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chore: use composite snakemake action [test] #345

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chore: use composite snakemake action [test] #345

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30 changes: 15 additions & 15 deletions .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -48,55 +48,55 @@ jobs:
- uses: actions/checkout@v2

- name: Test workflow (local FASTQs)
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true

- name: Test testcase generation
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
args: "results/testcases/one/freebayes/IX:314200 --configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true

- name: Test workflow (local FASTQs, target regions)
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-target-regions/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true

- name: Test workflow (local FASTQs, multiple target regions BED files)
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-target-regions/config_multiple_beds.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true

- name: Test workflow (local FASTQs, no candidate filtering)
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-no-candidate-filtering/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true

- name: Test workflow (local FASTQs primer)
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config_primers/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true

- name: Test workflow (SRA FASTQs)
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
Expand Down Expand Up @@ -129,31 +129,31 @@ jobs:
- uses: actions/checkout@v2

- name: Test workflow (local FASTQs)
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache"
show-disk-usage-on-error: true

- name: Test testcase generation
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
args: "results/testcases/one/freebayes/IX:314200 --configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache"
show-disk-usage-on-error: true

- name: Test report
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-simple/config.yaml --cores 1 --report report.zip"
show-disk-usage-on-error: true

- name: Test workflow (local FASTQs, target regions)
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
Expand All @@ -163,7 +163,7 @@ jobs:
show-disk-usage-on-error: true

- name: Test workflow (local FASTQs, multiple target regions BED files)
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
Expand All @@ -173,7 +173,7 @@ jobs:
show-disk-usage-on-error: true

- name: Test workflow (local FASTQs, no candidate filtering)
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
Expand All @@ -183,7 +183,7 @@ jobs:
show-disk-usage-on-error: true

- name: Test workflow (local FASTQs primer)
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
Expand Down Expand Up @@ -218,7 +218,7 @@ jobs:
- uses: actions/checkout@v2

- name: Test workflow (SRA FASTQs)
uses: snakemake/snakemake-github-action@v1
uses: snakemake/snakemake-github-action@use-conda-instead-of-docker
with:
directory: .test
snakefile: workflow/Snakefile
Expand Down
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