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@@ -23,78 +23,78 @@ concurrency: | |
cancel-in-progress: true | ||
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||
jobs: | ||
nf-test-changes: | ||
name: Check for changes | ||
runs-on: ubuntu-latest | ||
outputs: | ||
nf_test_files: ${{ steps.list.outputs.components }} | ||
# nf_test_files: ${{ env.TEST_SET }} | ||
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||
steps: | ||
- uses: actions/checkout@v4 | ||
with: | ||
fetch-depth: 0 | ||
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||
- name: List nf-test files | ||
id: list | ||
uses: adamrtalbot/[email protected] | ||
with: | ||
head: ${{ github.sha }} | ||
# TODO: check that the following works on pull_request | ||
base: ${{ github.ref_name }} | ||
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||
- name: print list of nf-test files | ||
run: | | ||
echo ${{ steps.list.outputs.components }} | ||
test: | ||
name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})" | ||
needs: [nf-test-changes] | ||
# Only run on push if this is the nf-core dev branch (merged PRs) | ||
if: "${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mcmicro')) && needs.nf-test-changes.outputs.nf_test_files != '[]' }}" | ||
runs-on: ubuntu-latest | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
NXF_VER: | ||
- "24.04.2" | ||
- "latest-everything" | ||
nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] | ||
profile: | ||
# - "conda" | ||
- "docker" | ||
- "singularity" | ||
test_name: | ||
- "test" | ||
isMaster: | ||
- ${{ github.base_ref == 'master' }} | ||
# Exclude conda and singularity on dev | ||
exclude: | ||
- isMaster: false | ||
profile: "conda" | ||
- isMaster: false | ||
profile: "singularity" | ||
steps: | ||
- name: install curl | ||
run: sudo apt update && sudo apt install -y curl wget | ||
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||
- name: Check out pipeline code | ||
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
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||
- name: Set up Nextflow | ||
uses: nf-core/setup-nextflow@v2 | ||
with: | ||
version: "${{ matrix.NXF_VER }}" | ||
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||
- name: Set up Apptainer | ||
if: matrix.profile == 'singularity' | ||
uses: eWaterCycle/setup-apptainer@main | ||
# nf-test-changes: | ||
# name: Check for changes | ||
# runs-on: ubuntu-latest | ||
# outputs: | ||
# nf_test_files: ${{ steps.list.outputs.components }} | ||
# # nf_test_files: ${{ env.TEST_SET }} | ||
# | ||
# steps: | ||
# - uses: actions/checkout@v4 | ||
# with: | ||
# fetch-depth: 0 | ||
# | ||
# - name: List nf-test files | ||
# id: list | ||
# uses: adamrtalbot/[email protected] | ||
# with: | ||
# head: ${{ github.sha }} | ||
# # TODO: check that the following works on pull_request | ||
# base: ${{ github.ref_name }} | ||
# | ||
# - name: print list of nf-test files | ||
# run: | | ||
# echo ${{ steps.list.outputs.components }} | ||
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||
- name: Set up Singularity | ||
if: matrix.profile == 'singularity' | ||
run: | | ||
mkdir -p $NXF_SINGULARITY_CACHEDIR | ||
mkdir -p $NXF_SINGULARITY_LIBRARYDIR | ||
# test: | ||
# name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})" | ||
# needs: [nf-test-changes] | ||
# # Only run on push if this is the nf-core dev branch (merged PRs) | ||
# if: "${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mcmicro')) && needs.nf-test-changes.outputs.nf_test_files != '[]' }}" | ||
# runs-on: ubuntu-latest | ||
# strategy: | ||
# fail-fast: false | ||
# matrix: | ||
# NXF_VER: | ||
# - "24.04.2" | ||
# - "latest-everything" | ||
# nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] | ||
# profile: | ||
# # - "conda" | ||
# - "docker" | ||
# - "singularity" | ||
# test_name: | ||
# - "test" | ||
# isMaster: | ||
# - ${{ github.base_ref == 'master' }} | ||
# # Exclude conda and singularity on dev | ||
# exclude: | ||
# - isMaster: false | ||
# profile: "conda" | ||
# - isMaster: false | ||
# profile: "singularity" | ||
# steps: | ||
# - name: install curl | ||
# run: sudo apt update && sudo apt install -y curl wget | ||
# | ||
# - name: Check out pipeline code | ||
# uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
# | ||
# - name: Set up Nextflow | ||
# uses: nf-core/setup-nextflow@v2 | ||
# with: | ||
# version: "${{ matrix.NXF_VER }}" | ||
# | ||
# - name: Set up Apptainer | ||
# if: matrix.profile == 'singularity' | ||
# uses: eWaterCycle/setup-apptainer@main | ||
# | ||
# - name: Set up Singularity | ||
# if: matrix.profile == 'singularity' | ||
# run: | | ||
# mkdir -p $NXF_SINGULARITY_CACHEDIR | ||
# mkdir -p $NXF_SINGULARITY_LIBRARYDIR | ||
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# - name: Set up Miniconda | ||
# if: matrix.profile == 'conda' | ||
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@@ -172,7 +172,7 @@ jobs: | |
# echo "toJSON(needs) = ${{ toJSON(needs) }}" | ||
# echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" | ||
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test_orig: | ||
test: | ||
name: Run pipeline with test data | ||
# Only run on push if this is the nf-core dev branch (merged PRs) | ||
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mcmicro') }}" | ||
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