Dear organizers,
I submitted my workflow on SBG-CGC last week. A few days later, I received a validation error from the scoring script:
```
Hello uhrigs,
Sorry, but we were unable to validate your submission to the SMC-RNA-Challenge evaluation queue- Challenge 2-Fusions.
Please refer to the challenge instructions which can be found at https://www.synapse.org/#!Synapse:syn2813589/wiki/70850 and to the error message below:
submission name: uhrigs-smc-rna-fusion-challenge-2017-03-08-14-33
submission ID: 8396553
'status'
If you have questions, please ask on the forums at https://www.synapse.org/#!Synapse:syn2813589/discussion/default.
Sincerely,
the scoring script
```
I tried troubleshooting the issue with the support staff from SBG-CGC, but everything seems okay on their side. My workflow runs fine and produces valid output files as far as I can tell (fusionToolEvaluator processes it without complaint). Can you kindly give me a hint why the submission was rejected? I am clueless at this point, because the error message is not really verbose and it is near impossible to do trial-and-error-style debugging, if it takes days for the scoring script to give feedback.
Many thanks in advance,
Sebastian
P. S. On a related note: The SBG-CGC supporter recommended to use the "DREAM Fusion Detection Evaluation Workflow" to test the output of my submission for validity. Strangely, the workflow does not produce any output (the output port is empty), even when I give it truth files as input. Can you confirm this or am I doing something wrong?
Created by uhrigs Dear Jeltje,
This error has been resolved. Thanks for bringing this to our attention.
Best,
Tom @thomas.yu this may be related to my issue:
When I run `SMC-RNA-Challenge/script/smc_rna_submit.py validate` on my merged workflow,
I get the warning `Not all of your inputs in your workflow are mapped`
This appears to be because I'm passing the fastq files as an array like so:
```
inputs:
TUMOR_FASTQ_1: File
TUMOR_FASTQ_2: File
steps:
fusioncatcher:
run: ../tools/fusioncatcher.cwl
in:
fastq: [TUMOR_FASTQ_1, TUMOR_FASTQ_2]
out: [output]
```
which works fine in my test runs, but gets validated (in line 156) as
`['#main/TUMOR_FASTQ_1', '#main/TUMOR_FASTQ_2'] in ['#main/TUMOR_FASTQ_1', '#main/TUMOR_FASTQ_2', '#main/convert/fusionout', '#main/convert/fusionout', '#main/fusioncatcher/output']`
and that obviously fails.
Do you have a version of `smc_rna_submit.py` that parses such arrays correctly? We are working through all of the submissions made before the deadline and working with the authors to make sure we can get them to run. We will contact you if we need to clarify or fix any minor points to get the pipeline to run and allow you to send minor fixes if needed. Hi Tom,
Thanks for looking into this issue! Assuming the submission is valid, I would appreciate it, if you considered my submission for round 3, since I submitted it before the deadline. But I could understand, if it were too late for that now and my submission could only be considered for round 4.
Regards,
Sebastian Dear Sebastian,
We are working on this issue. Your submission should be valid. After we fix this, a new validation email will be sent to you. Thanks in advance for your patience.
Best,
Tom