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Fix tools CI workflows #1363

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merged 3 commits into from
Dec 14, 2021
Merged

Fix tools CI workflows #1363

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fed2e9b
fix gh wf workflow
ggabernet Dec 14, 2021
f51c462
fix test wf
ggabernet Dec 14, 2021
cc54b9e
update changelog
ggabernet Dec 14, 2021
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21 changes: 16 additions & 5 deletions .github/workflows/create-lint-wf.yml
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Original file line number Diff line number Diff line change
@@ -1,15 +1,25 @@
name: Create a pipeline and lint it
on: [push, pull_request]

env:
NXF_ANSI_LOG: false
CAPSULE_LOG: none

jobs:
MakeTestWorkflow:
runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
strategy:
matrix:
# Nextflow versions: check pipeline minimum and latest edge version
nxf_ver: ["NXF_VER=21.10.3", "NXF_EDGE=1"]
# Nextflow versions
include:
# Test pipeline minimum Nextflow version
- NXF_VER: '21.10.3'
NXF_EDGE: ''
# Test latest edge release of Nextflow
- NXF_VER: ''
NXF_EDGE: '1'
steps:
- uses: actions/checkout@v2
name: Check out source-code repository
Expand All @@ -26,12 +36,13 @@ jobs:

- name: Install Nextflow
env:
CAPSULE_LOG: none
NXF_VER: ${{ matrix.NXF_VER }}
# Uncomment only if the edge release is more recent than the latest stable release
# See https://github.com/nextflow-io/nextflow/issues/2467
# NXF_EDGE: ${{ matrix.NXF_EDGE }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
export ${{ matrix.nxf_ver }}
nextflow self-update

- name: nf-core create
run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
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23 changes: 16 additions & 7 deletions .github/workflows/create-test-wf.yml
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Original file line number Diff line number Diff line change
@@ -1,17 +1,25 @@
name: Create a pipeline and test it
on: [push, pull_request]

env:
NXF_ANSI_LOG: false
CAPSULE_LOG: none

jobs:
RunTestWorkflow:
runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
strategy:
matrix:
# Nextflow versions: check pipeline minimum and latest edge version
nxf_ver:
- "NXF_VER=21.10.3"
# - "NXF_EDGE=1"
# Nextflow versions
include:
# Test pipeline minimum Nextflow version
- NXF_VER: '21.10.3'
NXF_EDGE: ''
# Test latest edge release of Nextflow
- NXF_VER: ''
NXF_EDGE: '1'
steps:
- uses: actions/checkout@v2
name: Check out source-code repository
Expand All @@ -28,12 +36,13 @@ jobs:

- name: Install Nextflow
env:
CAPSULE_LOG: none
NXF_VER: ${{ matrix.NXF_VER }}
# Uncomment only if the edge release is more recent than the latest stable release
# See https://github.com/nextflow-io/nextflow/issues/2467
# NXF_EDGE: ${{ matrix.NXF_EDGE }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
export ${{ matrix.nxf_ver }}
nextflow self-update

- name: Run nf-core/tools
run: |
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -40,6 +40,7 @@
* Erase temporary files and folders while performing Python tests (pytest)
* Remove base `Dockerfile` used for DSL1 pipeline container builds
* Run tests with Python 3.10
* [#1363](https://github.com/nf-core/tools/pull/1363) Fix tools CI workflow nextflow versions.

### Modules

Expand Down