From 7584b3b3365a01cf08660df0453f38bd4115b785 Mon Sep 17 00:00:00 2001
From: Andrey Prjibelski <andrewprzh@gmail.com>
Date: Tue, 20 Feb 2024 15:47:47 +0200
Subject: [PATCH] fix step name

---
 .github/workflows/ILP.PB.yml                       | 4 ++--
 .github/workflows/SIRVs.Set4.R10.yml               | 2 ++
 .github/workflows/SIRVs.Set4.simulated_R10.yml     | 6 +++---
 .github/workflows/SIRVs.Set4.simulated_R9.yml      | 4 ++--
 .github/workflows/SIRVs.Set4.simulated_perfect.yml | 4 ++--
 5 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/ILP.PB.yml b/.github/workflows/ILP.PB.yml
index 6c2b8341..0297a9df 100644
--- a/.github/workflows/ILP.PB.yml
+++ b/.github/workflows/ILP.PB.yml
@@ -34,7 +34,7 @@ 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
@@ -42,4 +42,4 @@ jobs:
           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
index 3b0b8097..af401f4d 100644
--- 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 ${{env.OUTPUT_BASE}}
diff --git a/.github/workflows/SIRVs.Set4.simulated_R10.yml b/.github/workflows/SIRVs.Set4.simulated_R10.yml
index cd0575ad..99301996 100644
--- a/.github/workflows/SIRVs.Set4.simulated_R10.yml
+++ b/.github/workflows/SIRVs.Set4.simulated_R10.yml
@@ -36,7 +36,7 @@ jobs:
           STEP_NAME: SIRVs.simulated_R10
         run: |
           export PATH=$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
@@ -44,7 +44,7 @@ jobs:
           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
@@ -52,4 +52,4 @@ jobs:
           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 ${{env.OUTPUT_BASE}}
diff --git a/.github/workflows/SIRVs.Set4.simulated_R9.yml b/.github/workflows/SIRVs.Set4.simulated_R9.yml
index 87843dee..1360afb0 100644
--- a/.github/workflows/SIRVs.Set4.simulated_R9.yml
+++ b/.github/workflows/SIRVs.Set4.simulated_R9.yml
@@ -36,7 +36,7 @@ jobs:
           STEP_NAME: SIRVs.simulated_R9_real_exp
         run: |
           export PATH=$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
@@ -44,4 +44,4 @@ 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 ${{env.OUTPUT_BASE}}
diff --git a/.github/workflows/SIRVs.Set4.simulated_perfect.yml b/.github/workflows/SIRVs.Set4.simulated_perfect.yml
index c865c864..9a3e823b 100644
--- a/.github/workflows/SIRVs.Set4.simulated_perfect.yml
+++ b/.github/workflows/SIRVs.Set4.simulated_perfect.yml
@@ -36,7 +36,7 @@ jobs:
           STEP_NAME: SIRVs.simulated_perfect
         run: |
           export PATH=$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
@@ -44,4 +44,4 @@ jobs:
           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}}