This thread is the designated place to ask questions about running the broad-gatk-validate-bam workflow.
Created by James Eddy jaeddy Apparently I had the sharing settings wrong on the evaluation queue, so only admins were able to submit. That's fixed now.
You should be able to submit your results through Synapse, without re-running the `synapse-submit` tool:
1. Navigate to the folder where you stored the results (https://www.synapse.org/#!Synapse:syn11638646);
2. Find the file that was uploaded (should be a zipped folder named `9607590_BioGenLink_.zip`), click on the file to open the Synapse page for that entity;
3. Click the **Tools** icon in the top right corner of the screen and select **Submit File to Challenge**;
4. Select `GA4GH-DREAM_broad-gatk-data-processing` from the list and proceed through the remaining steps.
You can also submit using the CWL tool as you did before ? whichever is easier! Let me know when you've re-submitted and I'll manually run the validation for that workflow.
Best,
James
Awesome, thanks! Hey @bernest - I'll take a look this morning and see if we can get the issue resolved. I'm certainly happy to count the submission!
Hi, I submitted results for this workflow a few days ago, and the result files were uploaded to the correct directory, but they were never validated. I see now that I got an error from running the submission command: `cwltool --non-strict dockstore-tool-synapse-submit.cwl ValidateBam_submit.cwl.json`.
My `ValidateBam_submit.cwl.json` file contains the following:
```
{
"config_file": {
"class": "File",
"path": ".synapseConfig"
},
"team_name": "BioGenLink",
"eval_id": "9607590",
"file": [
{
"class": "File",
"path": "H06HDADXX130110.1.ATCACGAT.20k_reads.validation_SUMMARY.txt"
},
{
"class": "File",
"path": "H06HDADXX130110.2.ATCACGAT.20k_reads.validation_SUMMARY.txt"
}
],
"parent_id": "syn11638646"
}
```
My two results files both contain the phrase "No errors found" in them.
I got the following error message:
```shell
SynapseHTTPError: 403 Client Error: Forbidden
User lacks SUBMIT access to Evaluation 9607590
```
But overall, it appears that the submission succeeded, because everything else looked normal and I got the following message at the end:
```
##################################################
Uploading file to Synapse storage
##################################################
[job dockstore-tool-synapse-submit.cwl] completed success
{}
Final process status is success
```
Any ideas? This happened before December 31st, so it doesn't appear to be because the submission queue was closed.
Drop files to upload
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