-
Notifications
You must be signed in to change notification settings - Fork 16
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
cbbb554
commit 7bcecd1
Showing
2 changed files
with
82 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,58 @@ | ||
name: mop3-CI | ||
# When this workflow is triggered | ||
on: | ||
push: | ||
paths-ignore: | ||
- 'docs/**' | ||
pull_request: | ||
paths-ignore: | ||
- 'docs/**' | ||
|
||
jobs: | ||
build: | ||
name: mop3 ci | ||
# This job runs on Linux | ||
runs-on: ubuntu-20.04 | ||
timeout-minutes: 90 | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
java_version: [11] | ||
|
||
steps: | ||
- name: Delete huge unnecessary tools folder | ||
uses: jlumbroso/free-disk-space@main | ||
with: | ||
tool-cache: true | ||
|
||
- name: Environment | ||
run: env | sort | ||
|
||
- name: Checkout | ||
uses: actions/checkout@v3 | ||
with: | ||
token: ${{ github.token }} | ||
repository: biocorecrg/master_of_pores | ||
fetch-depth: 1 | ||
submodules: true | ||
|
||
- name: Setup Java | ||
uses: actions/setup-java@v2 | ||
with: | ||
java-version: ${{ matrix.java_version }} | ||
distribution: 'adopt' | ||
architecture: x64 | ||
|
||
- name: MOP3 | ||
run: | | ||
curl -fsSL get.nextflow.io | bash | ||
bash INSTALL.sh | ||
cd mop_preprocess | ||
../nextflow run mop_preprocess.nf -params-file params.f5.yaml -with-docker -profile ci | ||
cd ../mop_mod | ||
../nextflow run mop_mod.nf -params-file params.yaml -with-docker -profile ci | ||
cd ../mop_tail | ||
../nextflow run mop_tail.nf -with-docker -params-file params.yaml -profile ci | ||
env: | ||
NXF_ANSI_LOG: false |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,24 @@ | ||
on: | ||
push: | ||
paths: | ||
- 'docs/**' | ||
pull_request: | ||
paths: | ||
- 'docs/**' | ||
jobs: | ||
build: | ||
runs-on: ubuntu-20.04 | ||
steps: | ||
- uses: actions/setup-python@v2 | ||
- uses: actions/checkout@master | ||
with: | ||
fetch-depth: 0 # otherwise, you will failed to push refs to dest repo | ||
- name: Build and Commit | ||
uses: sphinx-notes/pages@v2 | ||
with: | ||
requirements_path: "docs/requirements.txt" | ||
- name: Push changes | ||
uses: ad-m/github-push-action@master | ||
with: | ||
github_token: ${{ secrets.GITHUB_TOKEN }} | ||
branch: gh-pages |