GitHub actions - run nextflow in a docker image

.github/workflows/fastqc.yml

@@ -15,4 +15,5 @@ jobs:
     - uses: actions/checkout@v1
 
     # Test the module
-    - run: nextflow run ./tools/fastqc/test/
+    - uses: docker://quay.io/biocontainers/nextflow:19.10.0--hecc5488_0
+      run: nextflow run ./tools/fastqc/test/

.github/workflows/samtools_index.yml

@@ -15,4 +15,5 @@ jobs:
     - uses: actions/checkout@v1
 
     # Test the module
-    - run: nextflow run ./tools/samtools/index/test/
+    - uses: docker://quay.io/biocontainers/nextflow:19.10.0--hecc5488_0
+      run: nextflow run ./tools/samtools/index/test/

.github/workflows/samtools_sort.yml

@@ -15,4 +15,5 @@ jobs:
     - uses: actions/checkout@v1
 
     # Test the module
-    - run: nextflow run ./tools/samtools/sort/test/
+    - uses: docker://quay.io/biocontainers/nextflow:19.10.0--hecc5488_0
+      run: nextflow run ./tools/samtools/sort/test/

.github/workflows/trim_galore.yml

@@ -15,4 +15,5 @@ jobs:
     - uses: actions/checkout@v1
 
     # Test the module
-    - run: nextflow run ./tools/trim_galore/test/
+    - uses: docker://quay.io/biocontainers/nextflow:19.10.0--hecc5488_0
+      run: nextflow run ./tools/trim_galore/test/

tools/fastqc/test/main.nf

@@ -1 +1,13 @@
-/* A mini pipeline to test FastQC here */
+#!/usr/bin/env nextflow
+echo true
+
+cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola'
+
+process sayHello {
+  input:
+    val x from cheers
+  script:
+    """
+    echo '$x world!'
+    """
+}

tools/samtools/index/test/main.nf

@@ -1 +1,13 @@
-/* A mini pipeline to test samtools index here */
+#!/usr/bin/env nextflow
+echo true
+
+cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola'
+
+process sayHello {
+  input:
+    val x from cheers
+  script:
+    """
+    echo '$x world!'
+    """
+}

tools/samtools/sort/test/main.nf

@@ -1 +1,13 @@
-/* A mini pipeline to test samtools sort here */
+#!/usr/bin/env nextflow
+echo true
+
+cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola'
+
+process sayHello {
+  input:
+    val x from cheers
+  script:
+    """
+    echo '$x world!'
+    """
+}

tools/trim_galore/test/main.nf

@@ -1 +1,13 @@
-/* A mini pipeline to test FastQC here */
+#!/usr/bin/env nextflow
+echo true
+
+cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola'
+
+process sayHello {
+  input:
+    val x from cheers
+  script:
+    """
+    echo '$x world!'
+    """
+}