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Add CI to build mulled containers with Wave #115

Add CI to build mulled containers with Wave

Add CI to build mulled containers with Wave #115

Workflow file for this run

name: Wave
# When environment.yml is changed
on:
pull_request:
paths:
- "**/environment.yml"
# TODO On complete call testing CI
# TODO Skip testing CI if any changes to environment.yml
env:
WAVE_VER: "1.5.0"
NFTEST_VER: "0.9.1"
jobs:
gen-matrix:
name: generate-matrix
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
- name: Calculate file differences
id: diff
uses: tj-actions/changed-files@v44
with:
json: true
quotepath: false
# TODO Add Dockerfiles
files: |
modules/**/environment.yml
- name: Debug
run: echo ${{ steps.diff.outputs.all_changed_files }}
- id: set-matrix
run: echo "matrix={\"profile\":[\"docker\", \"singularity\"],\"files\":${{ steps.diff.outputs.all_changed_files }} }" >> "$GITHUB_OUTPUT"
outputs:
matrix: ${{ steps.set-matrix.outputs.matrix }}
build:
if: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"
needs: gen-matrix
name: build
runs-on: ubuntu-latest
timeout-minutes: 60
strategy:
fail-fast: false
matrix: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"
steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
- name: Install wave-cli
run: |
wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VER}/wave-${WAVE_VER}-linux-x86_64
sudo mv wave-${WAVE_VER}-linux-x86_64 /usr/local/bin/wave
chmod +x /usr/local/bin/wave
- name: Create a registry name
uses: actions/github-script@v7
id: registry-name
with:
result-encoding: string
script: |
return '${{ matrix.files }}'.replace('modules/nf-core/', '').replace('/environment.yml', '').replace('/', '_');
- name: Build container
if: matrix.profile == 'docker'
run: |
wave --conda-file "${{ matrix.files }}" \
--freeze \
--await \
--tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
--tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}
- name: Build Singularity
if: matrix.profile == 'singularity'
run: |
wave --conda-file "${{ matrix.files }}" \
--freeze \
--await \
--tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
--tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }} \
--singularity
# TODO Build from Dockerfiles
# bump-versions:
# needs: gen-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.NFTEST_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 "[email protected]"
# 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