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SHAPEIT5_LIGATE Migration to nf-test #690

SHAPEIT5_LIGATE Migration to nf-test

SHAPEIT5_LIGATE Migration to nf-test #690

Workflow file for this run

name: Wave
# When environment.yml is changed
on:
pull_request:
paths:
- "**/environment.yml"
- "**/Dockerfile"
# TODO On complete call testing CI
# TODO Skip testing CI if any changes to environment.yml
env:
# renovate: datasource=github-releases depName=seqeralabs/wave-cli versioning=semver
WAVE_VERSION: "1.5.0"
# renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
NFT_VER: "0.9.2"
# renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
NXF_VER: "24.10.1"
jobs:
generate-matrix:
name: generate-matrix
runs-on: ubuntu-latest
# Only run on Pull Requests within the same repository, and not from forks
if: github.event.pull_request.head.repo.full_name == github.repository
outputs:
conda-matrix: ${{ steps.conda-diff.outputs.all_changed_files }}
dockerfile-matrix: ${{ steps.docker-diff.outputs.all_changed_files }}
steps:
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Find conda differences
id: conda-diff
uses: tj-actions/changed-files@4edd678ac3f81e2dc578756871e4d00c19191daf # v45
with:
json: true
escape_json: false
files: |
modules/**/environment.yml
- name: Find Dockerfile differences
id: docker-diff
uses: tj-actions/changed-files@4edd678ac3f81e2dc578756871e4d00c19191daf # v45
with:
json: true
escape_json: false
files: |
modules/**/Dockerfile
conda-wave:
# NOTE This should get skipped because generate-matrix won't run
# if: github.repository == 'nf-core/modules'
if: ${{ needs.generate-matrix.outputs.conda-matrix != '[]' }}
needs: generate-matrix
name: Build ${{ matrix.profile }} ${{ matrix.platform }} Container
runs-on: ubuntu-latest
timeout-minutes: 60
strategy:
fail-fast: false
max-parallel: 4
matrix:
files: "${{ fromJson(needs.generate-matrix.outputs.conda-matrix) }}"
profile: [docker, singularity]
platform: ["linux/amd64", "linux/arm64"]
steps:
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Install wave-cli
run: |
wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VERSION}/wave-${WAVE_VERSION}-linux-x86_64
sudo mv wave-${WAVE_VERSION}-linux-x86_64 /usr/local/bin/wave
chmod +x /usr/local/bin/wave
- name: Build ${{ matrix.profile }} container
# FIXME Hack while iron out the CI
continue-on-error: true
env:
PROFILE: ${{ (contains(matrix.profile, 'singularity') && '--singularity') || '' }}
run: |
wave --conda-file "${{ matrix.files }}" \
$PROFILE \
--freeze \
--await \
--platform ${{ matrix.platform }} \
--tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
--tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}
dockerfile-wave:
# NOTE This should get skipped because generate-matrix won't run
# if: github.repository == 'nf-core/modules'
if: ${{ needs.generate-matrix.outputs.dockerfile-matrix != '[]' }}
needs: generate-matrix
name: Build Dockerfile-based ${{ matrix.platform }} Container
runs-on: ubuntu-latest
timeout-minutes: 60
strategy:
fail-fast: false
max-parallel: 4
matrix:
files: "${{ fromJson(needs.generate-matrix.outputs.dockerfile-matrix) }}"
# NOTE singularity build requires a Singularity definition file in place of Dockerfile
# https://nextflow.slack.com/archives/C0477AS31T5/p1731755350230149?thread_ts=1731697852.661849&cid=C0477AS31T5
# profile: [docker]
platform: ["linux/amd64", "linux/arm64"]
steps:
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Install wave-cli
run: |
wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VERSION}/wave-${WAVE_VERSION}-linux-x86_64
sudo mv wave-${WAVE_VERSION}-linux-x86_64 /usr/local/bin/wave
chmod +x /usr/local/bin/wave
- name: Create a registry name
uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
id: registry-name
with:
result-encoding: string
script: |
return '${{ matrix.files }}'.replace('modules/nf-core/', '').replace('/Dockerfile', '').replace('/', '_');
- name: Build ${{ matrix.platform }} container
# NOTE If you're changing a Dockerfile and this is running, try to update the Dockerfile to build with wave
continue-on-error: false
run: |
wave -f "${{ matrix.files }}" \
--freeze \
--await \
--platform ${{ matrix.platform }} \
--build-repo quay.io/nf-core/modules/${{steps.registry-name.outputs.result}} \
--cache-repository quay.io/nf-core/wave-cache/docker/${{ matrix.platform }} \
--tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
--tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}
# bump-versions:
# needs: generate-matrix
# name: bump-versions
# runs-on: ubuntu-latest
# steps:
# - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
# with:
# distribution: "temurin"
# java-version: "17"
# - uses: nf-core/setup-nextflow@v2
# - uses: nf-core/setup-nf-test@v1
# with:
# version: ${{ env.NFT_VER }}
# - name: Bump Snapshot Versions
# env:
# # NFT_DIFF: "pdiff"
# # NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
# SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
# SENTIEON_AUTH_MECH: "GitHub Actions - token"
# run: |
# # use "docker_self_hosted" if it runs on self-hosted runner and matrix.profile=docker
# if [ "${{ matrix.profile }}" == "docker" ]; then
# PROFILE="docker_self_hosted"
# else
# PROFILE=${{ matrix.profile }}
# fi
# NFT_WORKDIR=~ \
# nf-test test \
# --profile=${{ matrix.profile }} \
# --tap=test.tap \
# # --ci \
# --verbose \
# --only-changed \
# # --shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} \
# # --filter ${{ matrix.filter }} \
# --follow-dependencies \
# --tag version \
# --update-snapshot
# - name: Commit & push version bumps
# run: |
# git config user.email "core@nf-co.re"
# git config user.name "nf-core-bot"
# git config push.default upstream
# git add .
# git status
# git commit -m "[automated] Bump versions snapshot"
# git push