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ExpansionHunter extract sex from a ped file. #281

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merged 14 commits into from
Jan 11, 2022
Merged

ExpansionHunter extract sex from a ped file. #281

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b7e176c
ExpansionHunter extract sex from a ped file.
VJalili Jan 10, 2022
5370144
Update wdl/ExpansionHunter.wdl
VJalili Jan 10, 2022
45ab21d
Update wdl/ExpansionHunterScatter.wdl
VJalili Jan 10, 2022
afc9403
Update wdl/ExpansionHunter.wdl
VJalili Jan 10, 2022
08889d2
Update wdl/ExpansionHunterScatter.wdl
VJalili Jan 10, 2022
64245ed
Update wdl/ExpansionHunter.wdl
VJalili Jan 10, 2022
9f132cf
Add parameter metadata for few arguments.
VJalili Jan 10, 2022
3f6c266
Errout if sample ID or ped file are not defined & few bug fixes.
VJalili Jan 11, 2022
de3502a
Improve on determining sample sex.
VJalili Jan 11, 2022
82f2406
Remove output_prefix & make sample_id required.
VJalili Jan 11, 2022
5ea38f4
Update wdl/ExpansionHunter.wdl
VJalili Jan 11, 2022
de6a0bd
Update wdl/ExpansionHunterScatter.wdl
VJalili Jan 11, 2022
0e1f251
Update a comment.
VJalili Jan 11, 2022
7040314
Merge remote-tracking branch 'origin/eh_gender' into eh_gender
VJalili Jan 11, 2022
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17 changes: 16 additions & 1 deletion wdl/ExpansionHunter.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,8 @@ workflow ExpansionHunter {
File reference_fasta
File? reference_fasta_index
File variant_catalog
String? individual_id
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File? ped_filename
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File? output_prefix
String expansion_hunter_docker
RuntimeAttr? runtime_attr
Expand Down Expand Up @@ -52,6 +54,8 @@ workflow ExpansionHunter {
reference_fasta = reference_fasta,
reference_fasta_index = reference_fasta_index_,
variant_catalog = variant_catalog,
individual_id = individual_id,
ped_filename = ped_filename,
output_prefix = output_prefix_,
expansion_hunter_docker = expansion_hunter_docker,
runtime_attr_override = runtime_attr,
Expand All @@ -72,6 +76,8 @@ task RunExpansionHunter {
File reference_fasta
File reference_fasta_index
File variant_catalog
String? individual_id
File? ped_filename
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String output_prefix
String expansion_hunter_docker
RuntimeAttr? runtime_attr_override
Expand All @@ -87,13 +93,22 @@ task RunExpansionHunter {
command <<<
set -euxo pipefail

sex=""
if [ ! -z "~{ped_filename}" -a "~{ped_filename}" != " " ]; then
if [ -e "~{ped_filename}" ]; then
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sex=$(awk -F '\t' '{if ($2 == "~{individual_id}") {if ($5 == "1") {print "--sex male"; exit 0} else if ($5 == "2") {print "--sex female"; exit 0} else {exit 1}}}' < ~{ped_filename} )
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I would actually try to emit a helpful error message if the sex is undefined. I think it would be best to define sex="NA" if the ped file is provided. Then use print "NA"; exit 0 instead of exit 1 in the last if clause. Then check the value of sex below - if it's NA then warn that either the sample id was not found or the sex is undefined and fail.

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Please check if the updated condition would be equally good.

fi
fi
echo $sex

ExpansionHunter \
--reads ~{bam_or_cram} \
--reference ~{reference_fasta} \
--variant-catalog ~{variant_catalog} \
--output-prefix ~{output_prefix} \
--cache-mates \
--record-timing
--record-timing \
$sex
>>>

RuntimeAttr runtime_attr_str_profile_default = object {
Expand Down
9 changes: 9 additions & 0 deletions wdl/ExpansionHunterScatter.wdl
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Expand Up @@ -9,6 +9,7 @@ workflow ExpansionHunterScatter {
Array[File] bams_or_crams
Array[File]? bams_or_crams_indexes
Array[String]? sample_ids
File? ped_filename
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File reference_fasta
File? reference_fasta_index
File variant_catalog
Expand Down Expand Up @@ -37,13 +38,21 @@ workflow ExpansionHunterScatter {
else
basename(bam_or_cram_, ".cram")

String individual_id =
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if defined(sample_ids) then
select_first([sample_ids])[i]
else
output_prefix

call ExpansionHunter.ExpansionHunter as expanionHunter {
input:
bam_or_cram=bam_or_cram_,
bam_or_cram_index=bam_or_cram_index_,
reference_fasta=reference_fasta,
reference_fasta_index=reference_fasta_index_,
variant_catalog=variant_catalog,
individual_id=individual_id,
ped_filename=ped_filename,
output_prefix=output_prefix,
expansion_hunter_docker=expansion_hunter_docker,
runtime_attr=runtime_attr
Expand Down