From 22a3ba60b56dcb10bf13f32c0f60e01f6929dfb0 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 22 Jan 2026 16:49:25 +0000 Subject: [PATCH 1/3] Initial plan From dfea16af52a0716cbb2887379c4b3117607e93d0 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 22 Jan 2026 16:52:11 +0000 Subject: [PATCH 2/3] fix: address linting issues in BBGlab_new_protocol.md Co-authored-by: efigb <154223352+efigb@users.noreply.github.com> --- docs/BBGProtocols/BBGlab_new_protocol.md | 41 ++++++++++++++++-------- 1 file changed, 27 insertions(+), 14 deletions(-) diff --git a/docs/BBGProtocols/BBGlab_new_protocol.md b/docs/BBGProtocols/BBGlab_new_protocol.md index 2291181d..28c53dd9 100644 --- a/docs/BBGProtocols/BBGlab_new_protocol.md +++ b/docs/BBGProtocols/BBGlab_new_protocol.md @@ -4,7 +4,7 @@ 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). +Check the [cluster structure organization](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/`. @@ -14,39 +14,52 @@ This folder should contain all the files related to the analysis of your project 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/). +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). -Find further information about the BBG Datasets [here](https://bbglab.github.io/bbgwiki/Datasets/Datasets_BBGLAB/). - - +Find further information about the +[BBG Datasets](https://bbglab.github.io/bbgwiki/Datasets/Datasets_BBGLAB/). ## 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. +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: +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)** +1. Create a copy of the +**[Project Compilation template][project-compilation-template]** 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. + `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)**. +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 + +[project-compilation-template]: https://docs.google.com/spreadsheets/d/1jJleTek9eP4S6CCe5fO8_M4-vLuKhumgKjlQ58jP_rc/edit?gid=0#gid=0 From 72b04a5878edecc418d8d6b2c347f6061fa95419 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 22 Jan 2026 16:52:47 +0000 Subject: [PATCH 3/3] fix: correct spelling of 'instructions' in BBGlab_new_protocol.md Co-authored-by: efigb <154223352+efigb@users.noreply.github.com> --- docs/BBGProtocols/BBGlab_new_protocol.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/BBGProtocols/BBGlab_new_protocol.md b/docs/BBGProtocols/BBGlab_new_protocol.md index 28c53dd9..86381e7f 100644 --- a/docs/BBGProtocols/BBGlab_new_protocol.md +++ b/docs/BBGProtocols/BBGlab_new_protocol.md @@ -15,7 +15,7 @@ This folder should contain all the original data (or mildly processed data) of y (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/). +follow [these instructions](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).