chore: use composite snakemake action [test]

snakemake-workflows · Dec 10, 2024 · 17c0ad8 · 17c0ad8
1 parent d8f55ea
commit 17c0ad8
Showing 1 changed file with 15 additions and 15 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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