From 3288322976ac34c0faca13dd413671b014b473db Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Tue, 26 Nov 2024 12:25:12 +0000
Subject: [PATCH] Update Gitpod manifest with comments, and more tools

---
 .gitpod.yml | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/.gitpod.yml b/.gitpod.yml
index 81141e19..2a988980 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -1 +1,33 @@
+# A docker image supplied by nf-core. 
+# Defined at https://github.com/nf-core/tools/blob/main/nf_core/gitpod/gitpod.Dockerfile
+# Image contains:
+# - git
+# - conda
+# - docker
+# - apptainer
+# - nextflow
+# - nf-core (tools)
+# - nf-test
 image: nfcore/gitpod:latest
+
+tasks:
+  - name: Install Pixi
+    command: |
+      sudo chown gitpod -R /home/gitpod/
+      curl -fsSL https://pixi.sh/install.sh | bash
+      . /home/gitpod/.bashrc
+  - name: Update Nextflow
+    command: |
+      nextflow self-update
+      exit
+  - name: Install Snakemake
+    command: |
+      conda install snakemake -y
+      exit
+
+
+vscode:
+  extensions:
+    - nextflow.nextflow
+    - snakemake.snakemake-lang
+    - quarto.quarto