From 497573fc5d2903ea1ba44c085ba06a763c974d10 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 5 Dec 2019 15:44:10 +0100
Subject: [PATCH] Refactor GitHub actions workflows

---
 .github/workflows/fastqc.yml         | 18 ++++++++++++++++++
 .github/workflows/samtools_index.yml | 18 ++++++++++++++++++
 .github/workflows/samtools_sort.yml  | 18 ++++++++++++++++++
 .github/workflows/test-processes.yml | 26 --------------------------
 4 files changed, 54 insertions(+), 26 deletions(-)
 create mode 100644 .github/workflows/fastqc.yml
 create mode 100644 .github/workflows/samtools_index.yml
 create mode 100644 .github/workflows/samtools_sort.yml
 delete mode 100644 .github/workflows/test-processes.yml

diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml
new file mode 100644
index 00000000..14d75a2f
--- /dev/null
+++ b/.github/workflows/fastqc.yml
@@ -0,0 +1,18 @@
+on:
+  push:
+    paths: tools/fastqc/*
+  pull_request:
+    paths: tools/fastqc/*
+
+jobs:
+  run_multiqc:
+    runs-on: ubuntu-latest
+
+    steps:
+
+    # Check out the repository
+    - uses: actions/checkout@v1
+
+    # Test the module
+    - name: FastQC
+      run: nextflow run ./tools/fastqc/test/
diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml
new file mode 100644
index 00000000..fe7da6ae
--- /dev/null
+++ b/.github/workflows/samtools_index.yml
@@ -0,0 +1,18 @@
+on:
+  push:
+    paths: tools/samtools/sort*
+  pull_request:
+    paths: tools/samtools/sort*
+
+jobs:
+  run_multiqc:
+    runs-on: ubuntu-latest
+
+    steps:
+
+    # Check out the repository
+    - uses: actions/checkout@v1
+
+    # Test the module
+    - name: samtools sort
+      run: nextflow run ./tools/samtools/sort/test/
diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml
new file mode 100644
index 00000000..449a27f4
--- /dev/null
+++ b/.github/workflows/samtools_sort.yml
@@ -0,0 +1,18 @@
+on:
+  push:
+    paths: tools/samtools/index*
+  pull_request:
+    paths: tools/samtools/index*
+
+jobs:
+  run_multiqc:
+    runs-on: ubuntu-latest
+
+    steps:
+
+    # Check out the repository
+    - uses: actions/checkout@v1
+
+    # Test the module
+    - name: samtools index
+      run: nextflow run ./tools/samtools/index/test/
diff --git a/.github/workflows/test-processes.yml b/.github/workflows/test-processes.yml
deleted file mode 100644
index 9af40071..00000000
--- a/.github/workflows/test-processes.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-name: "nf-core/modules CI"
-on: [push, pull_request]
-
-jobs:
-  run_multiqc:
-    name: Test modules
-    runs-on: ubuntu-latest
-
-    steps:
-
-    # Check out the repository
-    - uses: actions/checkout@v1
-
-    # Test each module
-
-    - name: FastQC
-      paths: tools/fastqc/*
-      run: nextflow run ./tools/fastqc/test/
-
-    - name: samtools sort
-      paths: tools/samtoosl/sort*
-      run: nextflow run ./tools/samtools/sort/test/
-
-    - name: samtools index
-      paths: tools/samtoosl/index*
-      run: nextflow run ./tools/samtools/index/test/