diff --git a/.github/workflows/deprecated/cutadapt.yml b/.github/workflows/deprecated/cutadapt.yml
deleted file mode 100644
index ca756899..00000000
--- a/.github/workflows/deprecated/cutadapt.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-name: cutadapt
-on:
-  push:
-    paths:
-      - software/cutadapt/**
-      - .github/workflows/cutadapt.yml
-      - tests
-  pull_request:
-    paths:
-      - software/cutadapt/**
-      - .github/workflows/cutadapt.yml
-      - tests
-
-jobs:
-  run_ci_test:
-    runs-on: ubuntu-latest
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Test module with paired-end data
-        run: |
-          cd software/cutadapt/test/
-          nextflow run .
-
-      - name: Test module with single-end data
-        run: |
-          cd software/cutadapt/test/
-          nextflow run . --single_end
diff --git a/.github/workflows/deprecated/samtools_index.yml b/.github/workflows/deprecated/samtools_index.yml
deleted file mode 100644
index 1f952957..00000000
--- a/.github/workflows/deprecated/samtools_index.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-name: samtools index
-on:
-  push:
-    paths:
-      - software/samtools/index/**
-      - .github/workflows/samtools_index.yml
-      - tests
-  pull_request:
-    paths:
-      - software/samtools/index/**
-      - .github/workflows/samtools_index.yml
-      - tests
-
-jobs:
-  run_ci_test:
-    runs-on: ubuntu-latest
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-
-    - uses: actions/checkout@v2
-
-    - name: Install Nextflow
-      run: |
-        wget -qO- get.nextflow.io | bash
-        sudo mv nextflow /usr/local/bin/
-
-    # Test the module
-    - run: nextflow run ./software/samtools/index/test/
diff --git a/.github/workflows/deprecated/samtools_sort.yml b/.github/workflows/deprecated/samtools_sort.yml
deleted file mode 100644
index 81746f31..00000000
--- a/.github/workflows/deprecated/samtools_sort.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-name: samtools sort
-on:
-  push:
-    paths:
-      - software/samtools/sort**
-      - .github/workflows/samtools_sort.yml
-      - tests
-  pull_request:
-    paths:
-      - software/samtools/sort**
-      - .github/workflows/samtools_sort.yml
-      - tests
-
-jobs:
-  run_ci_test:
-    runs-on: ubuntu-latest
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-
-    - uses: actions/checkout@v2
-
-    - name: Install Nextflow
-      run: |
-        wget -qO- get.nextflow.io | bash
-        sudo mv nextflow /usr/local/bin/
-
-    # Test the module
-    - run: nextflow run ./software/samtools/sort/test/
diff --git a/.github/workflows/deprecated/tcoffee.yml b/.github/workflows/deprecated/tcoffee.yml
deleted file mode 100644
index 4a97cd40..00000000
--- a/.github/workflows/deprecated/tcoffee.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-name: tcoffee
-on:
-  push:
-    paths:
-      - software/tcoffee/**
-      - .github/workflows/tcoffee.yml
-      - tests
-  pull_request:
-    paths:
-      - software/tcoffee/**
-      - .github/workflows/tcoffee.yml
-      - tests
-
-jobs:
-  run_ci_test:
-    runs-on: ubuntu-latest
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-
-    - uses: actions/checkout@v2
-
-    - name: Install Nextflow
-      run: |
-        wget -qO- get.nextflow.io | bash
-        sudo mv nextflow /usr/local/bin/
-
-    # Test the module
-    - run: |
-        cd software/tcoffee/test/
-        nextflow run .