From 17c0ad890c97e0d143d4628d98d59d3397774dc5 Mon Sep 17 00:00:00 2001
From: Johannes Koester <johannes.koester@uni-due.de>
Date: Tue, 10 Dec 2024 13:25:55 +0100
Subject: [PATCH] chore: use composite snakemake action [test]

---
 .github/workflows/main.yml | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 43fd449dc..6802bef03 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -48,7 +48,7 @@ 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
@@ -56,7 +56,7 @@ jobs:
         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
@@ -64,7 +64,7 @@ jobs:
         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
@@ -72,7 +72,7 @@ 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
@@ -80,7 +80,7 @@ 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
@@ -88,7 +88,7 @@ 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
@@ -96,7 +96,7 @@ jobs:
         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
@@ -129,7 +129,7 @@ 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
@@ -137,7 +137,7 @@ jobs:
         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
@@ -145,7 +145,7 @@ jobs:
         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
@@ -153,7 +153,7 @@ jobs:
         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