From b22ec332e9ab619cbb3a49cbd0edf5976e487285 Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Fri, 7 Aug 2020 16:42:56 +0100
Subject: [PATCH] Add GitHub Actions

---
 .../picard_collectmultiplemetrics.yml         | 30 +++++++++++++++++++
 .github/workflows/picard_markduplicates.yml   | 30 +++++++++++++++++++
 .github/workflows/picard_mergesamfiles.yml    | 30 +++++++++++++++++++
 3 files changed, 90 insertions(+)
 create mode 100644 .github/workflows/picard_collectmultiplemetrics.yml
 create mode 100644 .github/workflows/picard_markduplicates.yml
 create mode 100644 .github/workflows/picard_mergesamfiles.yml

diff --git a/.github/workflows/picard_collectmultiplemetrics.yml b/.github/workflows/picard_collectmultiplemetrics.yml
new file mode 100644
index 00000000..292d01f7
--- /dev/null
+++ b/.github/workflows/picard_collectmultiplemetrics.yml
@@ -0,0 +1,30 @@
+name: picard_collectmultiplemetrics.yml
+on:
+  push:
+    paths:
+      - software/picard/collectmultiplemetrics/**
+      - .github/workflows/picard_collectmultiplemetrics.yml
+      - tests
+  pull_request:
+    paths:
+      - software/picard/collectmultiplemetrics/**
+      - .github/workflows/picard_collectmultiplemetrics.yml
+      - tests
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+
+    - uses: actions/checkout@v2
+
+    - name: Install Nextflow
+      run: |
+        export NXF_VER="20.07.1"
+        wget -qO- get.nextflow.io | bash
+        sudo mv nextflow /usr/local/bin/
+
+    # Test the module
+    - run: nextflow run ./software/picard/collectmultiplemetrics/test/ -profile docker
diff --git a/.github/workflows/picard_markduplicates.yml b/.github/workflows/picard_markduplicates.yml
new file mode 100644
index 00000000..fb0674f8
--- /dev/null
+++ b/.github/workflows/picard_markduplicates.yml
@@ -0,0 +1,30 @@
+name: picard_markduplicates
+on:
+  push:
+    paths:
+      - software/picard/markduplicates/**
+      - .github/workflows/picard_markduplicates.yml
+      - tests
+  pull_request:
+    paths:
+      - software/picard/markduplicates/**
+      - .github/workflows/picard_markduplicates.yml
+      - tests
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+
+    - uses: actions/checkout@v2
+
+    - name: Install Nextflow
+      run: |
+        export NXF_VER="20.07.1"
+        wget -qO- get.nextflow.io | bash
+        sudo mv nextflow /usr/local/bin/
+
+    # Test the module
+    - run: nextflow run ./software/picard/markduplicates/test/ -profile docker
diff --git a/.github/workflows/picard_mergesamfiles.yml b/.github/workflows/picard_mergesamfiles.yml
new file mode 100644
index 00000000..8cbf3645
--- /dev/null
+++ b/.github/workflows/picard_mergesamfiles.yml
@@ -0,0 +1,30 @@
+name: picard_mergesamfiles
+on:
+  push:
+    paths:
+      - software/picard/mergesamfiles/**
+      - .github/workflows/picard_mergesamfiles.yml
+      - tests
+  pull_request:
+    paths:
+      - software/picard/mergesamfiles/**
+      - .github/workflows/picard_mergesamfiles.yml
+      - tests
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+
+    - uses: actions/checkout@v2
+
+    - name: Install Nextflow
+      run: |
+        export NXF_VER="20.07.1"
+        wget -qO- get.nextflow.io | bash
+        sudo mv nextflow /usr/local/bin/
+
+    # Test the module
+    - run: nextflow run ./software/picard/mergesamfiles/test/ -profile docker