This repository has been archived by the owner on Mar 10, 2023. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 11
113 lines (101 loc) · 3.62 KB
/
ci.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
name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
jobs:
test:
name: Run workflow tests
# Only run on push if this is the nf-core dev branch (merged PRs)
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/kmermaid') }}
runs-on: ubuntu-latest
env:
NXF_VER: ${{ matrix.nxf_ver }}
NXF_ANSI_LOG: false
strategy:
matrix:
# Nextflow versions: check pipeline minimum and current latest
nxf_ver: ['20.11.0-edge', '']
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Check if Dockerfile or Conda environment changed
uses: technote-space/get-diff-action@v4
with:
FILES: |
Dockerfile
environment.yml
- name: Build new docker image
if: env.MATCHED_FILES
run: docker build --no-cache . -t nfcore/kmermaid:dev
- name: Pull docker image
if: ${{ !env.MATCHED_FILES }}
run: |
docker pull nfcore/kmermaid:dev
docker tag nfcore/kmermaid:dev nfcore/kmermaid:dev
- name: Install Nextflow
env:
CAPSULE_LOG: none
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Run pipeline with basic test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker
parameters:
name: Test workflow parameters
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/kmermaid') }}
runs-on: ubuntu-latest
env:
NXF_VER: '20.07.1'
NXF_ANSI_LOG: false
strategy:
matrix:
profile_flags:
- "test --sketch_scaled false --sketch_scaled_log2 2"
- "test --sketch_scaled false --sketch_num_hashes 20"
- "test --sketch_scaled false --sketch_num_hashes_log2 20"
- "test_bam --barcodes_file false --rename_10x_barcodes false --save_fastas false --write_barcodes_meta_csv false"
- "test_bam --rename_10x_barcodes false --write_barcodes_meta_csv false"
- "test_bam --skip_sig_merge"
- "test_bam --write_barcodes_meta_csv false"
- "test_bam --barcodes_file false --rename_10x_barcodes false"
- "test_bam --rename_10x_barcodes false"
- "test_fastas"
- "test_protein_fastas"
- "test_remove_ribo"
- "test_sig_merge"
- "test_tenx_tgz"
- "test_translate"
- "test_translate_bam"
- "test_translate_bam --skip_sig_merge"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Check if Dockerfile or Conda environment changed
uses: technote-space/get-diff-action@v4
with:
FILES: |
Dockerfile
environment.yml
- name: Build new docker image
if: env.MATCHED_FILES
run: docker build --no-cache . -t nfcore/kmermaid:dev
- name: Pull docker image
if: ${{ !env.MATCHED_FILES }}
run: |
docker pull nfcore/kmermaid:dev
docker tag nfcore/kmermaid:dev nfcore/kmermaid:dev
- name: Install Nextflow
env:
CAPSULE_LOG: none
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Run pipeline with various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.profile_flags }}