Scripts to create downsampled files #662
Open
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Outdated suggestions cannot be applied.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.
This PR adds utility scripts to create test data for the pipeline, which are created either by downsampling a larger file to contain information overlapping given test regions or by converting file types, whichever suits best. The resulting files are smaller than the input files, leading to faster and cheaper execution of workflows for testing purposes.
The following changes are implemented:
Create a
tests
folder containing all the tests, and move the Carrot-related files to this folder;Implement methods to downsample different types of files;
.cram
..vcf
,.interval_list
, and primary contigs file are the currently supported file types.Implement a script that iterates through given workflow JSON files, downsamples the set files, pushes them to the cloud if needed, and creates an output JSON file containing the downsampled files in addition to untouched inputs. For instance:
input JSON:
output json:
Add a BED file with default target regions such that resulting downsampled files run successfully through the
GatherSampleEvidence
workflow.The UUID of a test run on GCP:
dd8bc64f-7ac0-46b6-ae39-2af86f0fe573