We have tried to submit as your intruction but our submission still can not be scored:
"Your submission "smcIsoform_Hera_workflow_1476205723_merged.cwl" (ID: 7355484) to the SMC-RNA-Challenge evaluation queue- Challenge 1-Isoforms has been scored:
Thank you for your submission to the SMC-RNA Challenge!
If you have questions, please ask on the forums at https://www.synapse.org/#!Synapse:syn2813589/discussion/default"
Can you help us check up the reason? Our tool need at least 9Gb for running, is memory one of the reason?
Thank you
Created by Hoa Pham linuxpham Your submission "smcFusion_Hera_workflow_1478021629_merged.cwl" (ID: 7488045) to the SMC-RNA-Challenge evaluation queue- Challenge 2-Fusions has been scored:
Thank you for your submission to the SMC-RNA Challenge!
Can you help us to check if there is problem while running?
Thank you very much Thank you very much! @cndgf We were able to run your workflow without encountering any errors. @cndgf Your most recent submission (ID: 7378934) has been received, but the workflow has not yet been tested or scored. I will test your code today and let you know if there are any problems. submission "comb_workflow_v2_1476704303_merged.cwl" (ID: 7378934) to the SMC-RNA-Challenge evaluation queue- Challenge 2-Fusions has been scored:
Thank you for your submission to the SMC-RNA Challenge!
Would you let me know if there is problem running it?
Thanks Thank you a lot! Once all submissions have been scored, the results will be posted on the leaderboard. We still haven't seen it reported any score in the email.
Could you please clarify how can we see the score for the submission? @linuxpham We have tested your latest submission (ID: 7367548) and were able to run it without any problems. We have tried to re-submit as your guides but our submission still can not be scored:
"Your submission "smcIsoform_Hera_workflow_1476549574_merged.cwl" (ID: **7367548**) to the SMC-RNA-Challenge evaluation queue- Challenge 1-Isoforms has been scored:
Thank you for your submission to the SMC-RNA Challenge!"
Can you help us check up the reason?
Thank you Thank you a lot! Thank you! @tnv We have tested your submission (ID: 7269246 ) and have been able to run it without any problems. I have a similar notification as below. So that means our workflow has no score yet right? Can you check this pls?
Your submission "FusionRnadt_workflow_1474369510_merged.cwl" (ID: 7269246) to the SMC-RNA-Challenge evaluation queue- Challenge 2-Fusions has been scored: Thank you for your submission to the SMC-RNA Challenge! If you have questions, please ask on the forums at https://www.synapse.org/#!Synapse:syn2813589/discussion/default. Sincerely, the scoring script
Many thanks! Thank a lot for your help The CWL for entries 7252845 and 7255230 are missing the tar step to uncompress the custom reference files. Could you resubmit the workflows including this step so that we can evaluate? I got the same email notification below. Does it mean that my workflow cannot be scored?
<<
Your submission "comb_workflow_v1_1474289621_merged.cwl" (ID: 7255230) to the SMC-RNA-Challenge evaluation queue- Challenge 2-Fusions has been scored:
Thank you for your submission to the SMC-RNA Challenge!
If you have questions, please ask on the forums at https://www.synapse.org/#!Synapse:syn2813589/discussion/default.
Sincerely,
>>
Thanks, Looking at that entry we see few problems with the CWL.
The submitted version includes a docker requirement in the workflow 'hints' stanza, it looks like this (after being changed from YAML to JSON):
```
"hints": [
{
"input": "index",
"DockerRequirement": {
"dockerPull": "..."
},
"class": "file:///.../synData",
"entity": "..."
}
]
```
1. So the docker requirement is embedded in the syndata hint, and the evaluation system won't find it there.
2. that is the hints for the Workflow class. Docker hints need to be in the CommandLineTool classes.
So take the DockerRequirements stanza and move it to the tool.