-
Notifications
You must be signed in to change notification settings - Fork 6
211 lines (188 loc) · 9.06 KB
/
github-actions.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
name: DeepRVAT
run-name: DeepRVAT 🧬🧪💻🧑🔬
on: [ push ]
jobs:
DeepRVAT-Pipeline-Smoke-Tests:
runs-on: ubuntu-latest
steps:
- name: Check out repository code
uses: actions/checkout@v4
- uses: mamba-org/setup-micromamba@v1.8.1
with:
environment-name: deeprvat-gh-action
environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml
cache-environment: true
cache-downloads: true
- name: Smoketest training_association_testing pipeline
run: |
python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example \
--snakefile ${{ github.workspace }}/pipelines/training_association_testing.snakefile --show-failed-logs
shell: micromamba-shell {0}
- name: Link pretrained models
run: cd ${{ github.workspace }}/example && ln -s ../pretrained_models
shell: bash -el {0}
- name: Smoketest association_testing_pretrained pipeline
run: |
python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example \
--snakefile ${{ github.workspace }}/pipelines/association_testing_pretrained.snakefile --show-failed-logs
shell: micromamba-shell {0}
- name: Copy seed gene discovery snakemake config
run: cd ${{ github.workspace }}/example && cp ../deeprvat/seed_gene_discovery/config.yaml .
shell: bash -el {0}
- name: Smoketest seed_gene_discovery pipeline
run: |
python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example \
--snakefile ${{ github.workspace }}/pipelines/seed_gene_discovery.snakefile --show-failed-logs
shell: micromamba-shell {0}
DeepRVAT-Pipeline-Tests:
runs-on: ubuntu-latest
needs: DeepRVAT-Pipeline-Smoke-Tests
steps:
- name: Check out repository code
uses: actions/checkout@v4
- uses: mamba-org/setup-micromamba@v1.8.1
with:
environment-name: deeprvat-gh-action
environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml
cache-environment: true
cache-downloads: true
- name: Install DeepRVAT
run: pip install -e ${{ github.workspace }}
shell: micromamba-shell {0}
# There are no GPUs on the gh worker, so we disable it in the config
- name: Update config to use no gpus
run: "sed -i 's/gpus: 1/gpus: 0/' ${{ github.workspace }}/example/config.yaml"
shell: bash -el {0}
- name: Run training_association_testing pipeline
run: |
python -m snakemake -j 2 --directory ${{ github.workspace }}/example \
--snakefile ${{ github.workspace }}/pipelines/training_association_testing.snakefile --show-failed-logs
shell: micromamba-shell {0}
- name: Link pretrained models
run: cd ${{ github.workspace }}/example && ln -s ../pretrained_models
shell: bash -el {0}
- name: Run association_testing_pretrained pipeline
run: |
python -m snakemake -j 2 --directory ${{ github.workspace }}/example \
--snakefile ${{ github.workspace }}/pipelines/association_testing_pretrained.snakefile --show-failed-logs
shell: micromamba-shell {0}
- name: Copy seed gene discovery snakemake config
run: cd ${{ github.workspace }}/example && cp ../deeprvat/seed_gene_discovery/config.yaml .
shell: bash -el {0}
- name: Run seed_gene_discovery pipeline
run: |
python -m snakemake -j 2 --directory ${{ github.workspace }}/example \
--snakefile ${{ github.workspace }}/pipelines/seed_gene_discovery.snakefile --show-failed-logs
shell: micromamba-shell {0}
DeepRVAT-Preprocessing-Pipeline-Smoke-Tests:
runs-on: ubuntu-latest
steps:
- name: Check out repository code
uses: actions/checkout@v4
- uses: mamba-org/setup-micromamba@v1.8.1
with:
environment-name: deeprvat-preprocess-gh-action
environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml
cache-environment: true
cache-downloads: true
- name: Fake fasta data
if: steps.cache-fasta.outputs.cache-hit != 'true'
run: |
cd ${{ github.workspace }}/example/preprocess && touch workdir/reference/GRCh38.primary_assembly.genome.fa
- name: Run preprocessing pipeline no qc Smoke Test
run: |
python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example/preprocess \
--snakefile ${{ github.workspace }}/pipelines/preprocess_no_qc.snakefile \
--configfile ${{ github.workspace }}/pipelines/config/deeprvat_preprocess_config.yaml --show-failed-logs
shell: micromamba-shell {0}
- name: Preprocessing pipeline with qc Smoke Test
run: |
python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example/preprocess \
--snakefile ${{ github.workspace }}/pipelines/preprocess_with_qc.snakefile \
--configfile ${{ github.workspace }}/pipelines/config/deeprvat_preprocess_config.yaml --show-failed-logs
shell: micromamba-shell {0}
DeepRVAT-Annotation-Pipeline-Smoke-Tests:
runs-on: ubuntu-latest
steps:
- name: Check out repository code
uses: actions/checkout@v4
- uses: mamba-org/setup-micromamba@v1.8.1
with:
environment-name: deeprvat-preprocess-gh-action
environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml
cache-environment: true
cache-downloads: true
- name: Annotations Smoke Test
run: |
python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example/annotations \
--snakefile ${{ github.workspace }}/pipelines/annotations.snakefile \
--configfile ${{ github.workspace }}/pipelines/config/deeprvat_annotation_config.yaml --show-failed-logs
shell: micromamba-shell {0}
DeepRVAT-Preprocessing-Pipeline-Tests-No-QC:
runs-on: ubuntu-latest
needs: DeepRVAT-Preprocessing-Pipeline-Smoke-Tests
steps:
- name: Check out repository code
uses: actions/checkout@v4
- uses: mamba-org/setup-micromamba@v1.8.1
with:
environment-name: deeprvat-preprocess-gh-action
environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml
cache-environment: true
cache-downloads: true
- name: Install DeepRVAT
run: pip install -e ${{ github.workspace }}
shell: micromamba-shell {0}
- name: Cache Fasta file
id: cache-fasta
uses: actions/cache@v4
with:
path: example/preprocess/workdir/reference
key: ${{ runner.os }}-reference-fasta
- name: Download and unpack fasta data
if: steps.cache-fasta.outputs.cache-hit != 'true'
run: |
cd ${{ github.workspace }}/example/preprocess && \
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz \
-O workdir/reference/GRCh38.primary_assembly.genome.fa.gz \
&& gzip -d workdir/reference/GRCh38.primary_assembly.genome.fa.gz
- name: Run preprocessing pipeline
run: |
python -m snakemake -j 2 --directory ${{ github.workspace }}/example/preprocess \
--snakefile ${{ github.workspace }}/pipelines/preprocess_no_qc.snakefile \
--configfile ${{ github.workspace }}/pipelines/config/deeprvat_preprocess_config.yaml --show-failed-logs
shell: micromamba-shell {0}
DeepRVAT-Preprocessing-Pipeline-Tests-With-QC:
runs-on: ubuntu-latest
needs: DeepRVAT-Preprocessing-Pipeline-Smoke-Tests
steps:
- name: Check out repository code
uses: actions/checkout@v4
- uses: mamba-org/setup-micromamba@v1.8.1
with:
environment-name: deeprvat-preprocess-gh-action
environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml
cache-environment: true
cache-downloads: true
- name: Install DeepRVAT
run: pip install -e ${{ github.workspace }}
shell: micromamba-shell {0}
- name: Cache Fasta file
id: cache-fasta
uses: actions/cache@v4
with:
path: example/preprocess/workdir/reference
key: ${{ runner.os }}-reference-fasta
- name: Download and unpack fasta data
if: steps.cache-fasta.outputs.cache-hit != 'true'
run: |
cd ${{ github.workspace }}/example/preprocess && \
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz \
-O workdir/reference/GRCh38.primary_assembly.genome.fa.gz \
&& gzip -d workdir/reference/GRCh38.primary_assembly.genome.fa.gz
- name: Run preprocessing pipeline
run: |
python -m snakemake -j 2 --directory ${{ github.workspace }}/example/preprocess \
--snakefile ${{ github.workspace }}/pipelines/preprocess_with_qc.snakefile \
--configfile ${{ github.workspace }}/pipelines/config/deeprvat_preprocess_config.yaml --show-failed-logs
shell: micromamba-shell {0}