Add .tests-mock, update GH actions, synchronise generate_exclude_file…

…_for_mosaic_count
friendsofstrandseq · Jun 26, 2024 · d10143f · d10143f
1 parent 50d24dc
commit d10143f
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Showing 38 changed files with 101 additions and 1,189 deletions.
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -28,11 +28,11 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: "recursive" # Ensures all submodules are checked out
-          lfs: true # Ensures LFS objects for the main repo are pulled
+          # lfs: true # Ensures LFS objects for the main repo are pulled
 
       - name: Pull LFS objects in submodules
         run: |
-          git submodule foreach --recursive 'git lfs pull'
+          git submodule foreach --recursive 'git pull origin main'
 
       - name: List contents of .tests
         run: |
@@ -73,10 +73,10 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          lfs: true
+          # lfs: true
 
       - name: Pull LFS objects in submodules
-        run: git submodule foreach --recursive 'git lfs pull'
+        run: git submodule foreach --recursive 'git pull origin main'
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -123,10 +123,10 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          lfs: true
+          # lfs: true
 
       - name: Pull LFS objects in submodules
-        run: git submodule foreach --recursive 'git lfs pull'
+        run: git submodule foreach --recursive 'git pull origin main'
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -175,10 +175,10 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          lfs: true
+          # lfs: true
 
       - name: Pull LFS objects in submodules
-        run: git submodule foreach --recursive 'git lfs pull'
+        run: git submodule foreach --recursive 'git pull origin main'
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -215,10 +215,10 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          lfs: true
+          # lfs: true
 
       - name: Pull LFS objects in submodules
-        run: git submodule foreach --recursive 'git lfs pull'
+        run: git submodule foreach --recursive 'git pull origin main'
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -255,10 +255,10 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          lfs: true
+          # lfs: true
 
       - name: Pull LFS objects in submodules
-        run: git submodule foreach --recursive 'git lfs pull'
+        run: git submodule foreach --recursive 'git pull origin main'
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -295,10 +295,10 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          lfs: true
+          # lfs: true
 
       - name: Pull LFS objects in submodules
-        run: git submodule foreach --recursive 'git lfs pull'
+        run: git submodule foreach --recursive 'git pull origin main'
 
       - name: Setup Python
         uses: actions/setup-python@v5

diff --git a/github-actions-runner/.tests-mock/.gitattributes b/github-actions-runner/.tests-mock/.gitattributes
diff --git a/github-actions-runner/.tests-mock/.gitignore b/github-actions-runner/.tests-mock/.gitignore
diff --git a/github-actions-runner/.tests-mock/README.md b/github-actions-runner/.tests-mock/README.md
diff --git a/github-actions-runner/.tests-mock/config/simple_config_ashleys.yaml b/github-actions-runner/.tests-mock/config/simple_config_ashleys.yaml
diff --git a/github-actions-runner/.tests-mock/config/simple_config_mosaicatcher.yaml b/github-actions-runner/.tests-mock/config/simple_config_mosaicatcher.yaml
diff --git a/github-actions-runner/.tests-mock/config/slurm_config/config.yaml b/github-actions-runner/.tests-mock/config/slurm_config/config.yaml
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20301.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20301.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20302.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20302.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20303.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20303.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20304.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20304.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20305.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20305.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20306.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20306.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20307.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20307.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20308.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20308.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20309.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20309.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20310.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20310.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20311.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20311.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20312.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20312.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20313.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20313.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20314.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20314.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20316.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20316.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20317.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20317.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20318.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20318.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20319.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20319.sort.mdup.bam
diff --git a/github-actions-runner/.tests-mock/external_data/chr17.fa b/github-actions-runner/.tests-mock/external_data/chr17.fa
diff --git a/github-actions-runner/.tests-mock/external_data/chr17.fa.amb b/github-actions-runner/.tests-mock/external_data/chr17.fa.amb
diff --git a/github-actions-runner/.tests-mock/external_data/chr17.fa.ann b/github-actions-runner/.tests-mock/external_data/chr17.fa.ann
diff --git a/github-actions-runner/.tests-mock/external_data/chr17.fa.bwt b/github-actions-runner/.tests-mock/external_data/chr17.fa.bwt
diff --git a/github-actions-runner/.tests-mock/external_data/chr17.fa.fai b/github-actions-runner/.tests-mock/external_data/chr17.fa.fai
diff --git a/github-actions-runner/.tests-mock/external_data/chr17.fa.gzi b/github-actions-runner/.tests-mock/external_data/chr17.fa.gzi
diff --git a/github-actions-runner/.tests-mock/external_data/chr17.fa.log b/github-actions-runner/.tests-mock/external_data/chr17.fa.log
diff --git a/github-actions-runner/.tests-mock/external_data/chr17.fa.pac b/github-actions-runner/.tests-mock/external_data/chr17.fa.pac
diff --git a/github-actions-runner/.tests-mock/external_data/chr17.fa.sa b/github-actions-runner/.tests-mock/external_data/chr17.fa.sa
diff --git a/watchdog_pipeline/excluded_samples.yaml b/watchdog_pipeline/excluded_samples.yaml