping</a> and <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Sequence_Quality_Trimming">read trimming</a> as pre-processing steps
+            #elseif (trimCount == librariesCount && clipCount == 0)
+                You have selected only <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Sequence_Quality_Trimming">read trimming</a> as pre-processing step
+            #elseif (trimCount == 0 && clipCount == librariesCount)
+                You have selected only <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Alternative_clipping_strategies_.28Adaptor_clipping.29">adaptor clipping</a> as pre-processing step
+            #elseif (trimCount == 0 && clipCount == 0)
+                You have selected no pre-processing step to be performed
+            #elseif (trimCount > 0 && clipCount == 0)
+                You have selected <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Alternative_clipping_strategies_.28Adaptor_clipping.29">adaptor clipping</a> as pre-processing steps
+            #elseif (trimCount == 0 && clipCount > 0)
+                You have chosen to turn <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Alternative_clipping_strategies_.28Adaptor_clipping.29">adaptor clipping</a> for some libraries, but not all.
+            #else
+                You have chosen to turn <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Alternative_clipping_strategies_.28Adaptor_clipping.29">adaptor clipping</a> and <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Sequence_Quality_Trimming">read trimming</a> off for some libraries, but not all.
+            #end
+        </p>
+        <p>
+        #if (sampleId.isDefined && libId.isDefined)
+            Here we show aggregated quality statistics sequencing library ${libId} for sample ${sampleId}. It shows the total number of bases used after quality control, and the total number of bases discarded during quality control. This is done for both forward and reverse reads.
+        #elseif (sampleId.isDefined)
+            Here we show aggregated quality statistics for every sequencing library for sample ${sampleId}. It shows the total number of bases used after quality control, and the total number of bases discarded during quality control. This is done for both forward and reverse reads.
+        #else
+            Here we show aggregated quality statistics for every sequencing library. It shows the total number of bases used after quality control, and the total number of bases discarded during quality control. This is done for both forward and reverse reads.
+        #end
         </p>
     </div>
     </div>

public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp

@@ -15,14 +15,45 @@
         case Some(sample) => List(sample.toString)
         case _ => summary.samples.toList
     }
+    val trimCount = summary.getLibraryValues("flexiprep", "settings", "skip_trim").count(_._2 == Some(false))
+    val clipCount = summary.getLibraryValues("flexiprep", "settings", "skip_clip").count(_._2 == Some(false))
+    val librariesCount = summary.samples.foldLeft(0)(_ + summary.libraries(_).size)
 }#
+
 #if (showIntro)
     <br/>
     <div class="row">
     <div class="col-md-1"></div>
     <div class="col-md-6">
         <p>
-            Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+            #if (trimCount == librariesCount && clipCount == librariesCount)
+                You have selected both <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Alternative_clipping_strategies_.28Adaptor_clipping.29">adaptor clipping</a> and <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Sequence_Quality_Trimming">read trimming</a> as pre-processing steps
+            #elseif (trimCount == librariesCount && clipCount == 0)
+                You have selected only <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Sequence_Quality_Trimming">read trimming</a> as pre-processing step
+            #elseif (trimCount == 0 && clipCount == librariesCount)
+                You have selected only <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Alternative_clipping_strategies_.28Adaptor_clipping.29">adaptor clipping</a> as pre-processing step
+            #elseif (trimCount == 0 && clipCount == 0)
+                You have selected no pre-processing step to be performed
+            #elseif (trimCount > 0 && clipCount == 0)
+                You have selected <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Alternative_clipping_strategies_.28Adaptor_clipping.29">adaptor clipping</a> as pre-processing steps
+            #elseif (trimCount == 0 && clipCount > 0)
+                You have chosen to turn <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Alternative_clipping_strategies_.28Adaptor_clipping.29">adaptor clipping</a> for some libraries, but not all.
+            #else
+                You have chosen to turn <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Alternative_clipping_strategies_.28Adaptor_clipping.29">adaptor clipping</a> and <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Sequence_Quality_Trimming">read trimming</a> off for some libraries, but not all.
+            #end
+        </p>
+        <p>
+        #if(sampleId.isDefined && libId.isDefined)
+            Here we show aggregated quality statistics for sequencing library ${libId} for sample ${sampleId}. It shows the total number of reads used after quality control, and the total number of reads discarded during quality control. This is done for both forward and reverse reads.
+        #elseif(sampleId.isDefined)
+            Here we show aggregated quality statistics for every sequencing library for sample ${sampleId}. It shows the total number of reads used after quality control, and the total number of reads discarded during quality control. This is done for both forward and reverse reads.
+        #else
+            Here we show aggregated quality statistics for every sequencing library. It shows the total number of reads used after quality control, and the total number of reads discarded during quality control. This is done for both forward and reverse reads.
+            We show two plots; one for the forward read in the pair, and another one of the reverse read in the pair.
+            Red denotes number of reads left after QC. Green denotes reads filtered by adaptor clipping.
+            Blue denotes number of reads filtered by read trimming.
+            Purple denotes the amount of <em>synced</em> reads. That is, reads removed in one orientation should be removed in the other as well to ensure correctness.
+        #end
         </p>
     </div>
     </div>

public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp

@@ -23,7 +23,22 @@
     <div class="col-md-1"></div>
     <div class="col-md-6">
         <p>
-            Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+        #if(sampleId.isDefined)
+        This table shows aggregated <a href="http://gatkforums.broadinstitute.org/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk">variant</a> statistics for sample ${sampleId}.
+        <ul>
+            <li><em>Hom</em>: Denotes amount of homozygous positions in the resultant VCF file</li>
+            <li><em>HomVar</em>: Denotes amount of homozygous variant positions in the resultant VCF file</li>
+            <li><em>Het</em>: Denotes amount of heterozygous positions (and therefore variants) in the resultant VCF file</li>
+            <li><em>HomRef</em>: Denotes amount of homozygous reference positions in the resultant VCF file</li>
+            <li><em>NoCall</em>: Denotes amount of positions not found in this sample, but present in other samples</li>
+            <li><em>Variant</em>: Denotes amount of positions that were variant in the resultant VCF file</li>
+            <li><em>Total</em>: Denotes total amount of positions in the resultant VCF file</li>
+        </ul>
+        This can be also downloaded as a tab-delimited file.
+
+        #else
+        This plot shows aggregated <a href="http://gatkforums.broadinstitute.org/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk">variant</a> statistics for all of the ${samples.size} samples. Every sample is represent as a multi-colored bar. Red denotes the fraction of variants that are homozygous, whereas green denotes the fraction of variants that are heterozygous. Blue represents the number of variants that were called homozygous reference by the variant caller. #if(samples.size > 1) Purple denotes those <em>positions</em> at which no call was made for the given sample, but these positions <em>do</em> occur in (one of) the other sample(s). #end The values that were used for plot creation can also be seen in the table, and can be downloaded as a tab-delimited file.
+        #end
         </p>
     </div>
     </div>

public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp

@@ -21,7 +21,15 @@
     <div class="col-md-1"></div>
     <div class="col-md-6">
     <p>
-    Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+    In this web document you can find your Shiva pipeline report.
+    Different categories of data can be found in the left-side menu.
+    Statistics per sample and library can be accessed through the top-level menu.
+    Some statistics for target regions can be found in the regions tab.
+    Futhermore, you can view all versions of software tools used by selecting "Versions" from the top menu.
+    </p>
+
+    <p>
+    <small>Brought to you by <a href="https://sasc.lumc.nl">SASC</a> and <a href="https://www.lumc.nl/org/klinische-genetica/">KG</a>, LUMC. </small>
     </p>
     </div>
 </div>
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