A github action to check if a part is synthesizable from a given Genbank file.
dna-is-synthesizable is a Github Action that receives a path for an input directory, a regex pattern that should be used to filter genbank files or another interesting file name pattern, a directory where the output will be written, and also username, password, clientId and clientSecret from Integrated DNA Technologies (IDT) API. This action will use this information to annotate problematic parts of a given sequence.
Every argument is required.
| Option | Description | Default |
|---|---|---|
| input-dir | Directory where all the input genbank files will be read | input |
| input-pattern | Regex to filter files in the input directory | .*\.\(gb|gbk\) |
| output-dir | Directory where all the output genbank files will be written | output |
| input-username | IDT account username | |
| input-password | IDT account password | |
| input-client-id | IDT API ClientId | |
| input-client-secret | IDT API ClientSecret | |
| output-alert | Display an error when a non-synthesizable sequence is found |
This parameter is the path of the directory for your genbank files to read and annotate. You can use this parameter to setup different pipelines for different folders, so your project can be divided in folders with different processes. By default the action will use input as the input directory.
Default: input
This parameter is a regex pattern using re2 syntax to filter files from within input-dir. So even inside a given input directory, you can select a specific file or group of files for the current job. By default the action will match files with genbank extensions (.gb or .gbk).
Example: Match only BBF10k-prefixed files, freegene 10k gene project parts.
Default: .*\.\(gb\|gbk\)
This parameter is the path of the directory for outputting annotated sequences as genbank files. By default the action will use output as the output directory.
Default: output
Username from the IDT account. This parameter doesn't have any value by default.
Note: Don't commit secrets to git history in production!
When deploying in production, use GitHub secrets or a similar security mechanism to prevent leaking of access credentials and data.
Password from the IDT account. This parameter doesn't have any value by default.
Note: Don't commit secrets to git history in production!
When deploying in production, use GitHub secrets or a similar security mechanism to prevent leaking of access credentials and data.
ClientID from the IDT API account. This parameter doesn't have any value by default.
Note: Don't commit secrets to git history in production!
When deploying in production, use GitHub secrets or a similar security mechanism to prevent leaking of access credentials and data.
ClientSecret from the IDT API account. This parameter doesn't have any value by default.
Note: Don't commit secrets to git history in production!
When deploying in production, use GitHub secrets or a similar security mechanism to prevent leaking of access credentials and data.
This flag can be enabled to break your pipeline if one of the sequences isn't synthesizable by IDT. That way, the machine will alert you that some sequence is problematic.
Default: false
Basic:
- name: synthesizable
uses: Open-Science-Global/[email protected]See action.yml for a comprehensive list of all the options.
See Friendzymes Cookbook for further examples and sample data.