Scripts

Scripts that automate ENCORE tasks.

Create Encore Project Windows batch file and a Unix/MacOS bash script to automatically initialize an ENCORE project:

1. create a local directory
2. create a repository on GitHub
3. link the \Processing directory to the GitHub repository

Create AIRR-seq template ENCORE template for repertoire sequencing (AIRRseq) support projects. AIRRseq, or Adaptive Immune Receptor Repertoire sequencing, is a high-throughput sequencing technology used to analyze the diversity and specificity of B-cell and T-cell receptor repertoires in the immune system. It enables the study of immune responses, disease mechanisms, and the development of immunotherapies by providing detailed insights into the adaptive immune system's receptor sequences.

1. It will pull the latest version of the ENCORE template from its Git repository
2. The directory "ENCORE" is renamed to the name of the project (the sequence run)
3. It pulls the RESEDA repository and create a branch for this specific dataset. Next it adds the RESEDA code to the \Processing directory of the ENCORE directory.
4. The ".git" sub directory is removed
5. In the Processing directory the name of computation is renamed to the "outdir" that is specified in config.yml
6. All the README files are filled out and placed in the corresponding FSS directory (templates are located in the "templates" directory)
7. The directory is uploaded to a remote storage system when rclone is configured correctly (see below for an example of an owncloud based webdav server)