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Nuwah12
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proper bash escaping
1 parent f17d39e commit 5e9d541

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wdl_tasks/peak_calling.wdl

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -88,7 +88,7 @@ task MACS2_CallPeaks {
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~{if call_summits then "--call-summits" else ""} \
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~{broad_flag} \
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~{if defined(estimated_fragment_size) then "--nomodel" else ""} \
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~{if defined(estimated_fragment_size) then ("--shiftsize="+"${HALF_FRAG}") else ""}
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~{if defined(estimated_fragment_size) then ("--shiftsize="+$HALF_FRAG) else ""}
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~{if defined(estimated_fragment_size) then ("--bw="+Bandwidth) else ""} \
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~{if paired_end then "--format BAMPE" else "--format BAM"} \
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--keep-dup=1 \

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