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Update output names for ReblockGVCF #1443

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Update output names for ReblockGVCF #1443

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71d8002
Update output names for ReblockGVCF
jessicaway Dec 3, 2024
2e62ede
Updated pipeline_versions.txt with all pipeline version information
actions-user Dec 3, 2024
a8b7bfe
Update versions and changelogs
jessicaway Dec 3, 2024
1abe40b
Merge remote-tracking branch 'origin/jw_update_reblock' into jw_updat…
jessicaway Dec 3, 2024
e84d265
Updated pipeline_versions.txt with all pipeline version information
actions-user Dec 3, 2024
00955ad
update changelogs
jessicaway Dec 5, 2024
bfb58cf
Merge remote-tracking branch 'origin/jw_update_reblock' into jw_updat…
jessicaway Dec 5, 2024
f4e3b62
Updated pipeline_versions.txt with all pipeline version information
actions-user Dec 5, 2024
46168f4
Merge branch 'develop' into jw_update_reblock
jessicaway Dec 5, 2024
5badc4c
the most minor major change
jessicaway Dec 5, 2024
ed5064d
Merge remote-tracking branch 'origin/jw_update_reblock' into jw_updat…
jessicaway Dec 5, 2024
b9f8211
Updated pipeline_versions.txt with all pipeline version information
actions-user Dec 5, 2024
f53ba80
update version again
jessicaway Dec 5, 2024
a8dba53
Updated pipeline_versions.txt with all pipeline version information
actions-user Dec 5, 2024
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6 changes: 3 additions & 3 deletions pipeline_versions.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,19 +2,19 @@ Pipeline Name Version Date of Last Commit
CheckFingerprint 1.0.22 2024-10-28
RNAWithUMIsPipeline 1.0.18 2024-11-04
AnnotationFiltration 1.2.7 2024-11-04
UltimaGenomicsWholeGenomeGermline 1.1.2 2024-11-04
UltimaGenomicsWholeGenomeGermline 1.1.3 2024-12-05
WholeGenomeGermlineSingleSample 3.3.3 2024-11-04
ExomeGermlineSingleSample 3.2.3 2024-11-04
JointGenotypingByChromosomePartTwo 1.5.2 2024-11-04
JointGenotypingByChromosomePartOne 1.5.2 2024-11-04
ReblockGVCF 2.3.2 2024-11-04
ReblockGVCF 2.4.0 2024-12-05
JointGenotyping 1.7.2 2024-11-04
UltimaGenomicsJointGenotyping 1.2.2 2024-11-04
VariantCalling 2.2.4 2024-11-04
UltimaGenomicsWholeGenomeCramOnly 1.0.23 2024-11-04
GDCWholeGenomeSomaticSingleSample 1.3.4 2024-11-04
BroadInternalRNAWithUMIs 1.0.36 2024-11-04
BroadInternalUltimaGenomics 1.1.2 2024-11-04
BroadInternalUltimaGenomics 1.1.3 2024-12-05
BroadInternalArrays 1.1.14 2024-11-04
BroadInternalImputation 1.1.14 2024-11-04
Arrays 2.6.30 2024-11-04
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5 changes: 5 additions & 0 deletions ...nes/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md
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Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
# 2.4.0
2024-12-05 (Date of Last Commit)

* Updated output names for ReblockGVCF workflow from output_vcf and output_vcf_index to reblocked_gvcf and reblocked_gvcf_index respectively

# 2.3.2
2024-11-04 (Date of Last Commit)

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6 changes: 3 additions & 3 deletions pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl
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Expand Up @@ -6,7 +6,7 @@ import "../../../../../../tasks/broad/Utilities.wdl" as utils

workflow ReblockGVCF {

String pipeline_version = "2.3.2"
String pipeline_version = "2.4.0"


input {
Expand Down Expand Up @@ -70,8 +70,8 @@ workflow ReblockGVCF {
}

output {
File output_vcf = Reblock.output_vcf
File output_vcf_index = Reblock.output_vcf_index
File reblocked_gvcf = Reblock.output_vcf
File reblocked_gvcf_index = Reblock.output_vcf_index
}
meta {
allowNestedInputs: true
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5 changes: 5 additions & 0 deletions ...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md
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@@ -1,3 +1,8 @@
# 1.1.3
2024-12-05 (Date of Last Commit)

* Updated the name of the output for ReblockGVCFs; this does not affect this pipeline

# 1.1.2
2024-11-04 (Date of Last Commit)

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6 changes: 3 additions & 3 deletions pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.wdl
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Expand Up @@ -50,7 +50,7 @@ workflow UltimaGenomicsWholeGenomeGermline {
filtering_model_no_gt_name: "String describing the optional filtering model; default set to rf_model_ignore_gt_incl_hpol_runs"
}

String pipeline_version = "1.1.2"
String pipeline_version = "1.1.3"


References references = alignment_references.references
Expand Down Expand Up @@ -202,8 +202,8 @@ workflow UltimaGenomicsWholeGenomeGermline {

# Outputs that will be retained when execution is complete
output {
File output_gvcf = ReblockGVCF.output_vcf
File output_gvcf_index = ReblockGVCF.output_vcf_index
File output_gvcf = ReblockGVCF.reblocked_gvcf
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Do we need to change the outputs here to? I don't think we (GVS) ever direct consume the output of this WDL, so it's likely that maintaining its output naming scheme was deliberate. But I just wanted to verify that here

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This change is necessary since the output of the reblock workflow is being referenced. I left the output name for this workflow the same, but needed to update the reference to the output of ReblockGVCF

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yup, totally makes sense why this change was needed. As I don't know the users of this particular wdl, I mostly wanted to ensure that it wasn't something any end users would be running before sending the data into GVS (in which case we'd want to update its outputs as well). It sounds as though this is not expected behavior though, and this one has only been touched because it consumes ReblockGVCF for other reasons. Thanks!

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It's a good question. I'm not sure whether we expect the outputs of this workflow to be used in joint calling.
@rickymagner would you be able to comment on whether we expect the outputs of UltimaGenomicsWholeGenomeGermline to be used for joint calling in GVS?

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Hm I don't know if GVS has been used on Ultima samples before. Does anyone from the Variants team know if that's an existing/planned application for GVS?

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Thanks @rickymagner!
Sounds like this isn't currently a known issue @koncheto-broad, let me know if this becomes an issue in the future and we can change it here too.

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Thanks for clarifying, y'all! I think we pretty exclusively use Illumina samples at this point, so the Ultima pipeline is unlikely to affect us. And if we discover that it does, we can always just reach out then!

File output_gvcf_index = ReblockGVCF.reblocked_gvcf_index
File output_vcf = ConvertGVCFtoVCF.output_vcf
File output_vcf_index = ConvertGVCFtoVCF.output_vcf_index

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5 changes: 5 additions & 0 deletions .../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md
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Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
# 1.1.3
2024-12-05 (Date of Last Commit)

* Updated the name of the output for ReblockGVCFs; this does not affect this pipeline

# 1.1.2
2024-11-04 (Date of Last Commit)

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2 changes: 1 addition & 1 deletion ...ad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl
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Expand Up @@ -6,7 +6,7 @@ import "../../../../../../../pipelines/broad/qc/CheckFingerprint.wdl" as FP

workflow BroadInternalUltimaGenomics {

String pipeline_version = "1.1.2"
String pipeline_version = "1.1.3"

input {

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8 changes: 4 additions & 4 deletions verification/test-wdls/TestReblockGVCF.wdl
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Expand Up @@ -54,8 +54,8 @@ workflow TestReblockGVCF {
# Collect all of the pipeline outputs into single Array[String]
Array[String] pipeline_outputs = flatten([
[ # File outputs
ReblockGVCF.output_vcf_index,
ReblockGVCF.output_vcf,
ReblockGVCF.reblocked_gvcf_index,
ReblockGVCF.reblocked_gvcf,
],

])
Expand Down Expand Up @@ -86,13 +86,13 @@ workflow TestReblockGVCF {
if (!update_truth){
call Utilities.GetValidationInputs as GetGvcf {
input:
input_file = ReblockGVCF.output_vcf,
input_file = ReblockGVCF.reblocked_gvcf,
results_path = results_path,
truth_path = truth_path
}
call Utilities.GetValidationInputs as GetGvcfIndex {
input:
input_file = ReblockGVCF.output_vcf_index,
input_file = ReblockGVCF.reblocked_gvcf_index,
results_path = results_path,
truth_path = truth_path
}
Expand Down
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