Updated CI (a5b297f0) · Commits · Chaos / Cutandrun

.github/workflows/ci.yml

+43 −22

Original line number	Diff line number	Diff line
		@@ -18,6 +18,7 @@ jobs:
		if: ${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
		runs-on: ubuntu-latest
		env:
		NXF_VER: ${{ matrix.nxf_ver }}
		NXF_ANSI_LOG: false
		CAPSULE_LOG: none
		strategy:
		@@ -26,21 +27,13 @@ jobs:
		include:
		# Test pipeline minimum Nextflow version
		- NXF_VER: '21.10.3'
		NXF_EDGE: ''
		# Test pipeline latest Nextflow version
		# Test latest nextflow version
		- NXF_VER: ''
		NXF_EDGE: ''
		# Test latest edge release of Nextflow
		- NXF_VER: ''
		NXF_EDGE: 1
		steps:
		- name: Check out pipeline code
		uses: actions/checkout@v2

		- name: Install Nextflow
		env:
		NXF_VER: ${{ matrix.NXF_VER }}
		NXF_EDGE: ${{ matrix.NXF_EDGE }}
		run: \|
		wget -qO- get.nextflow.io \| bash
		sudo mv nextflow /usr/local/bin/
		@@ -69,28 +62,18 @@ jobs:
		if: ${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
		runs-on: ubuntu-latest
		env:
		NXF_VER: ${{ matrix.nxf_ver }}
		NXF_ANSI_LOG: false
		CAPSULE_LOG: none
		strategy:
		matrix:
		# Nextflow versions
		include:
		# Test pipeline minimum Nextflow version
		- NXF_VER: '21.10.3'
		NXF_EDGE: ''
		# Test pipeline latest Nextflow version
		- NXF_VER: ''
		NXF_EDGE: ''
		# Nextflow versions: check pipeline minimum and current latest
		nxf_ver: ['21.10.3', '']
		steps:
		- name: Check out pipeline code
		uses: actions/checkout@v2

		- name: Install Nextflow
		env:
		NXF_VER: ${{ matrix.NXF_VER }}
		# Uncomment only if the edge release is more recent than the latest stable release
		# See https://github.com/nextflow-io/nextflow/issues/2467
		# NXF_EDGE: ${{ matrix.NXF_EDGE }}
		run: \|
		wget -qO- get.nextflow.io \| bash
		sudo mv nextflow /usr/local/bin/
		@@ -110,6 +93,44 @@ jobs:
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small_local_zip

		#####################################
		### EDGE VERSION INTEGRATION TEST ###
		#####################################
		test_edge:
		name: Run standard pipeline test (edge version)
		# Only run on push if this is the nf-core dev branch (merged PRs)
		if: ${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
		runs-on: ubuntu-latest
		env:
		NXF_VER: ''
		NXF_EDGE: 1
		NXF_ANSI_LOG: false
		CAPSULE_LOG: none
		steps:
		- name: Check out pipeline code
		uses: actions/checkout@v2

		- name: Install Nextflow
		run: \|
		wget -qO- get.nextflow.io \| bash
		sudo mv nextflow /usr/local/bin/
		nextflow self-update

		# Work around for the unexpected end of file error that github actions seems to get when downloading compressed
		# files during pipelie execution
		- name: Download data
		run: \|
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz

		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip

		##############################
		### UNIT TESTS ###
		##############################

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