Stacky Glue / BCLConvert InteropQC / cttsoV2 Fixes / Deprecate ICAv2 Copy Batch Utility #337
Conversation
This file contains 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
…tabases Generated a dynamodb table with a sort key and one without a sort key
With latest changes to WRSC schema, update the icav2 handler and WRSC ready event handler Also added a SFN for generating ready events from a prior workflowrunstatechange Renamed icav2-table stack Also renamed dynamodb constructs in the bclconvert manager from the previous commit
Removed the icav2 copy batch utility stack
Removed remnants of icav2 copy batch utility stack. Use the new icav2 copy batch component inside the bssh fastq copy manager
CWL Pipeline that is triggered after the fastqs have landed in our bucket
Updated the inputs to match the new WRSC. Rely on the input glue to shrink the samplesheet and fastq list rows
Initialised stacky stateful components and stateless integration
Scotch integration for connecting the bclconvert manager success event to starting the bssh fastq event
Connect the completion of the bssh fastq copy manager to the start of the bclconvert interop qc pipeline and register the fastq list rows in the database
Now that the fastq list rows are in the database, find all samples that are tso500L samples and launch the cttso v2 analysis
This was
linked to
issues
May 31, 2024
8 tasks
This was
linked to
issues
May 31, 2024
Some wait steps for databases were set at the default '5' seconds
|
.. will take time & review today |
victorskl
approved these changes
Jun 3, 2024
|
Happy to merge this whenever you ready, Alexis. (I will take half the pizza 🍕 , if things go south) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
Generic Constructs
Added python lambda components (810f1f1)
Added partition table constructs (9f824cc)
Added ICAv2 workflow handlers (d9b6bc4)
Added ICAv2 Copy Batch Utility Construct (1cf7f2f)
BSSH Fastq Copy Manager
BCLConvert InterOp QC PIpeline Stack
ctTSO500 Pipeline Stack
StackyMcStackFace! (The Glue bits)
Scotch (bclconvert manager to bssh fastq copy)
Selleys (bssh fastq copy to BCLConvert InterOp QC)
Super (bssh fastq copy to cttsov2)