-
Notifications
You must be signed in to change notification settings - Fork 107
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Add support for artic primer set version V5.3.2 #373
Comments
Done! nf-core/configs@f84bc30 Are you able to test it out with the latest version of the pipeline and let us know if everything is working as expected please? |
I test it with the following configuration:
Which is the same configuration I always use, the only difference is between 4.1 and 5.3.2 but I get this error:
As I mentioned, this used to work with 4.1 and never complained about it being a string. I assume this is because of the two dots instead of one that makes the pipeline interpret it as a string? Perhaps this could be simply fixed by changing the nextflow_schema.json primer_set_version type to string instead of number, but not sure whether this would have any further consequences. |
Yep, this is a more complex issue with the way parameters are coerced by Nextflow and then mismatch the validation. Changing the line below to viralrecon/nextflow_schema.json Line 112 in 3731dd3
However, the pipeline fails when you provide older primer sets that are integers: ERROR: Validation of pipeline parameters failed!
* --primer_set_version: expected type: String, found: Integer (1) Any suggestions @ewels ? For now, I think the best solution is to provide the parameters via a
Haven't tested this so please let me know if the pipeline complains elsewhere! |
In general though, if you plan on using this primer set even more often it's worth downloading the files locally and updating the
|
When using the params-file do I just need to specify the genome and leave primer set etc as defaults? I actually never used it before but this could be useful for testing new primer sets that arent commercially available yet. |
I would add that in the ignore_params thingy |
Ok. Ignore everything I said about using a params file. Can you try with your original command in this comment and add this parameter too please?
Thanks @maxulysse ! |
Hello @drpatelh I'd like to hijack this thread, if I may. My lab has generated tiled-PCR amplfication assays using PrimalScheme for a couple of other viruses. I was wondering if there is a workaround to allow Viralrecon to take in completely custom schemes? They should be functionally the same as those being generated for SARS-CoV-2. I wasn't sure if the thoughts in this thread might be applicable to my scenario. Thanks in advance. -Cody |
Hi @Codes1985 . You might be able to use similar parameters to the ones suggested for the SWIFT panel with customisations for your genome reference and primer sets. You might need to check that the pipeline is using the primer sets as expected by checking some of the heatmaps / plots etc: Might be good to have something like this as generic docs in that section too. |
Sorry to further the hijacking but did @Codes1985 have any luck with custom schemes? I am looking to do the same kind of analysis with custom primer sets for other viruses as well. |
Hello @kneubehl I'm so sorry - I haven't had a chance to try it out yet! I will reply here as soon as I can. However, if you beat me to it, I 'd love to hear. Take care! |
Description of the bug
Hi, there has been a new primer set version uploaded to https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V5.3.2, would it be possible to add it to the genomes.config for viralrecon?
Command used and terminal output
No response
Relevant files
No response
System information
No response
The text was updated successfully, but these errors were encountered: