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add array imputation quota consumed wdl #1425

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Nov 13, 2024
Merged

add array imputation quota consumed wdl #1425

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1bcd8ca
add array imputation quota consumed wdl
Nov 13, 2024
dc9bb55
add changelogs for imputation array related workflows
Nov 13, 2024
af52bd9
fix bad file names and bad versions
Nov 13, 2024
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4 changes: 4 additions & 0 deletions .dockstore.yml
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Expand Up @@ -87,6 +87,10 @@ workflows:
subclass: WDL
primaryDescriptorPath: /pipelines/broad/arrays/imputation_beagle/LiftoverVcfs.wdl

- name: ArrayImputationQuotaConsumed
subclass: WDL
primaryDescriptorPath: /pipelines/broad/arrays/imputation_beagle/ArrayImputationQuotaConsumed.wdl

- name: RNAWithUMIsPipeline
subclass: WDL
primaryDescriptorPath: /pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl
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4 changes: 4 additions & 0 deletions pipelines/broad/arrays/imputation_beagle/ArrayImputationQuotaConsumed.changelog.md
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@@ -0,0 +1,4 @@
# 0.0.1
2024-11-13 (Date of Last Commit)

* Pipeline still in developmental state
34 changes: 34 additions & 0 deletions pipelines/broad/arrays/imputation_beagle/ArrayImputationQuotaConsumed.wdl
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@@ -0,0 +1,34 @@
version 1.0

import "../../../../tasks/broad/ImputationTasks.wdl" as tasks

workflow QuotaConsumed {
String pipeline_version = "0.0.1"

input {
Int chunkLength = 25000000
Int chunkOverlaps = 5000000

File multi_sample_vcf

File ref_dict
Array[String] contigs
String reference_panel_path_prefix
String genetic_maps_path
String output_basename
Boolean split_output_to_single_sample = false

# file extensions used to find reference panel files
String interval_list_suffix = ".interval_list"
String bref3_suffix = ".bref3"
}

call tasks.CountSamples {
input:
vcf = multi_sample_vcf
}

output {
Int quota_consumed = CountSamples.nSamples
}
}
4 changes: 4 additions & 0 deletions ...ines/broad/arrays/imputation_beagle/CreateImputationRefPanelBeagle.changelog.md
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# 0.0.1
2024-11-13 (Date of Last Commit)

* Pipeline still in developmental state
2 changes: 2 additions & 0 deletions pipelines/broad/arrays/imputation_beagle/CreateImputationRefPanelBeagle.wdl
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Expand Up @@ -2,6 +2,8 @@ version 1.0

# This script is under review. It is not actively tested or maintained at this time.
workflow CreateImputationRefPanelBeagle {
String pipeline_version = "0.0.1"

input {
Array[File] ref_vcf
Array[File] ref_vcf_index
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4 changes: 4 additions & 0 deletions pipelines/broad/arrays/imputation_beagle/ImputationBeagle.changelog.md
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# 0.0.1
2024-11-13 (Date of Last Commit)

* Pipeline still in developmental state
4 changes: 4 additions & 0 deletions pipelines/broad/arrays/imputation_beagle/ImputationBeaglePreChunk.changelog.md
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# 0.0.1
2024-11-13 (Date of Last Commit)

* Pipeline still in developmental state
4 changes: 4 additions & 0 deletions pipelines/broad/arrays/imputation_beagle/LiftoverVcfs.changelog.md
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# 0.0.1
2024-11-13 (Date of Last Commit)

* Pipeline still in developmental state
2 changes: 1 addition & 1 deletion pipelines/broad/arrays/imputation_beagle/LiftoverVcfs.wdl
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Expand Up @@ -3,7 +3,7 @@ version 1.0
# Liftover VCFs from hg19 to hg38
workflow LiftoverVcfs {

String pipeline_version = "1.0.0"
String pipeline_version = "0.0.1"

input {
File vcf_path
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