Merge pull request #169 from LUMC/nextflowfunctional

Functional tests for nextflow

Author: rhpvorderman

.github/workflows/ci.yml

@@ -60,38 +60,45 @@ jobs:
       - name: Upload coverage report
         uses: codecov/codecov-action@v1
 
-  test-functional:
+  test-functional-python-tools:
     runs-on: ubuntu-latest
-    needs: lint
     strategy:
       matrix:
         python-version: ["3.7"]
-        test-program: [cromwell, snakemake, miniwdl]
+        test-program: [snakemake, miniwdl]
     steps:
       - uses: actions/[email protected]
 
-      # Setup python program requirements
       - name: Set up Python ${{ matrix.python-version }}
-        if: ${{ matrix.test-program != 'cromwell' }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install tox
-        if: ${{ matrix.test-program != 'cromwell' }}
         run: pip install tox
 
-      # Setup cromwell requirements
+      - name: Test
+        shell: bash -l {0}  # Needed for conda
+        run: tox -e ${{ matrix.test-program }}
+
+  test-functional-other:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        test-program: [ cromwell, nextflow ]
+    steps:
+      - uses: actions/[email protected]
+
       - name: Install conda
-        if: ${{ matrix.test-program == 'cromwell' }}
         uses: conda-incubator/[email protected] # https://github.com/conda-incubator/setup-miniconda.
         with:
-          channels: conda-forge,defaults
-      - name: Install cromwell and tox
+          channels: conda-forge,bioconda,defaults
+          installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
+          channel-priority: true
+
+      - name: Install test program and tox
         shell: bash -l {0}  # Needed for conda
-        if: ${{ matrix.test-program == 'cromwell' }}
-        run: conda install cromwell tox
+        run: mamba install ${{ matrix.test-program }} tox
 
-      # Test
       - name: Test
         shell: bash -l {0}  # Needed for conda
-        run: tox -e ${{ matrix.test-program }}
+        run: tox -e ${{ matrix.test-program }}

tests/pipelines/nextflow/nextflow_testpipeline.nf

@@ -1,30 +1,31 @@
 #!/usr/bin/env nextflow
 
-# Copyright (C) 2018 Leiden University Medical Center
-# This file is part of pytest-workflow
-#
-# pytest-workflow is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Affero General Public License as
-# published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# pytest-workflow is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU Affero General Public License for more details.
-#
-# You should have received a copy of the GNU Affero General Public License
-# along with pytest-workflow.  If not, see <https://www.gnu.org/licenses/
+/* Copyright (C) 2018 Leiden University Medical Center
+   This file is part of pytest-workflow
 
-# Nextflow using the Snakemake test file as example.
-# Just a simple dummy pipeline that reads some data from /dev/urandom,
-# and does some transformations on it.
+   pytest-workflow is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Affero General Public License as
+   published by the Free Software Foundation, either version 3 of the
+   License, or (at your option) any later version.
+
+   pytest-workflow is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Affero General Public License for more details.
+
+   You should have received a copy of the GNU Affero General Public License
+   along with pytest-workflow.  If not, see <https://www.gnu.org/licenses/
+*/
+
+/* Nextflow using the Snakemake test file as example.
+   Just a simple dummy pipeline that reads some data from /dev/urandom,
+  and does some transformations on it. */
 
 params.N_LINES_TO_READ = 5
 
 process read_random {
 	publishDir = [
-                path: { "${params.outdir}/rand'}
+                path: { "${params.outdir}/rand" }
         ]
 
 	input:
@@ -40,7 +41,7 @@ process read_random {
 
 process base64_random {
 	publishDir = [
-                path: { "${params.outdir}/b64'}
+                path: { "${params.outdir}/b64" }
         ]
 
 	input:
@@ -57,7 +58,7 @@ process base64_random {
 
 process gzip_b64 {
 	publishDir = [
-                path: { "${params.outdir}/randgz'}
+                path: { "${params.outdir}/randgz" }
         ]
 
 	input:
@@ -73,7 +74,7 @@ process gzip_b64 {
 
 process concat_gzip {
 	publishDir = [
-                path: { "${params.outdir}'}
+                path: { "${params.outdir}" }
         ]
 
 	input: