fix step name

ablab · Feb 20, 2024 · 7584b3b · 7584b3b
1 parent 109f10d
commit 7584b3b
Show file tree

Hide file tree

Showing 5 changed files with 11 additions and 9 deletions.
diff --git a/.github/workflows/ILP.PB.yml b/.github/workflows/ILP.PB.yml
@@ -34,12 +34,12 @@ jobs:
           STEP_NAME: ILP.PB.Camk2b
         run: |
           export PATH=$PATH:${{env.BIN_PATH}}
-          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.RUN_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
+          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
 
       - name: 'ILP PacBio BIN1'
         shell: bash
         env:
           STEP_NAME: ILP.PB.BIN1
         run: |
           export PATH=$PATH:${{env.BIN_PATH}}
-          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.RUN_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
+          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
diff --git a/.github/workflows/SIRVs.Set4.R10.yml b/.github/workflows/SIRVs.Set4.R10.yml
@@ -32,6 +32,8 @@ jobs:
 
       - name: 'IsoQuant SIRVs'
         shell: bash
+        env:
+          STEP_NAME: SIRVs.Set4.R10
         run: |
           export PATH=$PATH:${{env.BIN_PATH}}
           python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.RUN_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

diff --git a/.github/workflows/SIRVs.Set4.simulated_R10.yml b/.github/workflows/SIRVs.Set4.simulated_R10.yml
@@ -36,20 +36,20 @@ jobs:
           STEP_NAME: SIRVs.simulated_R10
         run: |
           export PATH=$PATH:${{env.BIN_PATH}}
-          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.RUN_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
+          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
 
       - name: 'SIRVs.simulated_R10_no_trunc'
         shell: bash
         env:
           STEP_NAME: SIRVs.simulated_R10_no_trunc
         run: |
           export PATH=$PATH:${{env.BIN_PATH}}
-          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.RUN_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
+          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
 
       - name: 'SIRVs.simulated_R10_real_exp'
         shell: bash
         env:
           STEP_NAME: SIRVs.simulated_R10_real_exp
         run: |
           export PATH=$PATH:${{env.BIN_PATH}}
-          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.RUN_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
+          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
diff --git a/.github/workflows/SIRVs.Set4.simulated_R9.yml b/.github/workflows/SIRVs.Set4.simulated_R9.yml
@@ -36,12 +36,12 @@ jobs:
           STEP_NAME: SIRVs.simulated_R9_real_exp
         run: |
           export PATH=$PATH:${{env.BIN_PATH}}
-          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.RUN_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
+          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
 
       - name: 'SIRVs simulated ONT R9 real expression'
         shell: bash
         env:
           STEP_NAME: SIRVs.simulated_R9_real_exp
         run: |
           export PATH=$PATH:${{env.BIN_PATH}}
-          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.RUN_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
+          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
diff --git a/.github/workflows/SIRVs.Set4.simulated_perfect.yml b/.github/workflows/SIRVs.Set4.simulated_perfect.yml
@@ -36,12 +36,12 @@ jobs:
           STEP_NAME: SIRVs.simulated_perfect
         run: |
           export PATH=$PATH:${{env.BIN_PATH}}
-          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.RUN_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
+          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
 
       - name: 'IsoQuant: perfect reads with polyA'
         shell: bash
         env:
           STEP_NAME: SIRVs.simulated_perfect_polya
         run: |
           export PATH=$PATH:${{env.BIN_PATH}}
-          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.RUN_NAME}}.cfg -o ${{env.OUTPUT_BASE}}
+          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}