Add seqstat generate. ValidateFastq now validates files.

biopet/seqstat.wdl

+version 1.0
+
+# Copyright Sequencing Analysis Support Core - Leiden University Medical Center 2018
+
+task Generate {
+    input {
+        String? preCommand
+        File? toolJar
+        File fastqR1
+        File? fastqR2
+        String outputFile
+        String sample
+        String library
+        String readgroup
+
+        Int memory = 4
+        Float memoryMultiplier = 2.0
+    }
+
+    String toolCommand = if defined(toolJar)
+        then "java -Xmx" + memory + "G -jar " + toolJar
+        else "biopet-seqstat -Xmx" + memory + "G"
+
+    command {
+        set -e -o pipefail
+        ~{preCommand}
+        mkdir -p $(dirname ~{outputFile})
+        ~{toolCommand} Generate \
+        --fastqR1 ~{fastqR1} \
+        ~{"--fastqR2 " + fastqR2} \
+        --output ~{outputFile} \
+        ~{"--sample " + sample} \
+        ~{"--library " + library } \
+        ~{"--readgroup " + readgroup }
+    }
+
+    output {
+        File json = outputFile
+    }
+
+    runtime {
+        memory: ceil(memory * memoryMultiplier)
+    }
+}
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