TSPS-887 make low pass imputation workflow driven by contig input#1803
Merged
jsotobroad merged 14 commits intodevelopfrom Apr 1, 2026
Merged
TSPS-887 make low pass imputation workflow driven by contig input#1803jsotobroad merged 14 commits intodevelopfrom
jsotobroad merged 14 commits intodevelopfrom
Conversation
added 10 commits
March 25, 2026 10:49
…assed down to nested scatters
|
Remember to squash merge! |
🔍Changelog Validation Results: |
🔍Version Validation Results: |
|
Remember to squash merge! |
🔍Changelog Validation Results: |
🔍Version Validation Results: |
MatthewBemis
approved these changes
Mar 30, 2026
mmorgantaylor
approved these changes
Mar 31, 2026
Member
mmorgantaylor
left a comment
mmorgantaylor
left a comment
There was a problem hiding this comment.
nice, just a couple minor things
| File sites_table_index | ||
|
|
||
| Array[String] contigs | ||
| String reference_panel_prefix |
Member
There was a problem hiding this comment.
can we add a comment about what this is expected to look like, i.e. based on how it's used, should it end with a . ?
Contributor
Author
There was a problem hiding this comment.
yup yup, can add a comment
| calls_bcf = BcftoolsCall.output_bcf, | ||
| } | ||
| File phase_input_vcf = select_first([BcftoolsMerge.merged_vcf, BcftoolsNorm.output_vcf[0], input_vcf]) | ||
| File phase_input_vcf_index = select_first([BcftoolsMerge.merged_vcf_index, BcftoolsNorm.output_vcf_index[0],input_vcf_index]) |
Member
There was a problem hiding this comment.
Suggested change
| File phase_input_vcf_index = select_first([BcftoolsMerge.merged_vcf_index, BcftoolsNorm.output_vcf_index[0],input_vcf_index]) | |
| File phase_input_vcf_index = select_first([BcftoolsMerge.merged_vcf_index, BcftoolsNorm.output_vcf_index[0], input_vcf_index]) |
nit - add space after comma
| cpu: cpu | ||
| preemptible: preemptible | ||
| maxRetries: max_retries | ||
| maxRetries: max_retries |
|
Remember to squash merge! |
🔍Changelog Validation Results: |
🔍Version Validation Results: |
|
Remember to squash merge! |
🔍Version Validation Results: |
🔍Changelog Validation Results: |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
4 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Description
These changes make it so the computation done in the workflow is driven by the
contigsinput. The workflow becomes more user friendly for both our service and for users using the wdl directly. The downside is that now the reference related files need to live in the same cloud base path.chr20 run - https://app.terra.bio/#workspaces/allofus-drc-imputation/Imputation_Server_Hydrogen_Dev/submission_history/474ebcfe-5a0a-4e76-833a-c8df096e1f43
chr1 + chr20 run - https://app.terra.bio/#workspaces/allofus-drc-imputation/Imputation_Server_Hydrogen_Dev/submission_history/e0c5e12d-42c0-407d-972c-c203be894563
Checklist
If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP team by tagging @broadinstitute/warp-admins in a comment on this PR.