remove poretools.wdl

poretools.wdl

-task fastq {
-    Array[File]+ files # Files should exist! Also accepts multiple directories (unlike poretools).
-    String outputFile
-    String? preCommand
-    String? type
-    String? start
-    String? end
-    Int? minLength
-    Int? maxLength
-    Boolean? highQuality
-    Boolean? normalQuality
-    String? group
-    Boolean? gzip = true
-    command {
-    set -e -o pipefail
-    mkdir -p $(dirname ${outputFile})
-    ${preCommand}
-
-    (
-    # Allow for multiple directory input by looping over files
-    for file in ${sep=" " files}
-    do
-        poretools fastq \
-        ${"--type " + type} \
-        ${"--start " + start } \
-        ${"--end " + end } \
-        ${"--min-length " + minLength } \
-        ${"--max-length " + maxLength } \
-        ${true="--high-quality" false="" highQuality} \
-        ${true="--normal-quality" false="" normalQuality} \
-        ${"--group " + group} \
-        $file
-    done
-    ) ${true="| gzip " false="" gzip}> ${outputFile}
-    }
-
-    output {
-    File fastq = outputFile
-    }
-}
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