Update iChor WDLs for WDL 1.0 #77
Open
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
geoffjentry
commented
Jan 6, 2025
| Float maxFracCNASubclone | ||
| Float maxFracGenomeSubclone | ||
| input { | ||
| File bam_file |
There was a problem hiding this comment.
These weren't modified, they're just tabbed over one level
geoffjentry
commented
Jan 6, 2025
| String sample_id | ||
| Int bin_size | ||
|
|
||
| Int min_qual = 20 |
There was a problem hiding this comment.
As mentioned, the optionals with a default were converted to standard types
geoffjentry
commented
Jan 6, 2025
| Float altFracThreshold | ||
| Int lambdaScaleHyperParam | ||
| Int rmCentromereFlankLength | ||
| String plotFileType = "pdf" |
There was a problem hiding this comment.
This is one other example of the de-optioning
geoffjentry
commented
Jan 6, 2025
|
|
||
| call bundle_plots { | ||
| input: CNA_plots = CNA_plots, | ||
| summary_script = summary_script, | ||
| sample_set_name = sample_set_name | ||
| } | ||
| output { | ||
| bundle_plots.* | ||
| File bundledPDF = bundle_plots.bundledPDF |
There was a problem hiding this comment.
There's only this one output from bundle_plots, so I just kept the same name from the task
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Outdated suggestions cannot be applied.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.
This PR does a couple of things:
The removal of the optionals was useful because of constructs like
disks: "local-disk " + diskGB + " HDD"which is not technically valid (e.g. what ifdiskGBisNone?) although Cromwell does allow it. It also removed some warnings fromminiwdl checklisting.I don't have access to the docker containers at the moment so can't run this to verify the changes are valid. They shouldn't be modifying any behavior, but it'd be good to run this first before merging.