Added unit testing to CI (4c2e98d1) · Commits · Chaos / Cutandrun

.github/workflows/ci.yml

+88 −1

Original line number	Diff line number	Diff line
		@@ -9,6 +9,9 @@ on:
		types: [published]

		jobs:
		##############################
		### SMALL INTEGRATION TEST ###
		##############################
		test:
		name: Run standard pipeline test
		# Only run on push if this is the nf-core dev branch (merged PRs)
		@@ -33,6 +36,9 @@ jobs:
		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test
		##############################
		### LARGE INTEGRATION TEST ###
		##############################
		test_full_small:
		name: Run extended pipeline test
		# Only run on push if this is the nf-core dev branch (merged PRs)
		@@ -57,3 +63,84 @@ jobs:
		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small
		##############################
		### UNIT TESTS ###
		##############################
		unit_tests:
		name: ${{ matrix.nxf_version }} ${{ matrix.tags }}
		if: ${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
		runs-on: ubuntu-20.04
		env:
		NXF_ANSI_LOG: false
		strategy:
		matrix:
		nxf_version: ["21.04.0", '']
		tags: ["samplesheet", "verify_output/input", "verify_output/align", "verify_output/peak_calling", "verify_output/reporting", verify_output/save", "verify_output/skip"]
		steps:
		- uses: actions/checkout@v2

		- name: Set up Python
		uses: actions/setup-python@v2
		with:
		python-version: "3.x"

		- uses: actions/cache@v2
		with:
		path: ~/.cache/pip
		key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
		restore-keys: \|
		${{ runner.os }}-pip-
		- name: Set up Python
		uses: actions/setup-python@v2
		with:
		python-version: "3.x"

		- name: Install Python dependencies
		run: python -m pip install --upgrade pip pytest-workflow

		- uses: actions/cache@v2
		with:
		path: /usr/local/bin/nextflow
		key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
		restore-keys: \|
		${{ runner.os }}-nextflow-
		- name: Install Nextflow
		env:
		NXF_VER: ${{ matrix.nxf_version }}
		CAPSULE_LOG: none
		run: \|
		wget -qO- get.nextflow.io \| bash
		sudo mv nextflow /usr/local/bin/
		- name: Set up Singularity
		if: matrix.profile == 'singularity'
		uses: eWaterCycle/setup-singularity@v5
		with:
		singularity-version: 3.7.1

		- name: Setup miniconda
		if: matrix.profile == 'conda'
		uses: conda-incubator/setup-miniconda@v2
		with:
		auto-update-conda: true
		channels: conda-forge,bioconda,defaults
		python-version: ${{ matrix.python-version }}

		- name: Conda clean
		if: matrix.profile == 'conda'
		run: conda clean -a

		# Test the module
		- name: Run pytest-workflow
		# only use one thread for pytest-workflow to avoid race condition on conda cache.
		run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof

		- name: Upload logs on failure
		if: failure()
		uses: actions/upload-artifact@v2
		with:
		name: logs-${{ matrix.tags }}-${{ matrix.profile }}-${{ matrix.nxf_version }}
		path: \|
		/home/runner/pytest_workflow_//.nextflow.log
		/home/runner/pytest_workflow_//log.out
		/home/runner/pytest_workflow_//log.err
		/home/runner/pytest_workflow_//work
		No newline at end of file

tests/test_verify_output_save_merged.yml

+1 −0

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		@@ -2,6 +2,7 @@
		command: nextflow run main.nf -profile docker,test_tech_reps --save_merged_fastq true --only_preqc true
		tags:
		- verify_output
		- verify_output/save
		- verify_output/save_merged
		files:
		- path: results/01_prealign/merged_fastq/h3k27me3_R1_1.merged.fastq.gz

tests/test_verify_output_save_ref.yml

+1 −0

Original line number	Diff line number	Diff line
		@@ -2,6 +2,7 @@
		command: nextflow run main.nf -profile docker,test --save_reference true --only_genome true
		tags:
		- verify_output
		- verify_output/save
		- verify_output/save_ref
		files:
		- path: results/00_genome/target/hg38-chr20-genes.bed

tests/test_verify_output_save_trimmed.yml

+1 −0

Original line number	Diff line number	Diff line
		@@ -2,6 +2,7 @@
		command: nextflow run main.nf -profile docker,test --only_preqc true --save_trimmed true
		tags:
		- verify_output
		- verify_output/save
		- verify_output/save_trimmed
		files:
		- path: results/01_prealign/trimgalore/h3k27me3_R1_1.trimmed.fastq.gz
		No newline at end of file

tests/test_verify_output_skip_fastqc.yml

+1 −0

Original line number	Diff line number	Diff line
		@@ -2,6 +2,7 @@
		command: nextflow run main.nf -profile docker,test --only_preqc true --skip_fastqc true
		tags:
		- verify_output
		- verify_output/skip
		- verify_output/skip_fastqc
		- verify_output/skip_fastqc/true
		files:

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