written fastqc task

fastqc.wdl

+task fastqc {
+    File seqFile
+    String outdirPath
+    String? condaEnv
+    Boolean? casava
+    Boolean? nano
+    Boolean? noFilter
+    Boolean? extract = true
+    Boolean? nogroup
+    Int? minLength
+    String? format
+    Int? threads = 1
+    File? contaminants
+    File? adapters
+    File? limits
+    Int? kmers
+    String? dir
+
+    command {
+    set -e -o pipefail
+    ${"source activate " + condaEnv}
+    mkdir -p ${outdirPath}
+    fastqc \
+    ${"--outdir " + outdirPath}
+    ${true="--casava" false="" casava} \
+    ${true="--nano" false="" nano} \
+    ${true="--nofilter" false="" noFilter} \
+    ${true="--extract" false="" extract} \
+    ${true="--nogroup" false="" nogroup} \
+    ${"--min_length " + minLength } \
+    ${"--format " + format} \
+    ${"--threads " + threads} \
+    ${"--contaminants " + contaminants} \
+    ${"--adapters " + adapters} \
+    ${"--limits " + limits} \
+    ${"--kmers " + kmers} \
+    ${"--dir " + dir} \
+    ${seqFile}
+    }
+
+    output {
+        String reportDir = outdirPath + "/" + sub(basename(seqFile),"\..*$","_fastqc")
+        File rawReport = reportDir + "/fastqc_data.txt"
+        File htmlReport = reportDir + "fastqc_report.html"
+        File summary = reportDir + "/summary.txt"
+        File adapterContent = reportDir + "/Images/adapter_content.png"
+        File duplicationLevels = reportDir + "/Images/duplication_levels.png"
+        File perBaseNContent = reportDir + "/Images/per_base_n_content.png"
+        File perBaseQuality = reportDir + "/Images/per_base_quality.png"
+        File perBaseSequenceContent = reportDir + "/Images/per_base_sequence_content.png"
+        File perSequenceGCContent = reportDir + "/Images/per_sequence_gc_content.png"
+        File perSequenceQuality = reportDir + "/Images/per_sequence_quality.png"
+        File perTileQuality = reportDir + "/Images/per_tile_quality.png"
+        File sequenceLengthDistribution = reportDir + "/Images/sequence_length_distribution.png"
+    }
+
+    runtime {
+        cpu: select_first(threads)
+    }
+}