add mouse R9 tests with correct truncation

.github/workflows/Group_tests.yml

@@ -3,7 +3,7 @@ name: Read grouping tests
 on:
   workflow_dispatch:
   schedule:
-  - cron: '0 6 * * 0,4'
+  - cron: '0 2 * * 0,4'
 
 env:
   RUN_NAME: Resume_tests
@@ -70,3 +70,12 @@ jobs:
           export PATH=$PATH:${{env.BIN_PATH}}
           python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
 
+      - name: 'Grouping by CSV file'
+        if: always()
+        shell: bash
+        env:
+          STEP_NAME: GROUP5.CSV.SIRVs.R10
+        run: |
+          export PATH=$PATH:${{env.BIN_PATH}}
+          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
+

.github/workflows/Mouse.ONT_simulated.R10.no_gtf.yml

@@ -3,7 +3,7 @@ name: Mouse ONT R10 simulated no annotation
 on:
   workflow_dispatch:
   schedule:
-  - cron: '0 23 * * 5'
+  - cron: '0 3 * * 0'
 
 env:
   RUN_NAME: Mouse.ONT_simulated.R10.no_gtf

.github/workflows/Mouse.ONT_simulated.R10.reduced_db.yml

@@ -3,7 +3,7 @@ name: Mouse ONT R10 simulated reduced annotation
 on:
   workflow_dispatch:
   schedule:
-  - cron: '0 4 * * 1'
+  - cron: '0 3 * * 3'
 
 env:
   RUN_NAME: Mouse.ONT_simulated.R10.reduced_db

.github/workflows/Mouse.ONT_simulated.R9.no_gtf.yml

@@ -3,7 +3,7 @@ name: Mouse ONT R9 simulated no annotation
 on:
   workflow_dispatch:
   schedule:
-  - cron: '0 23 * * 1'
+  - cron: '0 3 * * 4'
 
 env:
   RUN_NAME: Mouse.ONT_simulated.R9.no_gtf

.github/workflows/Mouse.ONT_simulated.R9.reduced_db.yml

@@ -3,7 +3,7 @@ name: Mouse ONT R9 simulated reduced annotation
 on:
   workflow_dispatch:
   schedule:
-  - cron: '0 4 * * 3'
+  - cron: '0 3 * * 1'
 
 env:
   RUN_NAME: Mouse.ONT_simulated.R9.reduced_db

.github/workflows/Mouse.ONT_simulated.R9.trunc.no_gtf.yml

@@ -0,0 +1,45 @@
+name: Mouse ONT R9 correct truncation simulated no annotation
+
+on:
+  workflow_dispatch:
+  schedule:
+  - cron: '0 3 * * 2'
+
+env:
+  RUN_NAME: Mouse.ONT_simulated.R9.trunc.no_gtf
+  LAUNCHER: ${{github.workspace}}/tests/github/run_pipeline.py
+  CFG_DIR: /abga/work/andreyp/ci_isoquant/data
+  BIN_PATH: /abga/work/andreyp/ci_isoquant/bin/
+  OUTPUT_BASE: /abga/work/andreyp/ci_isoquant/output/${{github.ref_name}}/
+
+concurrency:
+  group: ${{github.workflow}}
+  cancel-in-progress: false
+
+jobs:
+  launch-runner:
+    runs-on:
+      labels: [self-hosted]
+    name: 'Running IsoQuant and QC'
+
+    steps:
+      - name: 'Cleanup'
+        run: >
+          set -e &&
+          shopt -s dotglob &&
+          rm -rf *
+
+      - name: 'Checkout'
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 1
+
+      - name: 'IsoQuant'
+        if: always()
+        shell: bash
+        env:
+          STEP_NAME: Mouse.ONT_simulated.R9.trunc.no_gtf
+        run: |
+          export PATH=$PATH:${{env.BIN_PATH}}
+          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
+

.github/workflows/Mouse.ONT_simulated.R9.trunc.reduced_db.yml

@@ -0,0 +1,45 @@
+name: Mouse ONT R9 correct truncation simulated reduced annotation
+
+on:
+  workflow_dispatch:
+  schedule:
+  - cron: '0 3 * * 6'
+
+env:
+  RUN_NAME: Mouse.ONT_simulated.R9.trunc.reduced_db
+  LAUNCHER: ${{github.workspace}}/tests/github/run_pipeline.py
+  CFG_DIR: /abga/work/andreyp/ci_isoquant/data
+  BIN_PATH: /abga/work/andreyp/ci_isoquant/bin/
+  OUTPUT_BASE: /abga/work/andreyp/ci_isoquant/output/${{github.ref_name}}/
+
+concurrency:
+  group: ${{github.workflow}}
+  cancel-in-progress: false
+
+jobs:
+  launch-runner:
+    runs-on:
+      labels: [self-hosted]
+    name: 'Running IsoQuant and QC'
+
+    steps:
+      - name: 'Cleanup'
+        run: >
+          set -e &&
+          shopt -s dotglob &&
+          rm -rf *
+
+      - name: 'Checkout'
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 1
+
+      - name: 'IsoQuant'
+        if: always()
+        shell: bash
+        env:
+          STEP_NAME: Mouse.ONT_simulated.R9.trunc.reduced_db
+        run: |
+          export PATH=$PATH:${{env.BIN_PATH}}
+          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
+

.github/workflows/Mouse.ONT_simulated.R9.uniform_cov.polyA.yml

@@ -3,7 +3,7 @@ name: Mouse ONT R9 simulated uniform coverage polyA
 on:
   workflow_dispatch:
   schedule:
-  - cron: '0 10 * * 4'
+  - cron: '0 6 * * 5'
 
 env:
   RUN_NAME: Mouse.ONT_simulated.R9.uniform_cov.polyA