Kathleen Morrill
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Latest activity by Kathleen Morrill
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Kathleen Morrill commented,
The second approach, feeding bcftools write_lines(${inputSetVCF}), does indeed make a .tmp file containing a localized input per line. But the workflow errors out there, throwing "Array value was g...
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Kathleen Morrill commented,
I'll try that out later!I've run into a different problem with the merge workflow. Trying to get BCFtools to accept my Array[File] for input to merge. Done in this way, write_lines is making a file...
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Kathleen Morrill commented,
I ended up splitting into two workflows, filter VCF workflow for individual samples and a merge VCFs workflow for sample sets, which seems to be the better approach!But, still might be curious abou...
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Kathleen Morrill commented,
Ok, update, this appears to have just been a WDL versioning issue. Declaring version 1.0 at the top of the WDL allowed for struct definitions but other syntax had to change like input {} wrappers f...
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Kathleen Morrill created a post,
Struct Definition and sample_set entity
Hi, I am trying to make a workflow that uses entity `sample_set`, scatters over samples to filter and replace the IDs of their VCFs, and then merges said filtered VCFs. I'm getting parsing errors f...
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Kathleen Morrill commented,
Found a solution! Rather than inputting existing attributes and outputting those, I set the Task for if(!download) to run the command `exit 1`, forcing a fail state for the workflow. Failed workflo...
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Kathleen Morrill commented,
So, I have tried the solution of requesting the current data model attributes as outputs for a task that runs only if !download. However, I've found that the successful workflow will attempt to upd...
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Kathleen Morrill commented,
Thank you!Another suggested feature request, which might help with the same goal in mind, is the ability to sort the data model by multiple columns when selecting samples for a sample set. That way...
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Kathleen Morrill commented,
Thanks Samantha, I have added the support email to the workspace. Here is the workspace name: Dog Aging Project - Sequencing DataThe following submission has examples of samples for which the con...
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Kathleen Morrill created a post,
Only copy outputs to data model for conditional call
I've written a workflow (entity: sample) that downloads data from our partner sequencing platform. This workflow has a conditional call, namely... Boolean download = (sample_status == "succeeded" &...
- Kathleen Morrill
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