From fc6efaf7c02cd6dbc10e0c4fb5715764edb67518 Mon Sep 17 00:00:00 2001 From: Peter van 't Hof Date: Mon, 22 Jun 2015 16:48:42 +0200 Subject: [PATCH] Added temp intro texts --- .../pipelines/bammetrics/alignmentSummary.ssp | 13 ++++++++++++- .../sasc/biopet/pipelines/bammetrics/insertSize.ssp | 13 +++++++++++++ .../pipelines/bammetrics/BammetricsReport.scala | 1 - .../pipelines/flexiprep/flexiprepBaseSummary.ssp | 12 ++++++++++++ .../pipelines/flexiprep/flexiprepReadSummary.ssp | 12 ++++++++++++ .../sasc/biopet/pipelines/shiva/sampleVariants.ssp | 13 +++++++++++++ .../lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp | 9 +++++++++ 7 files changed, 71 insertions(+), 2 deletions(-) diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp index 7a9bbe178..d5931c4b8 100644 --- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp +++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp @@ -10,6 +10,7 @@ <%@ var outputDir: File %> <%@ var showPlot: Boolean = false %> <%@ var showTable: Boolean = true %> +<%@ var showIntro: Boolean = true%> #{ val samples = sampleId match { case Some(sample) => { @@ -18,7 +19,17 @@ case _ => summary.samples.toList } }# - +#if (showIntro) +
+
+
+
+

+ 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. +

+
+
+#end #if (showPlot) #{ BammetricsReport.alignmentSummaryPlot(outputDir, "alignmentSummary", summary, !sampleLevel, sampleId = sampleId) }# diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp index 266c63876..47491d042 100644 --- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp +++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp @@ -13,6 +13,7 @@ <%@ var fields: List[String] = List("mean_insert_size", "standard_deviation", "median_insert_size")%> <%@ var showPlot: Boolean = false %> <%@ var showTable: Boolean = true %> +<%@ var showIntro: Boolean = true%> #{ val samples = sampleId match { case Some(sample) => { @@ -22,6 +23,18 @@ } }# +#if (showIntro) +
+
+
+
+

+ 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. +

+
+
+#end + #if (showPlot) #{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId) }# diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala index d06fcc7ca..247308993 100644 --- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala +++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala @@ -33,7 +33,6 @@ object BammetricsReport extends ReportBuilder { Map()))), List( "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"), - "Bam Stats" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp"), "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true)) ), Map() diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp index 7edb7df76..9bb6408cd 100644 --- a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp +++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp @@ -9,12 +9,24 @@ <%@ var outputDir: File %> <%@ var showPlot: Boolean = false %> <%@ var showTable: Boolean = true %> +<%@ var showIntro: Boolean = true %> #{ val samples = sampleId match { case Some(sample) => List(sample.toString) case _ => summary.samples.toList } }# +#if (showIntro) +
+
+
+
+

+ 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. +

+
+
+#end #if (showPlot) #{ FlexiprepReport.baseSummaryPlot(outputDir, "QC_Bases_R1","R1", summary, sampleId = sampleId) diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp index 33f115a68..d8b3c7b86 100644 --- a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp +++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp @@ -9,12 +9,24 @@ <%@ var outputDir: File %> <%@ var showPlot: Boolean = false %> <%@ var showTable: Boolean = true %> +<%@ var showIntro: Boolean = true %> #{ val samples = sampleId match { case Some(sample) => List(sample.toString) case _ => summary.samples.toList } }# +#if (showIntro) +
+
+
+
+

+ 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. +

+
+
+#end #if (showPlot) #{ diff --git a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp index 17eb37477..27121ca4e 100644 --- a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp +++ b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp @@ -8,6 +8,7 @@ <%@ var outputDir: File %> <%@ var showPlot: Boolean = false %> <%@ var showTable: Boolean = true %> +<%@ var showIntro: Boolean = true%> #{ val fields = List("Hom", "HomVar", "Het", "HomRef", "NoCall", "Variant", "Total") val samples = sampleId match { @@ -16,6 +17,18 @@ } }# +#if (showIntro) +
+
+
+
+

+ 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. +

+
+
+#end + #if (showPlot) #{ ShivaReport.variantSummaryPlot(outputDir, "variantSummary", summary, sampleId = sampleId) }#
diff --git a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp index 339f9e171..0c9781c0a 100644 --- a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp +++ b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp @@ -15,3 +15,12 @@ +
+
+
+
+

+ 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. +

+
+
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