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Apply easy module updates #734

Apply easy module updates

Apply easy module updates #734

Workflow file for this run

# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
name: nf-core CI
on:
push:
branches:
- "dev"
pull_request:
branches:
- "dev"
- "master"
release:
types:
- "published"
env:
NXF_ANSI_LOG: false
NFTEST_VER: "0.7.3"
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test:
name: Run pipeline with test data
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
aligner:
- "bismark"
- "bismark_hisat"
- "bwameth"
profile:
- "docker"
steps:
# Skip if it's a pull_request to dev and NXF_VER is '22.10.1'
- name: Skip condition
id: condition
run: |
if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
echo "skip=true" >> $GITHUB_OUTPUT
fi
- name: Check out pipeline code
if: steps.condition.outputs.skip != 'true'
uses: actions/checkout@v3
- name: Hash Github Workspace
if: steps.condition.outputs.skip != 'true'
id: hash_workspace
run: |
echo "digest=$(echo methylseq2_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
- name: Cache test data
if: steps.condition.outputs.skip != 'true'
id: cache-testdata
uses: actions/cache@v3
with:
path: test-datasets/
key: ${{ steps.hash_workspace.outputs.digest }}
- name: Check out test data
if: steps.cache-testdata.outputs.cache-hit != 'true' && steps.condition.outputs.skip != 'true'
uses: actions/checkout@v3
with:
repository: nf-core/test-datasets
ref: methylseq
path: test-datasets/
- name: Replace remote paths in samplesheets
if: steps.condition.outputs.skip != 'true'
run: |
for f in ./test-datasets/samplesheet/*csv; do
sed -i 's=https://github.com/nf-core/test-datasets/raw/methylseq/=./test-datasets/=g' $f
sed -i 's=https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/=./test-datasets/=g' $f
echo "========== $f ============"
cat $f
echo "========================================"
done;
- name: Install Nextflow
if: steps.condition.outputs.skip != 'true'
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Install nf-test
if: steps.condition.outputs.skip != 'true'
run: |
wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
sudo mv nf-test /usr/local/bin/
- name: Run nf-test
if: steps.condition.outputs.skip != 'true'
run: |
nf-test test tests/pipeline/${{ matrix.aligner }}/ --profile "test,${{ matrix.profile }}" --tap=test.tap
# If the test fails, output the software_versions.yml using the 'batcat' utility
- name: Output log on failure
if: failure()
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml