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Ensure index files are stored under the same dir/bucket as their respective file in EH WDL #282

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Jan 12, 2022
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Ensure index files are stored under the same dir/bucket as their respective file in EH WDL #282

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13 changes: 12 additions & 1 deletion wdl/ExpansionHunter.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -86,6 +86,17 @@ task RunExpansionHunter {
command <<<
set -euxo pipefail

BAM_OR_CRAM_DIR="$(dirname "~{bam_or_cram}")"
BAM_OR_CRAM_INDEX_FILENAME="$(basename "~{bam_or_cram_index}")"
DEST="$BAM_OR_CRAM_DIR/$BAM_OR_CRAM_INDEX_FILENAME"
if [ $DEST != ~{bam_or_cram_index} ]; then
mv ~{bam_or_cram_index} $DEST
fi
Comment on lines +92 to +94
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Do you need the if?

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in my tests, mv exits with fail code if the file is already there.


REF="$(basename "~{reference_fasta}")"
mv ~{reference_fasta} $REF
mv ~{reference_fasta_index} $REF.fai

sex=""
if ~{defined(ped_file)}; then
sex=$(awk -F '\t' '{if ($2 == "~{sample_id}") {if ($5 == "1") {print "--sex male"; exit 0} else if ($5 == "2") {print "--sex female"; exit 0}}}' < ~{ped_file} )
Expand All @@ -97,7 +108,7 @@ task RunExpansionHunter {

ExpansionHunter \
--reads ~{bam_or_cram} \
--reference ~{reference_fasta} \
--reference $REF \
--variant-catalog ~{variant_catalog} \
--output-prefix ~{sample_id} \
--cache-mates \
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