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prettier fix
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RobJY committed Nov 7, 2024
1 parent 5c65c21 commit e0a3183
Showing 1 changed file with 72 additions and 72 deletions.
144 changes: 72 additions & 72 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -23,78 +23,78 @@ concurrency:
cancel-in-progress: true

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 }}

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 ${{ steps.list.outputs.components }}
test:
name: "Run tests (${{ 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
# 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 }}

- 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

# - name: Set up Miniconda
# if: matrix.profile == 'conda'
Expand Down Expand Up @@ -172,7 +172,7 @@ jobs:
# echo "toJSON(needs) = ${{ toJSON(needs) }}"
# echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"

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') }}"
Expand Down

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