Commit a2c870b2 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding more output files to gearssingle

parent b118cadf
...@@ -85,8 +85,8 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -85,8 +85,8 @@ object GearsReport extends MultisampleReportBuilder {
def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = { def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = {
val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", "krakenreport", sample = sampleId, library = NoLibrary), Duration.Inf) == 1 val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", "krakenreport", sample = sampleId, library = NoLibrary), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", "centrifuge_report", sample = sampleId, library = None), Duration.Inf) == 1 val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", "centrifuge_report", sample = sampleId, library = None), Duration.Inf) == 1
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears", NoModule, sampleId, NoLibrary, "qiime_closed_otu_table"), Duration.Inf) val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gearssingle", NoModule, sampleId, NoLibrary, "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears", NoModule, sampleId, NoLibrary, "qiime_open_otu_table"), Duration.Inf) val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gearssingle", NoModule, sampleId, NoLibrary, "qiime_open_otu_table"), Duration.Inf)
ReportPage((if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", ReportPage((if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_report") Map("summaryStatsTag" -> "centrifuge_report")
......
...@@ -150,6 +150,7 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript ...@@ -150,6 +150,7 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
centrifuge.fastqR2 = r2 centrifuge.fastqR2 = r2
centrifuge.outputName = outputName centrifuge.outputName = outputName
add(centrifuge) add(centrifuge)
outputFiles += "centrifuge_output" -> centrifuge.centrifugeOutput
} }
qiimeRatx foreach { qiimeRatx => qiimeRatx foreach { qiimeRatx =>
...@@ -163,18 +164,21 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript ...@@ -163,18 +164,21 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
qiimeClosed.outputDir = new File(outputDir, "qiime_closed") qiimeClosed.outputDir = new File(outputDir, "qiime_closed")
qiimeClosed.fastqInput = combinedFastq qiimeClosed.fastqInput = combinedFastq
add(qiimeClosed) add(qiimeClosed)
outputFiles += "qiime_closed_otu_table" -> qiimeClosed.otuTable
} }
qiimeOpen foreach { qiimeOpen => qiimeOpen foreach { qiimeOpen =>
qiimeOpen.outputDir = new File(outputDir, "qiime_open") qiimeOpen.outputDir = new File(outputDir, "qiime_open")
qiimeOpen.fastqInput = combinedFastq qiimeOpen.fastqInput = combinedFastq
add(qiimeOpen) add(qiimeOpen)
outputFiles += "qiime_open_otu_table" -> qiimeOpen.otuTable
} }
seqCount.foreach { seqCount => seqCount.foreach { seqCount =>
seqCount.fastqInput = combinedFastq seqCount.fastqInput = combinedFastq
seqCount.outputDir = new File(outputDir, "seq_count") seqCount.outputDir = new File(outputDir, "seq_count")
add(seqCount) add(seqCount)
outputFiles += "seq_count_count_file" -> seqCount.countFile
} }
addSummaryJobs() addSummaryJobs()
......
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