-
Notifications
You must be signed in to change notification settings - Fork 719
343 lines (321 loc) · 11.1 KB
/
pytest-workflow.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
name: Run pytest-workflow
on:
push:
branches:
# https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
- "renovate/**" # branches Renovate creates
pull_request:
branches: [master]
merge_group:
types: [checks_requested]
branches: [master]
workflow_dispatch:
inputs:
runners:
description: "Runners to test on"
type: choice
options:
- "ubuntu-latest"
- "self-hosted"
default: "self-hosted"
# Cancel if a newer run is started
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
env:
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
jobs:
pytest-changes:
name: pytest-changes
runs-on: ubuntu-latest
outputs:
tags: ${{ steps.filter.outputs.changes }}
modules: ${{ steps.tags.outputs.modules }}
subworkflows: ${{ steps.tags.outputs.subworkflows }}
steps:
- uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
with:
fetch-depth: 2 # To retrieve the preceding commit.
# TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented
- uses: mirpedrol/paths-filter@main
id: filter
with:
filters: "tests/config/pytest_modules.yml"
token: ""
- name: Fetch module tags
id: tags
run: |
echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT
echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT
- name: debug
run: |
echo ${{ steps.tags.outputs.modules }}
echo ${{ steps.tags.outputs.subworkflows }}
pytest:
runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
name: pytest
needs: [pytest-changes]
if: needs.pytest-changes.outputs.tags != '[]'
strategy:
fail-fast: false
matrix:
tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"]
profile: [conda, docker, singularity]
exclude:
- tags: nf-test
- profile: conda
tags: backsub
- profile: conda
tags: bases2fastq
- profile: singularity
tags: bases2fastq
- profile: conda
tags: basicpy
- profile: conda
tags: bcl2fastq
- profile: conda
tags: bclconvert
- profile: conda
tags: bwa/aln
- profile: conda
tags: bwa/index
- profile: conda
tags: bwa/mem
- profile: conda
tags: bwa/sampe
- profile: conda
tags: bwa/samse
- profile: conda
tags: cellpose
- profile: conda
tags: cellrangerarc/count
- profile: conda
tags: cellrangerarc/mkfastq
- profile: conda
tags: cellrangerarc/mkref
- profile: conda
tags: cellrangeratac/count
- profile: conda
tags: cellrangeratac/mkfastq
- profile: conda
tags: cellrangeratac/mkref
- profile: conda
tags: checkm2/databasedownload
- profile: conda
tags: checkm2/predict
- profile: conda
tags: controlfreec/makegraph2
- profile: conda
tags: coreograph
- profile: conda
tags: deepcell/mesmer
- profile: conda
tags: deepvariant
- profile: conda
tags: fastani
- profile: conda
tags: fastk/fastk
- profile: conda
tags: fastk/histex
- profile: conda
tags: fastk/merge
- profile: conda
tags: fcs/fcsadaptor
- profile: conda
tags: fcs/fcsgx
- profile: conda
tags: gatk4/cnnscorevariants
- profile: conda
tags: gatk4/determinegermlinecontigploidy
- profile: singularity
tags: gatk4/determinegermlinecontigploidy
- profile: conda
tags: gatk4/germlinecnvcaller
- profile: conda
tags: gatk4/postprocessgermlinecnvcalls
- profile: conda
tags: genescopefk
- profile: conda
tags: happy/sompy
- profile: conda
tags: hlala/preparegraph
- profile: conda
tags: ilastik/multicut
- profile: conda
tags: ilastik/pixelclassification
- profile: conda
tags: imputeme/vcftoprs
- profile: conda
tags: islandpath
- profile: conda
tags: manta/convertinversion
- profile: conda
tags: mcstaging/imc2mc
- profile: conda
tags: mcquant
- profile: conda
tags: medaka
- profile: conda
tags: merquryfk/katcomp
- profile: conda
tags: merquryfk/katgc
- profile: conda
tags: merquryfk/merquryfk
- profile: conda
tags: merquryfk/ploidyplot
- profile: conda
tags: minimap2/align
- profile: conda
tags: mitohifi/findmitoreference
- profile: conda
tags: mitohifi/mitohifi
- profile: conda
tags: nanoplot
- profile: conda
tags: ncbitools/vecscreen
- profile: conda
tags: parabricks/applybqsr
- profile: conda
tags: parabricks/dbsnp
- profile: conda
tags: parabricks/deepvariant
- profile: conda
tags: parabricks/fq2bam
- profile: conda
tags: parabricks/genotypegvcf
- profile: conda
tags: parabricks/haplotypecaller
- profile: conda
tags: parabricks/indexgvcf
- profile: conda
tags: parabricks/mutectcaller
- profile: conda
tags: picard/collecthsmetrics
- profile: conda
tags: picard/collectwgsmetrics
- profile: conda
tags: sentieon/applyvarcal
- profile: conda
tags: sentieon/datametrics
- profile: conda
tags: sentieon/dnamodelapply
- profile: conda
tags: sentieon/dnascope
- profile: conda
tags: sentieon/readwriter
- profile: conda
tags: sentieon/tnfilter
- profile: conda
tags: sentieon/tnhaplotyper2
- profile: conda
tags: sentieon/tnscope
- profile: conda
tags: sentieon/varcal
- profile: conda
tags: sentieon/wgsmetrics
- profile: conda
tags: subworkflows/bam_qc_picard
- profile: conda
tags: subworkflows/bcl_demultiplex
- profile: conda
tags: subworkflows/fasta_clean_fcs
- profile: conda
tags: svanalyzer/svbenchmark
- profile: conda
tags: universc
- profile: singularity
tags: universc
- profile: conda
tags: vt/decompose
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Set up Python
uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
with:
python-version: "3.11"
- uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
id: cache-pip-pytest
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-pytest
restore-keys: |
${{ runner.os }}-pip-pytest
- name: Install Python dependencies
run: python -m pip install --upgrade pip pytest-workflow cryptography
- uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
with:
distribution: "temurin"
java-version: "17"
- name: Setup Nextflow
uses: nf-core/setup-nextflow@v2
- name: Setup 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
uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3
with:
miniconda-version: "latest"
channels: conda-forge,bioconda
python-version: "3.11"
- name: Conda setup
run: |
conda clean -a
conda install -n base conda-libmamba-solver
conda config --set solver libmamba
echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
echo $(realpath python) >> $GITHUB_PATH
# Test the module
- name: Run pytest-workflow
# only use one thread for pytest-workflow to avoid race condition on conda cache.
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
- name: Output log on failure
if: failure()
run: |
sudo apt-get update > /dev/null
sudo apt-get install bat > /dev/null
batcat --decorations=always --color=always /home/ubuntu/pytest_workflow_*/*/log.{out,err}
- name: Setting global variables
uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
id: parsed
with:
script: |
return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
result-encoding: string
- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
with:
name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
path: |
/home/ubuntu/pytest_workflow_*/*/.nextflow.log
/home/ubuntu/pytest_workflow_*/*/log.out
/home/ubuntu/pytest_workflow_*/*/log.err
/home/ubuntu/pytest_workflow_*/*/work
!/home/ubuntu/pytest_workflow_*/*/work/conda
!/home/ubuntu/pytest_workflow_*/*/work/singularity
!${{ github.workspace }}/.singularity
confirm-pass:
runs-on: ubuntu-latest
needs: [pytest-changes, pytest]
if: always()
steps:
- name: All tests ok
if: ${{ success() || !contains(needs.*.result, 'failure') }}
run: exit 0
- name: One or more tests failed
if: ${{ contains(needs.*.result, 'failure') }}
run: exit 1
- name: debug-print
if: always()
run: |
echo "toJSON(needs) = ${{ toJSON(needs) }}"
echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"