From a037c62620a5f8c8b761b1e279a9a66665ae5d07 Mon Sep 17 00:00:00 2001 From: efiguerola Date: Thu, 22 Jan 2026 15:09:37 +0100 Subject: [PATCH 1/3] added explanation to clarify project compilation template and fixed typos and formatting --- docs/BBGProtocols/BBGlab_new_protocol.md | 38 +++++++++++++----------- 1 file changed, 20 insertions(+), 18 deletions(-) diff --git a/docs/BBGProtocols/BBGlab_new_protocol.md b/docs/BBGProtocols/BBGlab_new_protocol.md index a297573e..a04fccc0 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 @@ -14,34 +13,37 @@ 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. Download the **[Project Compilation template](https://drive.google.com/drive/u/0/folders/1vGfO8B-vU-QRRf4ho4B5_Tnfe4neS7Y9)** +2. Change the name of the document 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/drive/folders/1veXAAucPqNQ2KIVFLyEJqPVjEeDcqsR-)**. ## 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 From 9b307ed1f68f1ce25b5a91e92a55f3aac5e7e94c Mon Sep 17 00:00:00 2001 From: efiguerola Date: Thu, 22 Jan 2026 17:40:11 +0100 Subject: [PATCH 2/3] updated links to files on bbglab shared drive and modified descriptions --- docs/BBGProtocols/BBGlab_new_protocol.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/BBGProtocols/BBGlab_new_protocol.md b/docs/BBGProtocols/BBGlab_new_protocol.md index a04fccc0..2291181d 100644 --- a/docs/BBGProtocols/BBGlab_new_protocol.md +++ b/docs/BBGProtocols/BBGlab_new_protocol.md @@ -28,13 +28,13 @@ Remember to follow the **[BBGlab best practices](https://bbglab.github.io/bbgwik 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. Download the **[Project Compilation template](https://drive.google.com/drive/u/0/folders/1vGfO8B-vU-QRRf4ho4B5_Tnfe4neS7Y9)** -2. Change the name of the document as follow: +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/drive/folders/1veXAAucPqNQ2KIVFLyEJqPVjEeDcqsR-)**. +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 @@ -48,4 +48,5 @@ You can create a github account if you don't have one yet. Check the [Git guidel ## Reference - Elisabet Figuerola +- Ferriol Calvet - Mònica Sánchez From ce97535992c14a2efdb7c24a54d36fdf36a1b61f Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 22 Jan 2026 17:53:12 +0000 Subject: [PATCH 3/3] Initial plan