8000 ci: Move tmpdir to ~ by edmundmiller · Pull Request #791 · nf-core/sarek · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

ci: Move tmpdir to ~ #791

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Oct 11, 2022
Merged

ci: Move tmpdir to ~ #791

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
32 changes: 15 additions & 17 deletions .github/workflows/ci.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -89,21 +89,20 @@ jobs:
if: failure()
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always /tmp/pytest_workflow_*/*/log.{out,err}
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: |
/tmp/pytest_workflow_*/*/.nextflow.log
/tmp/pytest_workflow_*/*/log.out
/tmp/pytest_workflow_*/*/log.err
/tmp/pytest_workflow_*/*/work
/tmp/pytest_workflow_*/**/.command.log
!/tmp/pytest_workflow_*/*/work/conda
!/tmp/pytest_workflow_*/*/work/singularity
/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

test_all:
name: Run pipeline with test data (complete)
Expand Down Expand Up @@ -168,25 +167,24 @@ jobs:
- name: Run pipeline with tests settings
uses: Wandalen/wretry.action@v1.0.11
with:
command: PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes
command:TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes
attempt_limit: 3

- name: Output log on failure
if: failure()
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always /tmp/pytest_workflow_*/*/log.{out,err}
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: |
/tmp/pytest_workflow_*/*/.nextflow.log
/tmp/pytest_workflow_*/*/log.out
/tmp/pytest_workflow_*/*/log.err
/tmp/pytest_workflow_*/*/work
/tmp/pytest_workflow_*/**/.command.log
!/tmp/pytest_workflow_*/*/work/conda
!/tmp/pytest_workflow_*/*/work/singularity
/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
0