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Update "unsorted" to "queryname" #32

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Update "unsorted" to "queryname" #32

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9ba205e
Update "unsorted" to "queryname"
jason-cerrato Aug 10, 2022
18b73d6
add ".wdl"
jason-cerrato Aug 10, 2022
fa7fba9
Update .dockstore.yml
jason-cerrato Aug 10, 2022
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2 changes: 1 addition & 1 deletion .dockstore.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ version: 1.2
workflows:
- name: processing-for-variant-discovery-gatk4
subclass: WDL
primaryDescriptorPath: /processing-for-variant-discovery-gatk4
primaryDescriptorPath: /processing-for-variant-discovery-gatk4.wdl
testParameterFiles:
- /processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json
- /processing-for-variant-discovery-gatk4.b37.wgs.inputs.json
6 changes: 3 additions & 3 deletions processing-for-variant-discovery-gatk4.wdl
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Expand Up @@ -124,7 +124,7 @@ workflow PreProcessingForVariantDiscovery_GATK4 {
bwa_commandline = bwa_commandline,
bwa_version = GetBwaVersion.version,
aligned_bam = SamToFastqAndBwaMem.output_bam,
output_bam_basename = bam_basename + ".aligned.unsorted",
output_bam_basename = bam_basename + ".aligned.queryname",
ref_fasta = ref_fasta,
ref_fasta_index = ref_fasta_index,
ref_dict = ref_dict,
Expand All @@ -142,7 +142,7 @@ workflow PreProcessingForVariantDiscovery_GATK4 {
call MarkDuplicates {
input:
input_bams = MergeBamAlignment.output_bam,
output_bam_basename = base_file_name + ".aligned.unsorted.duplicates_marked",
output_bam_basename = base_file_name + ".aligned.queryname.duplicates_marked",
metrics_filename = base_file_name + ".duplicate_metrics",
docker_image = gatk_docker,
gatk_path = gatk_path,
Expand Down Expand Up @@ -376,7 +376,7 @@ task MergeBamAlignment {
--OUTPUT ~{output_bam_basename}.bam \
--REFERENCE_SEQUENCE ~{ref_fasta} \
--PAIRED_RUN true \
--SORT_ORDER "unsorted" \
--SORT_ORDER "queryname" \
--IS_BISULFITE_SEQUENCE false \
--ALIGNED_READS_ONLY false \
--CLIP_ADAPTERS false \
Expand Down