forked from EBI-Metagenomics/workflow-is-cwl
-
Notifications
You must be signed in to change notification settings - Fork 1
/
.travis.yml
184 lines (168 loc) · 5.31 KB
/
.travis.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
sudo: true
matrix:
include:
- language: java
jdk: openjdk8
env: TOOL=InterProScan-v5
services:
- docker
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/run-interproscan5.sh
- language: java
jdk: openjdk8
env: TOOL=FastQC-v0.11.7
install: travis/install-fastqc-v0.11.7.sh
script:
- bash travis/run-fastqc-v0.11.7.sh
- if [ -f A1_left_fastqc.html ] ; then exit 0; fi
- language: perl
perl: 5.24
env: TOOL=TransDecoder.Longorfs-v5.0.2
services:
- docker
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/run-transdecoder.longorfs-v5.0.2.sh
- language: perl
perl: 5.24
env: TOOL=TransDecoder.Predict-v5.0.2
services:
- docker
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/run-transdecoder.predict-v5.0.2.sh
- language: perl
perl: 5.24
env: TOOL=TransDecoder-Workflow-v5.0.2
services:
- docker
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/run-transdecoder-v5.0.2.sub-workflow.sh
- language: cpp
compiler: clang
env: TOOL=Diamond.blastx-v0.9.21
services:
- docker
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/run-diamond.blastx-v0.9.21.sh
- if ! [ -e tools/Diamond/test_transcripts.fasta.diamond_matches ]; then exit 1; fi
- if ! diff -q tools/Diamond/test_transcripts.fasta.diamond_matches tools/Diamond/expected_output/test_transcripts.fasta.diamond_matches &>/dev/null; then exit 1; fi
- language: cpp
compiler: clang
env: TOOL=Diamond.makedb-v0.9.21
services:
- docker
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/run-diamond.makedb-v0.9.21.sh
- language: c
compiler: clang
env: TOOL=phmmer-v3.2.1
services:
- docker
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/run-phmmer-v3.2.1.sh
- language: c
compiler: clang
env: TOOL=cmsearch-v1.1.2
services:
- docker
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/run-cmsearch-v1.1.2.sh
- language: perl
perl: 5.24
env: TOOL=cmsearch-deoverlap
services:
- docker
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/run-cmsearch-deoverlap-v0.02.sh
- language: c
compiler: clang
env: TOOL=cmsearch-multimodel-Workflow
services:
- docker
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/run-cmsearch.multimodel-wf.sh
- language: python
env: TOOL=Utils - FASTA chunker
services:
- docker
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/run-utils-fasta_chunker.sh
- if ! [ -e utils/test_01_b_test_01_b.fasta ]; then exit 1; fi
- if ! diff -q utils/test_01_b_test_01_b.fasta utils/expected_output/fasta_chunker/test_01_b_test_01_b.fasta &>/dev/null; then exit 1; fi
- if ! diff -q utils/test_02_test_02.fasta utils/expected_output/fasta_chunker/test_02_test_02.fasta &>/dev/null; then exit 1; fi
# TODO: Fix integration test
# - language: python
# env: TOOL=Utils - FASTA header cutter
# services:
# - docker
# install:
# - travis/install-cwl-runner.sh
# script:
# - bash travis/run-utils-cut_fasta_headers.sh
# - if ! [ -e utils/test_seq_cut_fasta_headers.cut.fasta ]; then exit 1; fi
# - if ! diff -q utils/test_seq_cut_fasta_headers.cut.fasta utils/expected_output/fasta_header_cutter/test_seq_cut_fasta_headers.cut.fasta &>/dev/null; then exit 1; fi
- language: python
env: TOOL=BUSCO v3
services:
- docker
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/run-BUSCO-v3.0.2.sh
- if ! [ -e tools/BUSCO/missing_busco_list_TEST.tsv ]; then exit 1; fi
- if ! [ -e tools/BUSCO/short_summary_TEST.txt ]; then exit 1; fi
- if ! [ -e tools/BUSCO/translated_proteins/sample.faa ]; then exit 1; fi
- language: python
env: TOOL=Workflow validation tests
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/workflow-cwl-validation-tests.sh
- language: python
env: TOOL=Tool validation tests
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/tools-validation-tests.sh
- language: python
env: TOOL=Utils validation tests
install:
- travis/install-nodejs.sh
- travis/install-cwl-runner.sh
script:
- bash travis/utils-validation-tests.sh