11name : Run nf-test
22on :
3- push :
4- branches :
5- - dev
6- - master
7- - main
8- paths-ignore :
9- - " docs/**"
10- - " **/meta.yml"
11- - " **/*.md"
12- - " **/*.png"
13- - " **/*.svg"
143 pull_request :
154 paths-ignore :
165 - " docs/**"
3928 nf-test-changes :
4029 name : nf-test-changes
4130 runs-on : # use self-hosted runners
42- - runs-on=$-nf-test-changes
31+ - runs-on=${{ github.run_id }} -nf-test-changes
4332 - runner=4cpu-linux-x64
33+ - disk=large
4434 outputs :
4535 shard : ${{ steps.set-shards.outputs.shard }}
4636 total_shards : ${{ steps.set-shards.outputs.total_shards }}
7464 needs : [nf-test-changes]
7565 if : ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
7666 runs-on : # use self-hosted runners
77- - runs-on=$-nf-test
67+ - runs-on=${{ github.run_id }} -nf-test
7868 - runner=4cpu-linux-x64
7969 - disk=large
8070 strategy :
9181 - isMain : false
9282 profile : " singularity"
9383 NXF_VER :
94- - " 24.04.2 "
84+ - " 24.10.5 "
9585 - " latest-everything"
9686 env :
9787 NXF_ANSI_LOG : false
@@ -103,138 +93,39 @@ jobs:
10393 fetch-depth : 0
10494
10595 - name : Run nf-test
96+ id : run_nf_test
10697 uses : ./.github/actions/nf-test
98+ continue-on-error : ${{ matrix.NXF_VER == 'latest-everything' }}
10799 env :
108100 NFT_WORKDIR : ${{ env.NFT_WORKDIR }}
109101 with :
110102 profile : ${{ matrix.profile }}
111103 shard : ${{ matrix.shard }}
112104 total_shards : ${{ env.TOTAL_SHARDS }}
113- tags : modules_local,subworkflows_local
114-
115- pipeline-tests :
116- name : " Pipeline Test | ${{ matrix.test_name }} | ${{ matrix.NXF_VER }} | ${{ matrix.profile }}"
117- runs-on : ubuntu-latest
118- strategy :
119- fail-fast : false
120- matrix :
121- test_name :
122- - " default"
123- - " main_pipeline_build"
124- - " main_pipeline_extend"
125- - " main_pipeline_sub"
126- - " main_pipeline_qc"
127- - " main_pipeline_reference_mapping"
128- profile : [conda, docker, singularity]
129- isMain :
130- - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
131- # Exclude conda and singularity on dev
132- exclude :
133- - isMain : false
134- profile : " conda"
135- - isMain : false
136- profile : " singularity"
137- NXF_VER :
138- - " 24.04.2"
139- - " latest-everything"
140- steps :
141- - uses : actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
142- with :
143- fetch-depth : 0
144-
145- - name : Disk space cleanup
146- uses : jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
147105
148- - name : Setup Nextflow
149- uses : nf-core/setup-nextflow@v2
150- with :
151- version : " ${{ matrix.NXF_VER }}"
152-
153- - name : Set up Python
154- uses : actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
155- with :
156- python-version : " 3.13"
157-
158- - name : Install nf-test
159- uses : nf-core/setup-nf-test@v1
160- with :
161- version : ${{ env.NFT_VER }}
162- install-pdiff : true
163-
164- - name : Setup apptainer
165- if : contains(matrix.profile, 'singularity')
166- uses : eWaterCycle/setup-apptainer@main
167-
168- - name : Set up Singularity
169- if : contains(matrix.profile, 'singularity')
170- shell : bash
171- run : |
172- mkdir -p $NXF_SINGULARITY_CACHEDIR
173- mkdir -p $NXF_SINGULARITY_LIBRARYDIR
174-
175- name : Conda setup
176- if : contains(matrix.profile, 'conda')
177- uses : conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
178- with :
179- auto-update-conda : true
180- conda-solver : libmamba
181- conda-remove-defaults : true
182-
183- - name : Run nf-test
184- shell : bash
185- env :
186- NFT_DIFF : ${{ env.NFT_DIFF }}
187- NFT_DIFF_ARGS : ${{ env.NFT_DIFF_ARGS }}
188- NFT_WORKDIR : ${{ env.NFT_WORKDIR }}
106+ - name : Report test status
107+ if : ${{ always() }}
189108 run : |
190- # Make it clear that we're ONLY running tests from the tests directory
191- # and not including any module or subworkflow tests
192- nf-test test \
193- --profile=+${{ matrix.profile }} \
194- --ci \
195- --verbose \
196- --tap=test.tap \
197- tests/${{ matrix.test_name }}.nf.test
198-
199- name : Generate test summary
200- if : always()
201- shell : bash
202- run : |
203- # Add header if it doesn't exist (using a token file to track this)
204- if [ ! -f ".summary_header" ]; then
205- echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY
206- echo "" >> $GITHUB_STEP_SUMMARY
207- echo "| Status | Test Name | Profile | Nextflow Version |" >> $GITHUB_STEP_SUMMARY
208- echo "|:------:|-----------|---------|-----------------|" >> $GITHUB_STEP_SUMMARY
209- touch .summary_header
210- fi
211-
212- if [ -f test.tap ]; then
213- while IFS= read -r line; do
214- if [[ $line =~ ^ok ]]; then
215- test_name="${line#ok }"
216- # Remove the test number from the beginning
217- test_name="${test_name#* }"
218- echo "| ✅ | ${test_name} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} |" >> $GITHUB_STEP_SUMMARY
219- elif [[ $line =~ ^not\ ok ]]; then
220- test_name="${line#not ok }"
221- # Remove the test number from the beginning
222- test_name="${test_name#* }"
223- echo "| ❌ | ${test_name} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} |" >> $GITHUB_STEP_SUMMARY
224- fi
225- done < test.tap
226- else
227- echo "| ⚠️ | No test results found | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} |" >> $GITHUB_STEP_SUMMARY
109+ if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then
110+ echo "::error::Test with ${{ matrix.NXF_VER }} failed"
111+ # Add to workflow summary
112+ echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY
113+ if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then
114+ echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing."
115+ fi
116+ if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
117+ exit 1
118+ fi
228119 fi
229120
230121confirm-pass :
231122 needs : [nf-test, pipeline-tests]
232123 if : always()
233124 runs-on : # use self-hosted runners
234- - runs-on=$-confirm-pass
125+ - runs-on=${{ github.run_id }} -confirm-pass
235126 - runner=2cpu-linux-x64
236127 steps :
237- - name : One or more tests failed
128+ - name : One or more tests failed (excluding latest-everything)
238129 if : ${{ contains(needs.*.result, 'failure') }}
239130 run : exit 1
240131
@@ -253,11 +144,3 @@ jobs:
253144 echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
254145 echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
255146 echo "::endgroup::"
256-
257- name : Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
258- if : always()
259- run : |
260- ls -la ./
261- rm -rf ./* || true
262- rm -rf ./.??* || true
263- ls -la ./
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