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Github Actions uses fixed job names for branch protection rules #3677

Merged
merged 15 commits into from
Jul 28, 2023
Merged

Github Actions uses fixed job names for branch protection rules #3677

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7e04b5c
Add wait-for-status workflow
adamrtalbot Jul 28, 2023
568afbc
Rename and tidy all GHA workflows for branch protection
adamrtalbot Jul 28, 2023
f8e5c94
Changing some stuff to kick off real CI/CD
adamrtalbot Jul 28, 2023
628df3e
Apply suggestions from code review
adamrtalbot Jul 28, 2023
881259b
Update .github/workflows/nf-core-linting.yml
adamrtalbot Jul 28, 2023
54eaddb
Update .github/workflows/code-linting.yml
adamrtalbot Jul 28, 2023
2a252dd
Update nf-core-linting.yml
drpatelh Jul 28, 2023
4b5a160
Update nf-core-linting.yml
drpatelh Jul 28, 2023
dbe0b2c
Update nf-core-linting.yml
drpatelh Jul 28, 2023
8022f6d
Add FASTQC fake test
adamrtalbot Jul 28, 2023
6ed5696
Revert "Changing some stuff to kick off real CI/CD"
adamrtalbot Jul 28, 2023
1e8ada8
Change to fix-linting for consistency
adamrtalbot Jul 28, 2023
bb3f253
Remove fake nf-test change
adamrtalbot Jul 28, 2023
8531e7c
Delete main.nf.test
adamrtalbot Jul 28, 2023
e5f3c58
Bump setup-python version to v4
adamrtalbot Jul 28, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/code-linting.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
name: Code Linting
name: code-linting
on:
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push:
branches: [master]
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5 changes: 3 additions & 2 deletions .github/workflows/fix-linting.yml
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
name: Fix linting from a comment
name: fix-linting
run-name: fix linting (automated)
on:
issue_comment:
types: [created]

jobs:
deploy:
fix_linting:
# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
if: >
contains(github.event.comment.html_url, '/pull/') &&
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5 changes: 3 additions & 2 deletions .github/workflows/nf-core-linting.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
name: nf-core linting
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run-name: nf-core linting
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# This workflow is triggered on pushes and PRs to the repository.
# It runs the `nf-core lint` tests to ensure that the module code meets the nf-core guidelines
on:
Expand All @@ -14,7 +15,7 @@ concurrency:

jobs:
changes:
name: Check for changes
name: check-for-changes
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runs-on: ubuntu-latest
outputs:
# Expose matched filters as job 'modules' output variable
Expand All @@ -29,7 +30,7 @@ jobs:

lint:
runs-on: ubuntu-20.04
name: ${{ matrix.tags }}
name: nf-core-lint
needs: changes
if: needs.changes.outputs.modules != '[]'
strategy:
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8 changes: 4 additions & 4 deletions .github/workflows/nf-test.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
name: nf-test
run-name: nf-test
on:
push:
branches: [master]
Expand All @@ -15,7 +16,7 @@ concurrency:

jobs:
changes:
name: Check for changes
name: check-for-changes
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runs-on: ubuntu-latest
outputs:
# Expose matched filters as job 'modules' output variable
Expand All @@ -28,10 +29,9 @@ jobs:
with:
filters: "tests/config/nftest_modules.yml"

test:
nf_test:
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runs-on: ubuntu-20.04

name: ${{ matrix.tags }} ${{ matrix.profile }}
name: nf-test
needs: changes
if: needs.changes.outputs.modules != '[]'
strategy:
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10 changes: 5 additions & 5 deletions .github/workflows/pytest-workflow.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
name: Pytest-workflow
name: pytest-workflow
run-name: pytest-workflow
on:
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push:
branches: [master]
Expand All @@ -15,7 +16,7 @@ concurrency:

jobs:
changes:
name: Check for changes
name: check-for-changes
runs-on: ubuntu-latest
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outputs:
# Expose matched filters as job 'modules' output variable
Expand All @@ -28,10 +29,9 @@ jobs:
with:
filters: "tests/config/pytest_modules.yml"

test:
pytest_workflow:
runs-on: ubuntu-20.04
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name: ${{ matrix.tags }} ${{ matrix.profile }}
name: pytest-workflow
needs: changes
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if: needs.changes.outputs.modules != '[]'
strategy:
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2 changes: 1 addition & 1 deletion modules/nf-core/gatk4/haplotypecaller/main.nf
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Expand Up @@ -5,7 +5,7 @@ process GATK4_HAPLOTYPECALLER {
conda "bioconda::gatk4=4.4.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
'quay.io/biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"

input:
tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model)
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2 changes: 1 addition & 1 deletion modules/nf-core/samtools/sort/main.nf
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Expand Up @@ -5,7 +5,7 @@ process SAMTOOLS_SORT {
conda "bioconda::samtools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
'biocontainers/samtools:1.17--h00cdaf9_0' }"
'quay.io/biocontainers/samtools:1.17--h00cdaf9_0' }"

input:
tuple val(meta), path(bam)
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