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Commit 6cccf353 authored by Ruben Vorderman's avatar Ruben Vorderman
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work with adapterlist

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cutadapt.wdl
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...@@ -60,9 +60,12 @@ task cutadapt { ...@@ -60,9 +60,12 @@ task cutadapt {
${"source activate " + condaEnv} ${"source activate " + condaEnv}
cutadapt \ cutadapt \
${"--cores=" + cores} \ ${"--cores=" + cores} \
${sep="-a " "-a " + adapter} ${"-A " + adapterRead2} \ ${true="-a " false="" defined(adapter)} ${sep=" -a " adapter} \
${"-g" + front} ${"-G" + frontRead2} \ ${true="-A " false="" defined(adapterRead2)} ${sep=" -A " adapterRead2} \
${"-b " + anywhere} ${"-B" + anywhereRead2} \ ${true="-g " false="" defined(front)} ${sep=" -g " front} \
${true="-G " false="" defined(frontRead2)} ${sep=" -G " frontRead2} \
${true="-b " false="" defined(anywhere)} ${sep=" -a " anywhere} \
${true="-B " false="" defined(anywhereRead2)} ${sep=" -B " anywhereRead2} \
--output ${read1output} ${"--paired-output " + read2output} \ --output ${read1output} ${"--paired-output " + read2output} \
${"--to-short-output " + tooShortOutputPath} ${"--to-short-paired-output " + tooShortPairedOutputPath} \ ${"--to-short-output " + tooShortOutputPath} ${"--to-short-paired-output " + tooShortPairedOutputPath} \
${"--to-long-output " + tooLongOutputPath} ${"--to-long-paired-output " + tooLongPairedOutputPath} \ ${"--to-long-output " + tooLongOutputPath} ${"--to-long-paired-output " + tooLongPairedOutputPath} \
......
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