diff --git a/docs/BBGProtocols/BBGlab_new_protocol.md b/docs/BBGProtocols/BBGlab_new_protocol.md index a297573e..2291181d 100644 --- a/docs/BBGProtocols/BBGlab_new_protocol.md +++ b/docs/BBGProtocols/BBGlab_new_protocol.md @@ -4,9 +4,8 @@ These guidelines will help you to create a new project in the lab. ## Create project folders in the cluster -Check the cluster structure organization -[here](https://bbglab.github.io/bbgwiki/Cluster_basics/Structure/#description). -You can create the corresponding project folders within main directories: +Check the cluster structure organization [here](https://bbglab.github.io/bbgwiki/Cluster_basics/Structure/#description). +You can create the corresponding project folders within these main directories: - Create **project folder** in `/data/bbg/projects/`. This folder should contain all the files related to the analysis of your project @@ -14,36 +13,40 @@ This folder should contain all the files related to the analysis of your project - Create **dataset folder** in `/data/bbg/datasets/` or `/data/bbg/datasafe/` or s3. This folder should contain all the original data (or mildly processed data) of your project (fastq files, bam files, vcf files, maf files, etc.). + +To create these folders in the cluster, follow [these instrucions](https://bbglab.github.io/bbgwiki/Cluster_basics/NewFolders/). + Remember to add the dataset to the **BBG Datasets spreadsheet**, either if it is external (downloaded from a repository, from a collaborator) or internal (in house sequenced). -Please find further information about the BBG Datasets -[here](https://bbglab.github.io/bbgwiki/Datasets/Datasets_BBGLAB/). +Find further information about the BBG Datasets [here](https://bbglab.github.io/bbgwiki/Datasets/Datasets_BBGLAB/). + -To create these folders, follow -[these instrucions](https://bbglab.github.io/bbgwiki/Cluster_basics/NewFolders/). ## Properly organize your project folder -Remember to follow the -[BBGlab best practices](https://bbglab.github.io/bbgwiki/BBGProtocols/BBglab_data_organization/). -when organizing your project directory. -In addition, you should create a copy of the **Project Compilation spreadsheet** with your name, -fill it up with the information of your project/s and keep updating it whenever needed. -Please find the Project Compilation files -[here](https://drive.google.com/drive/u/0/folders/1vGfO8B-vU-QRRf4ho4B5_Tnfe4neS7Y9). +Remember to follow the **[BBGlab best practices](https://bbglab.github.io/bbgwiki/BBGProtocols/BBglab_data_organization/)** when organizing your project directory. + +Additionally, you should fill the **Project Compilation spreadsheet** that indicates all the paths in the cluster that you have been working in across all your projects. For that: + +1. Create a copy of the **[Project Compilation template](https://docs.google.com/spreadsheets/d/1jJleTek9eP4S6CCe5fO8_M4-vLuKhumgKjlQ58jP_rc/edit?gid=0#gid=0)** +2. Change the name of the document with your information as follow: + `ProjectCompilation-202X-NameSurename` +3. Store it in your Google drive folder (to be updated once the bbglab shared drive is available to store it accordingly) +4. Modify the document by removing the rows showing the examples, and adding our own entries. + +Remember to keep updating the file regularly so that information is available for everyone at any time. Note that this file will be needed once you do the **[BBGlab Exit Protocol](https://drive.google.com/file/d/1BnhLZCygroJ-dfamuZw8YvDgndIFmzzP/view?usp=drive_link)**. ## Properly organize your google drive -You can also follow the -[BBGlab best practices](https://bbglab.github.io/bbgwiki/BBGProtocols/BBglab_data_organization/) for that. +You can also follow the [BBGlab best practices](https://bbglab.github.io/bbgwiki/BBGProtocols/BBglab_data_organization/) for that. ## Track changes in Git You should have a Github account to track all your code in terms of version control and collaboration. -You can create a github account if you don't have one yet. Check the -[Git guidelines](https://bbglab.github.io/bbgwiki/Tools/Programming/git/). +You can create a github account if you don't have one yet. Check the [Git guidelines](https://bbglab.github.io/bbgwiki/Tools/Programming/git/). ## Reference - Elisabet Figuerola +- Ferriol Calvet - Mònica Sánchez