From a113b7546b5605e476abeabf6dd9e8b683d5d0be Mon Sep 17 00:00:00 2001
From: Zohaib Anwar <zohaib_anwar@ymail.com>
Date: Wed, 27 Nov 2024 15:38:39 -0800
Subject: [PATCH] finding local modules too

---
 .github/actions/nf-test-action/action.yml |  4 +-
 .github/workflows/ci.yml                  | 50 +++++++++++++++--------
 2 files changed, 35 insertions(+), 19 deletions(-)

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index 6b47677..3b1ef66 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -69,7 +69,7 @@ runs:
         TAGS: ${{ inputs.tags && format('--tag {0}', inputs.tags) || '' }}
         NFT_WORKDIR: "~"
       run: |
-        module_path="$GITHUB_WORKSPACE/modules/nf-core/${{ inputs.module }}"
+        module_path="$GITHUB_WORKSPACE/${{ inputs.module }}"
         echo "Testing module: $module_path"
         ls -R $module_path
 
@@ -87,7 +87,7 @@ runs:
     - uses: pcolby/tap-summary@v1
       if: always()
       with:
-        path: ${{ github.workspace }}/modules/nf-core/${{ inputs.module }}/test.tap
+        path: ${{ github.workspace }}/${{ inputs.module }}/test.tap
 
     - name: Clean up
       if: always()
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ec947fe..098d40e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,3 +1,31 @@
+name: Test nf-core Modules and Sub-workflows
+
+on:
+  push:
+    branches:
+      - 'github_actions_mza'
+  workflow_dispatch:
+    inputs:
+      runners:
+        description: 'Runners to test on'
+        type: choice
+        options:
+          - 'ubuntu-latest'
+          - 'self-hosted'
+        default: 'ubuntu-latest'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  NFT_VER: '0.9.2'
+  NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  NXF_VER: '24.10.1'
+
 jobs:
   discover-modules:
     name: Discover Modules with Tests
@@ -11,7 +39,7 @@ jobs:
       - name: List Modules with Tests
         id: get-modules
         run: |
-          modules=$(find . -type d -path "*/modules/*" | while read module; do
+          modules=$(find modules -maxdepth 3 -mindepth 3 -type d | while read module; do
             if [ -d "$module/tests" ]; then
               echo "$module"
             fi
@@ -60,22 +88,10 @@ jobs:
       - name: Display Test Summary
         if: always()
         run: |
-          echo "Module path: ${{ matrix.module }}"
-          if [ -d "${{ matrix.module }}" ]; then
-            echo "Module directory exists"
-            if [ -f "${{ matrix.module }}/tests/main.nf.test" ]; then
-              echo "Test file exists: ${{ matrix.module }}/tests/main.nf.test"
-              if [ -f "${{ matrix.module }}/test.tap" ]; then
-                echo "Test Summary for ${{ matrix.module }} (${{ matrix.profile }}):"
-                cat ${{ matrix.module }}/test.tap | grep -E '^(not )?ok'
-              else
-                echo "No test.tap file found for ${{ matrix.module }}"
-              fi
-            else
-              echo "No test file found at ${{ matrix.module }}/tests/main.nf.test"
-            fi
+          if [ -f "${{ matrix.module }}/test.tap" ]; then
+            echo "Test Summary for ${{ matrix.module }} (${{ matrix.profile }}):"
+            cat ${{ matrix.module }}/test.tap | grep -E '^(not )?ok'
           else
-            echo "Module directory does not exist: ${{ matrix.module }}"
-            ls -R $GITHUB_WORKSPACE/modules
+            echo "No test.tap file found for ${{ matrix.module }}"
           fi
         shell: bash