Commit 7a45bbcd authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge commit 'cde8f1a6' into peter

parents e7f818e2 cde8f1a6
dependency-reduced-pom.xml dependency-reduced-pom.xml
*~
*.swp
...@@ -92,4 +92,4 @@ object Fastqc { ...@@ -92,4 +92,4 @@ object Fastqc {
fastqcCommand.afterGraph fastqcCommand.afterGraph
return fastqcCommand return fastqcCommand
} }
} }
\ No newline at end of file
...@@ -82,12 +82,14 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript { ...@@ -82,12 +82,14 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
if (paired) addSha1sum(outputFiles("fastq_input_R2"), "sha1_R2") if (paired) addSha1sum(outputFiles("fastq_input_R2"), "sha1_R2")
var fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/") var fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
add(fastqc_R1)
outputFiles += ("fastqc_R1" -> fastqc_R1.output) outputFiles += ("fastqc_R1" -> fastqc_R1.output)
outputFiles += ("qualtype_R1" -> getQualtype(fastqc_R1, R1_name)) outputFiles += ("qualtype_R1" -> getQualtype(fastqc_R1, R1_name))
outputFiles += ("contams_R1" -> getContams(fastqc_R1, R1_name)) outputFiles += ("contams_R1" -> getContams(fastqc_R1, R1_name))
if (paired) { if (paired) {
var fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/") var fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/")
add(fastqc_R2)
outputFiles += ("fastqc_R2" -> fastqc_R2.output) outputFiles += ("fastqc_R2" -> fastqc_R2.output)
outputFiles += ("qualtype_R2" -> getQualtype(fastqc_R2, R2_name)) outputFiles += ("qualtype_R2" -> getQualtype(fastqc_R2, R2_name))
outputFiles += ("contams_R2" -> getContams(fastqc_R2, R2_name)) outputFiles += ("contams_R2" -> getContams(fastqc_R2, R2_name))
...@@ -232,9 +234,14 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript { ...@@ -232,9 +234,14 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
addSha1sum(R1, "sha1_qc_R1") addSha1sum(R1, "sha1_qc_R1")
if (paired) addSha1sum(R2, "sha1_qc_R2") if (paired) addSha1sum(R2, "sha1_qc_R2")
val fastqc_R1 = Fastqc(this, outputFiles("output_R1"), outputDir + "/" + R1_name + ".qc.fastqc/")
outputFiles += ("fastqc_R1_final" -> Fastqc(this, outputFiles("output_R1"), outputDir + "/" + R1_name + ".qc.fastqc/").output) add(fastqc_R1)
if (paired) outputFiles += ("fastqc_R2_final" -> Fastqc(this, outputFiles("output_R2"), outputDir + "/" + R2_name + ".qc.fastqc/").output) outputFiles += ("fastqc_R1_final" -> fastqc_R1.output)
if (paired) {
val fastqc_R2 = Fastqc(this, outputFiles("output_R2"), outputDir + "/" + R2_name + ".qc.fastqc/")
add(fastqc_R2)
outputFiles += ("fastqc_R2_final" -> fastqc_R2.output)
}
} }
if (!skipSummary) { if (!skipSummary) {
......
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