From bb23c62b21d194355e4630885bc038b75051136d Mon Sep 17 00:00:00 2001
From: Zohaib Anwar <zohaib_anwar@ymail.com>
Date: Sun, 15 Dec 2024 16:15:58 -0800
Subject: [PATCH] updated github actions testing

---
 .github/workflows/nextflow_CI.yml | 22 ++++++++++++++++++++++
 .gitignore                        |  4 ----
 2 files changed, 22 insertions(+), 4 deletions(-)
 create mode 100644 .github/workflows/nextflow_CI.yml

diff --git a/.github/workflows/nextflow_CI.yml b/.github/workflows/nextflow_CI.yml
new file mode 100644
index 00000000..d6b51d0d
--- /dev/null
+++ b/.github/workflows/nextflow_CI.yml
@@ -0,0 +1,22 @@
+name: Nextflow CI
+
+on:
+  push:
+    branches:
+      - development
+
+jobs:
+  test:
+    name: Run pipeline test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline test
+        run: |
+          nextflow run main.nf -profile docker -profile singularity,eagle --prefix "covidmvp-user-$(date +%Y-%m-%d)" -params-file covidmvp_user.yaml
diff --git a/.gitignore b/.gitignore
index fdd7e974..3bbbacae 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,11 +1,7 @@
 .nextflow*
-work/*
 results/*
 .idea/*
-.github/data/metadata
-.github/data/sequence
 .DS_store
-testing/*
 *.ipynb
 weekly*
 *.error