diff --git a/.github/workflows/gerp.yaml b/.github/workflows/gerp.yaml
index 686e53c..5dab7ea 100644
--- a/.github/workflows/gerp.yaml
+++ b/.github/workflows/gerp.yaml
@@ -31,15 +31,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       
       - uses: eWaterCycle/setup-apptainer@v2
         with:
-          apptainer-version: 1.1.4
+          apptainer-version: 1.3.5
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           channels: conda-forge,bioconda
           activate-environment: generode
           environment-file: environment.yml
diff --git a/.github/workflows/mitogenome_mapping.yaml b/.github/workflows/mitogenome_mapping.yaml
index 9381fe7..c6f9244 100644
--- a/.github/workflows/mitogenome_mapping.yaml
+++ b/.github/workflows/mitogenome_mapping.yaml
@@ -55,15 +55,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       
       - uses: eWaterCycle/setup-apptainer@v2
         with:
-          apptainer-version: 1.1.4
+          apptainer-version: 1.3.5
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           channels: conda-forge,bioconda
           activate-environment: generode
           environment-file: environment.yml
diff --git a/.github/workflows/mlRho_options.yaml b/.github/workflows/mlRho_options.yaml
index 41a939a..f3d0705 100644
--- a/.github/workflows/mlRho_options.yaml
+++ b/.github/workflows/mlRho_options.yaml
@@ -37,15 +37,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       
       - uses: eWaterCycle/setup-apptainer@v2
         with:
-          apptainer-version: 1.1.4
+          apptainer-version: 1.3.5
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           channels: conda-forge,bioconda
           activate-environment: generode
           environment-file: environment.yml
diff --git a/.github/workflows/pca_roh.yaml b/.github/workflows/pca_roh.yaml
index 6aba2f0..d51d6ad 100644
--- a/.github/workflows/pca_roh.yaml
+++ b/.github/workflows/pca_roh.yaml
@@ -29,15 +29,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       
       - uses: eWaterCycle/setup-apptainer@v2
         with:
-          apptainer-version: 1.1.4
+          apptainer-version: 1.3.5
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           channels: conda-forge,bioconda
           activate-environment: generode
           environment-file: environment.yml
diff --git a/.github/workflows/snpeff.yaml b/.github/workflows/snpeff.yaml
index bff3fe1..22a5588 100644
--- a/.github/workflows/snpeff.yaml
+++ b/.github/workflows/snpeff.yaml
@@ -31,15 +31,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       
       - uses: eWaterCycle/setup-apptainer@v2
         with:
-          apptainer-version: 1.1.4
+          apptainer-version: 1.3.5
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           channels: conda-forge,bioconda
           activate-environment: generode
           environment-file: environment.yml