From eea04f4fc7bc02c662e75083dc47ea0738655ba0 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 19 Jan 2018 14:54:30 +0100
Subject: [PATCH] written fastqc task
---
fastqc.wdl | 60 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 60 insertions(+)
diff --git a/fastqc.wdl b/fastqc.wdl
index e69de29..2b4cd87 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -0,0 +1,60 @@
+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)
+ }
+}
--
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