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umccr / cwl-ica

A collection of cwl-ica workflows along with a user guide for the commands to use and contributions guide
MIT License
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Germline params update #565

Closed skanwal closed 4 weeks ago

skanwal commented 4 weeks ago

Added in parameters to test Dragen tool with long read data. I haven't yet been able to setup the new cwl-ica-cli version (conda solver error) to sync definition in dev for the resource requirements issue.

@alexiswl - can you please sync the dev definition with this change https://github.com/umccr/cwl-ica/commit/cb076b018659fdd8db78230bb2ecc387b85f85d1?

alexiswl commented 4 weeks ago

I haven't yet been able to setup the new cwl-ica-cli version (conda solver error) to sync definition in dev for the resource requirements issue.

Likely an issue with mamba, uninstall mamba and your issue should be resolved

alexiswl commented 4 weeks ago

Added in parameters to test Dragen tool with long read data.

Cool, noted you've just updated the CommandLineTool, not the workflow, I'll do that.

Also noted --repeat-genotype-specs has not been added in to be either a string (an internal path) or a file (an external path) as previously discussed. Will add these in now too

alexiswl commented 4 weeks ago

Once this is merged @minw2828 I'll make an ICAv2 bundle for this pipeline to put into your ICAv2 project