Commit 613343f7 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix on fastqc jobs

parent 1395457c
...@@ -81,16 +81,18 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript { ...@@ -81,16 +81,18 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
addSha1sum(outputFiles("fastq_input_R1"), "sha1_R1") addSha1sum(outputFiles("fastq_input_R1"), "sha1_R1")
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/") val fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
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))
add(fastqc_R1)
if (paired) { if (paired) {
var fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/") val fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/")
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))
add(fastqc_R2)
} }
} }
...@@ -233,8 +235,14 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript { ...@@ -233,8 +235,14 @@ 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")
outputFiles += ("fastqc_R1_final" -> Fastqc(this, outputFiles("output_R1"), outputDir + "/" + R1_name + ".qc.fastqc/").output) val fastqc_R1 = Fastqc(this, outputFiles("output_R1"), outputDir + "/" + R1_name + ".qc.fastqc/")
if (paired) outputFiles += ("fastqc_R2_final" -> Fastqc(this, outputFiles("output_R2"), outputDir + "/" + R2_name + ".qc.fastqc/").output) add(fastqc_R1)
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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