forked from nf-core/modules
-
Notifications
You must be signed in to change notification settings - Fork 0
164 lines (148 loc) · 4.89 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
name: Pytest-workflow
on:
push:
branches: [master]
pull_request:
branches: [master]
# Cancel if a newer run is started
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
jobs:
changes:
name: Check for changes
runs-on: ubuntu-latest
outputs:
# Expose matched filters as job 'modules' output variable
modules: ${{ steps.filter.outputs.changes }}
steps:
- uses: actions/checkout@v3
- uses: dorny/paths-filter@v2
id: filter
with:
filters: "tests/config/pytest_modules.yml"
test:
runs-on: ubuntu-20.04
name: ${{ matrix.tags }} ${{ matrix.profile }}
needs: changes
if: needs.changes.outputs.modules != '[]'
strategy:
fail-fast: false
matrix:
tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
profile: ["docker", "singularity", "conda"]
exclude:
- profile: "conda"
tags: bases2fastq
- profile: "conda"
tags: bcl2fastq
- profile: "conda"
tags: bclconvert
- profile: "conda"
tags: cellranger/count
- profile: "conda"
tags: cellranger/mkfastq
- profile: "conda"
tags: cellranger/mkgtf
- profile: "conda"
tags: cellranger/mkref
- profile: "conda"
tags: deepvariant
- profile: "conda"
tags: ensemblvep/vep
- 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: "conda"
tags: genescopefk
- profile: "conda"
tags: imputeme/vcftoprs
- profile: "conda"
tags: merquryfk/katcomp
- profile: "conda"
tags: merquryfk/katgc
- profile: "conda"
tags: merquryfk/merquryfk
- profile: "conda"
tags: merquryfk/ploidyplot
- profile: "conda"
tags: subworkflows/vcf_annotate_ensemblvep
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- uses: actions/cache@v2
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
${{ runner.os }}-pip-
- name: Install Python dependencies
run: python -m pip install --upgrade pip pytest-workflow
- uses: actions/cache@v2
with:
path: /usr/local/bin/nextflow
key: ${{ runner.os }}
restore-keys: |
${{ runner.os }}-nextflow-
- name: Install Nextflow
env:
CAPSULE_LOG: none
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Singularity
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-singularity@v5
with:
singularity-version: 3.7.1
- name: Set up miniconda
if: matrix.profile == 'conda'
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
channels: conda-forge,bioconda,defaults
python-version: ${{ matrix.python-version }}
- name: Conda setup
if: matrix.profile == 'conda'
run: |
conda clean -a
conda install -n base conda-libmamba-solver
conda config --set solver libmamba
# Test the module
- name: Run pytest-workflow
# only use one thread for pytest-workflow to avoid race condition on conda cache.
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
- name: Output log on failure
if: failure()
run: |
sudo apt-get update > /dev/null
sudo apt-get install bat > /dev/null
batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v2
with:
name: logs-${{ matrix.profile }}
path: |
/home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity