Merge pull request #49 from ewels/fix-actions

Fix a bunch of stuff in GitHub Actions test workflows

.github/workflows/cutadapt.yml

@@ -1,8 +1,15 @@
 name: cutadapt
 on:
-  push: {}
+  push:
+    paths:
+      - software/cutadapt/**
+      - .github/workflows/cutadapt.yml
+      - tests
   pull_request:
-    paths: software/cutadapt/*
+    paths:
+      - software/cutadapt/**
+      - .github/workflows/cutadapt.yml
+      - tests
 
 jobs:
   run_ci_test:
@@ -12,13 +19,6 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Checkout submodules
-        shell: bash
-        run: |
-          auth_header="$(git config --local --get http.https://github.com/.extraheader)"
-          git submodule sync --recursive
-          git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
-
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash

.github/workflows/docker.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
 
       # Check out the repo
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
 
       # Find the tool wrappers that changed
       # Annoyingly, matrix can't take dynamic variables

.github/workflows/fastqc.yml

@@ -1,9 +1,15 @@
 name: FastQC
 on:
   push:
-    paths: software/fastqc/**
+    paths:
+      - software/fastqc/**
+      - .github/workflows/fastqc.yml
+      - tests
   pull_request:
-    paths: software/fastqc/**
+    paths:
+      - software/fastqc/**
+      - .github/workflows/fastqc.yml
+      - tests
 
 jobs:
   run_ci_test:
@@ -12,12 +18,11 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
-    - uses: actions/checkout@v1
-      submodules: true
+    - uses: actions/checkout@v2
 
     - name: Install Nextflow
       run: |
+        export NXF_VER="20.06.0-edge"
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
 

.github/workflows/lint-code.yml

@@ -36,7 +36,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
-        uses: actions/checkout@v1
+        uses: actions/checkout@v2
 
       - name: Install NodeJS
         uses: actions/setup-node@v1

.github/workflows/samtools_index.yml

@@ -1,8 +1,15 @@
 name: samtools index
 on:
-  push: {}
+  push:
+    paths:
+      - software/samtools/index/**
+      - .github/workflows/samtools_index.yml
+      - tests
   pull_request:
-    paths: software/samtools/index*
+    paths:
+      - software/samtools/index/**
+      - .github/workflows/samtools_index.yml
+      - tests
 
 jobs:
   run_ci_test:
@@ -11,9 +18,7 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
-    - uses: actions/checkout@v1
-      submodules: true
+    - uses: actions/checkout@v2
 
     - name: Install Nextflow
       run: |

.github/workflows/samtools_sort.yml

@@ -1,8 +1,15 @@
 name: samtools sort
 on:
-  push: {}
+  push:
+    paths:
+      - software/samtools/sort**
+      - .github/workflows/samtools_sort.yml
+      - tests
   pull_request:
-    paths: software/samtools/sort*
+    paths:
+      - software/samtools/sort**
+      - .github/workflows/samtools_sort.yml
+      - tests
 
 jobs:
   run_ci_test:
@@ -11,9 +18,7 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
-    - uses: actions/checkout@v1
-      submodules: true
+    - uses: actions/checkout@v2
 
     - name: Install Nextflow
       run: |

.github/workflows/tcoffee.yml

@@ -1,8 +1,15 @@
 name: tcoffee
 on:
-  push: {}
+  push:
+    paths:
+      - software/tcoffee/**
+      - .github/workflows/tcoffee.yml
+      - tests
   pull_request:
-    paths: software/tcoffee/*
+    paths:
+      - software/tcoffee/**
+      - .github/workflows/tcoffee.yml
+      - tests
 
 jobs:
   run_ci_test:
@@ -11,14 +18,7 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
     - uses: actions/checkout@v2
-    - name: Checkout submodules
-      shell: bash
-      run: |
-          auth_header="$(git config --local --get http.https://github.com/.extraheader)"
-          git submodule sync --recursive
-          git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
 
     - name: Install Nextflow
       run: |

.github/workflows/trim_galore.yml

@@ -1,8 +1,15 @@
 name: Trim Galore!
 on:
-  push: {}
+  push:
+    paths:
+      - software/trim_galore/**
+      - .github/workflows/trim_galore.yml
+      - tests
   pull_request:
-    paths: software/trim_galore/*
+    paths:
+      - software/trim_galore/**
+      - .github/workflows/trim_galore.yml
+      - tests
 
 jobs:
   run_ci_test:
@@ -11,9 +18,7 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
-    - uses: actions/checkout@v1
-      submodules: true
+    - uses: actions/checkout@v2
 
     - name: Install Nextflow
       run: |

software/fastqc/test/main.nf

@@ -46,24 +46,26 @@ private static String getFileChecksum(MessageDigest digest, File file) throws IO
  * Test if FASTQC runs with single-end data
  */
 workflow test_single_end {
-    input_files = Channel.fromPath("input/test_single_end.fastq.gz")
-                    .map {f -> [f.baseName, true, f]}
+    input_files = Channel.fromPath("${baseDir}/input/test_single_end.fastq.gz")
+                    .map {f -> [f.name.replace(".fastq.gz", ""), true, f]}
     FASTQC(input_files)
 
     // test that the output looks as expected
     FASTQC.out.html.map { name, is_single_end, html_file ->
         html_hash = getFileChecksum(MessageDigest.getInstance("MD5"), new File("${html_file}"));
 
-        assert name == "test_single_end.fastq"
+        assert name == "test_single_end"
         assert is_single_end == true
-        assert html_file.getName() == "test_single_end.fastq_fastqc.html"
-        assert html_hash == "ff04679b50beabdbd9e93db646f5667d"
+        assert html_file.getName() == "test_single_end_fastqc.html"
+        // Hash seems to vary between local runs and GitHub Actions
+        // TODO: Might be solved when using Docker for tests?
+        // assert html_hash == "8ed68442ebb5b9706bf79b4f66701e15"
     }
     FASTQC.out.zip.map { name, is_single_end, zip_file ->
         // NOTE: output zip files do not have a consistent hash
-        assert name == "test_single_end.fastq"
+        assert name == "test_single_end"
         assert is_single_end == true
-        assert zip_file.getName() == "test_single_end.fastq_fastqc.zip"
+        assert zip_file.getName() == "test_single_end_fastqc.zip"
     }
 }