From 97eaa1e3937312a23d8948ec55058fd6f10a5eb8 Mon Sep 17 00:00:00 2001
From: LiaOb21 <liaobinu@gmail.com>
Date: Wed, 15 May 2024 20:02:54 +0100
Subject: [PATCH] Revert file to previous version

---
 .github/workflows/main.yml | 51 ++++++++------------------------------
 1 file changed, 10 insertions(+), 41 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index d5f0a79..4f62e3f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -39,50 +39,19 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Download busco lineage
-      run: |
-        mkdir -p test_data/busco_db
-        cd test_data/busco_db
-        wget https://busco-data.ezlab.org/v5/data/lineages/saccharomycetes_odb10.2024-01-08.tar.gz
-        tar -xzf saccharomycetes_odb10.2024-01-08.tar.gz
-
-    - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: ncbi_fcsgx
-        environment-file: workflow/envs/fcsgx.yaml
-        auto-activate-base: false
-
-    - name: Download FCS-GX test database
-      shell: bash -l {0}
-      run: |
-        conda activate ncbi_fcsgx
-        mkdir -p test_data/gx_test_db
-        cd test_data/gx_test_db
-        sync_files.py get --mft https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.manifest --dir ./test-only
-
-    - name: Install and set up time command
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y time
-        echo "/usr/bin/time" | sudo tee /usr/local/bin/time
-        sudo chmod +x /usr/local/bin/time
-
-    - name: Concatenate ont files
-      run: |
-        cd test_data/raw_ont/
-        cat ont_test_SPSC01_SRR27947616_PRJNA1075684aa.fastq.gz ont_test_SPSC01_SRR27947616_PRJNA1075684ab.fastq.gz ont_test_SPSC01_SRR27947616_PRJNA1075684ac.fastq.gz > ont_test_SPSC01_SRR27947616_PRJNA1075684.fastq.gz
-
     - name: Test workflow
       uses: snakemake/snakemake-github-action@v1.24.0
       with:
         directory: .
         snakefile: workflow/Snakefile
-        args: "--configfile config/config_test.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"
+        args: "--configfile config/config_test.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp --dry-run"
 
-    - name: Test report
-      uses: snakemake/snakemake-github-action@v1.24.0
-      with:
-        directory: .
-        snakefile: workflow/Snakefile
-        args: "--report report.zip"
\ No newline at end of file
+
+# excluding this step for now (because of --dry-run option in the previous step)        
+
+#    - name: Test report
+#      uses: snakemake/snakemake-github-action@v1.24.0
+#      with:
+#        directory: .
+#        snakefile: workflow/Snakefile
+#        args: "--report report.zip"
\ No newline at end of file