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Add separate test actions for Snakemake versions 7 to 9
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-94
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-94
lines changed

‎.github/workflows/install.yml‎

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Original file line numberDiff line numberDiff line change
@@ -4,23 +4,7 @@ on: [push, pull_request]
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jobs:
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skip_duplicate:
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permissions:
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actions: write
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contents: read
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runs-on: ubuntu-latest
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outputs:
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should_skip: ${{ steps.skip_check.outputs.should_skip }}
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steps:
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- id: skip_check
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uses: fkirc/skip-duplicate-actions@v5.3.0
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with:
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cancel_others: 'true'
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concurrent_skipping: 'same_content_newer'
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Install:
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needs: skip_duplicate
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if: ${{ needs.skip_duplicate.outputs.should_skip != 'true' }}
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
@@ -31,14 +15,12 @@ jobs:
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channel-priority: strict
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activate-environment: snakemake
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auto-activate-base: false
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environment-file: .test/environment_7.32.4.yaml
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environment-file: .test/environment_v7.yaml
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- name: Create environments
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shell: bash -el {0}
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run: snakemake --snakefile workflow/Snakefile --directory .test --configfile config/config.yaml .test/targets.yaml --conda-create-envs-only --use-conda -c1 --conda-frontend conda
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run: snakemake --snakefile .test/Snakefile --configfile config/config.yaml .test/targets.yaml --conda-create-envs-only --use-conda -c1 --conda-frontend conda
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Dry_run:
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needs: skip_duplicate
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if: ${{ needs.skip_duplicate.outputs.should_skip != 'true' }}
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
@@ -49,7 +31,7 @@ jobs:
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channel-priority: strict
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activate-environment: snakemake
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auto-activate-base: false
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environment-file: .test/environment_7.32.4.yaml
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environment-file: .test/environment_v7.yaml
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- name: Dry run
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shell: bash -el {0}
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run: snakemake --snakefile workflow/Snakefile --directory .test --configfile config/config.yaml .test/targets.yaml --dry-run
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run: snakemake --snakefile .test/Snakefile --configfile config/config.yaml .test/targets.yaml --dry-run

‎.github/workflows/test.yml‎

Lines changed: 0 additions & 56 deletions
This file was deleted.

‎.github/workflows/test_v7.yml‎

Lines changed: 39 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,39 @@
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name: Test Sm v7
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on:
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workflow_dispatch:
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push:
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branches:
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- main
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- dev
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pull_request:
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branches:
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- "**"
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jobs:
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run_test_pipeline:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v3
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- name: Setup environment
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uses: conda-incubator/setup-miniconda@v3
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with:
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channel-priority: strict
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activate-environment: snakemake
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auto-activate-base: false
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miniforge-version: latest
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environment-file: .test/environment_v7.yaml
27+
- name: Run test pipeline
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shell: bash -el {0}
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run: snakemake --snakefile .test/Snakefile --configfile config/config.yaml .test/targets.yaml --use-conda -c1 --conda-frontend conda
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- name: Pack logs
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if: success() || failure()
32+
shell: bash -el {0}
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run: tar czf logs.tar.gz .test/output .snakemake/log
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- name: Upload output file
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if: success() || failure()
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uses: actions/upload-artifact@v4
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with:
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name: output-logs
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path: logs.tar.gz

‎.github/workflows/test_v8.yml‎

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@@ -0,0 +1,39 @@
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name: Test Sm v8
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on:
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workflow_dispatch:
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push:
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branches:
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- main
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- dev
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pull_request:
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branches:
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- "**"
12+
13+
jobs:
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run_test_pipeline:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v3
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- name: Setup environment
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uses: conda-incubator/setup-miniconda@v3
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with:
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channel-priority: strict
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activate-environment: snakemake
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auto-activate-base: false
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miniforge-version: latest
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environment-file: .test/environment_v8.yaml
27+
- name: Run test pipeline
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shell: bash -el {0}
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run: snakemake --snakefile .test/Snakefile --configfile config/config.yaml .test/targets.yaml --use-conda -c1 --conda-frontend conda
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- name: Pack logs
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if: success() || failure()
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shell: bash -el {0}
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run: tar czf logs.tar.gz .test/output .snakemake/log
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- name: Upload output file
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if: success() || failure()
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uses: actions/upload-artifact@v4
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with:
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name: output-logs
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path: logs.tar.gz

‎.github/workflows/test_v9.yml‎

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@@ -0,0 +1,39 @@
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name: Test Sm v9
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on:
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workflow_dispatch:
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push:
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branches:
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- main
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- dev
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pull_request:
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branches:
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- "**"
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jobs:
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run_test_pipeline:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v3
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- name: Setup environment
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uses: conda-incubator/setup-miniconda@v3
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with:
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channel-priority: strict
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activate-environment: snakemake
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auto-activate-base: false
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miniforge-version: latest
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environment-file: .test/environment_v9.yaml
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- name: Run test pipeline
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shell: bash -el {0}
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run: snakemake --snakefile .test/Snakefile --configfile config/config.yaml .test/targets.yaml -c1 --sdm conda
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- name: Pack logs
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if: success() || failure()
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shell: bash -el {0}
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run: tar czf logs.tar.gz .test/output .snakemake/log
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- name: Upload output file
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if: success() || failure()
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uses: actions/upload-artifact@v4
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with:
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name: output-logs
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path: logs.tar.gz

‎.test/Snakefile‎

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import sys
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import re
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from pathlib import Path
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from snakemake.utils import min_version
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import subprocess
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min_version("7.19")
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# Workflow version
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__version__ = "1.2.1"
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# Rules
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include: "../workflow/core.smk"
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include: "../workflow/rules/context.smk"
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include: "../workflow/rules/report.smk"
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rule all:
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input:
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OUTDIR/f"{OUTPUT_NAME}.report.html"

.test/environment_7.32.4.yaml renamed to .test/environment_v7.yaml

File renamed without changes.

‎.test/environment_v8.yaml‎

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@@ -0,0 +1,8 @@
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name: snakemake
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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- python==3.11.6
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- snakemake==8.30.0

‎.test/environment_v9.yaml‎

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@@ -0,0 +1,8 @@
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name: snakemake
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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- python==3.11.6
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- snakemake==9.1.6

‎.test/targets.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -1,25 +1,25 @@
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SAMPLES:
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sample1:
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bam: "data/bam/sample1.bam"
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fasta: "data/fasta/sample1.fasta"
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bam: ".test/data/bam/sample1.bam"
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fasta: ".test/data/fasta/sample1.fasta"
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sample2:
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bam: "data/bam/sample2.bam"
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fasta: "data/fasta/sample2.fasta"
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bam: ".test/data/bam/sample2.bam"
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fasta: ".test/data/fasta/sample2.fasta"
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sample3:
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bam: "data/bam/sample3.bam"
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fasta: "data/fasta/sample3.fasta"
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bam: ".test/data/bam/sample3.bam"
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fasta: ".test/data/fasta/sample3.fasta"
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METADATA:
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"data/metadata.csv"
12+
".test/data/metadata.csv"
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OUTPUT_DIRECTORY:
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"output"
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".test/output"
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CONTEXT_FASTA:
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"data/context.fasta"
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".test/data/context.fasta"
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OUTPUT_NAME:
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"test"
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DIVERSITY_REPS:
2020
10
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PLOTS:
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"../config/design_plots.R"
22+
"config/design_plots.R"
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PROBLEMATIC_VCF:
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"https://raw.githubusercontent.com/W-L/ProblematicSites_SARS-CoV2/da322c32004f7b16bdaa6a8ee7fd24d56e79d9dc/problematic_sites_sarsCov2.vcf"
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VC:
@@ -34,10 +34,10 @@ DEMIX:
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MIN_ABUNDANCE: 0.0001
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USE_BIONJ: false
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PLOT_GENOME_REGIONS:
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"../config/nsp_annotation.csv"
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"config/nsp_annotation.csv"
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REPORT_QMD:
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"../template.qmd"
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"template.qmd"
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FEATURES_JSON:
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"../config/sarscov2_features.json"
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"config/sarscov2_features.json"
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GENETIC_CODE_JSON:
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"../config/standard_genetic_code.json"
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"config/standard_genetic_code.json"

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