diff --git a/.github/workflows/cutadapt.yml b/.github/workflows/cutadapt.yml
index ba92681d..dfb15238 100644
--- a/.github/workflows/cutadapt.yml
+++ b/.github/workflows/cutadapt.yml
@@ -2,7 +2,7 @@ name: cutadapt
 on:
   push: {}
   pull_request:
-    paths: tools/cutadapt/*
+    paths: software/cutadapt/*
 
 jobs:
   run_ci_test:
@@ -25,10 +25,10 @@ jobs:
 
       - name: Test module with paired-end data
         run: |
-          cd tools/cutadapt/test_paired/
+          cd software/cutadapt/test_paired/
           nextflow run . -ansi-log false
 
       - name: Test module with single-end data
         run: |
-          cd tools/cutadapt/test_single/
+          cd software/cutadapt/test_single/
           nextflow run . -ansi-log false
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index c4a39fe1..d63a83a3 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -5,8 +5,8 @@ on:
     branches: master
     # Only if a conda environment file or a docker build file has been updated
     paths:
-      - tools/*/environment.yml
-      - tools/*/Dockerfile
+      - software/*/environment.yml
+      - software/*/Dockerfile
 
 jobs:
   build_docker:
@@ -36,7 +36,7 @@ jobs:
             echo $TOOL
           done;
           echo '-----'
-          for d in tools/*; do
+          for d in software/*; do
             for TOOL in $TOOLS; do
               echo "$d -- $TOOL"
               if echo $d/ | grep -q "$TOOL"; then
diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml
index 9cfcfa55..4ddcbefe 100644
--- a/.github/workflows/fastqc.yml
+++ b/.github/workflows/fastqc.yml
@@ -2,7 +2,7 @@ name: FastQC
 on:
   push: {}
   pull_request:
-    paths: tools/fastqc/*
+    paths: software/fastqc/*
 
 jobs:
   run_ci_test:
@@ -20,4 +20,4 @@ jobs:
         sudo mv nextflow /usr/local/bin/
 
     # Test the module
-    - run: nextflow run ./tools/fastqc/test/ -ansi-log false
+    - run: nextflow run ./software/fastqc/test/ -ansi-log false
diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml
index 302e0b6d..260c868d 100644
--- a/.github/workflows/samtools_index.yml
+++ b/.github/workflows/samtools_index.yml
@@ -2,7 +2,7 @@ name: samtools index
 on:
   push: {}
   pull_request:
-    paths: tools/samtools/index*
+    paths: software/samtools/index*
 
 jobs:
   run_ci_test:
@@ -20,4 +20,4 @@ jobs:
         sudo mv nextflow /usr/local/bin/
 
     # Test the module
-    - run: nextflow run ./tools/samtools/index/test/ -ansi-log false
+    - run: nextflow run ./software/samtools/index/test/ -ansi-log false
diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml
index cc9ce4f8..b020dfbd 100644
--- a/.github/workflows/samtools_sort.yml
+++ b/.github/workflows/samtools_sort.yml
@@ -2,7 +2,7 @@ name: samtools sort
 on:
   push: {}
   pull_request:
-    paths: tools/samtools/sort*
+    paths: software/samtools/sort*
 
 jobs:
   run_ci_test:
@@ -20,4 +20,4 @@ jobs:
         sudo mv nextflow /usr/local/bin/
 
     # Test the module
-    - run: nextflow run ./tools/samtools/sort/test/ -ansi-log false
+    - run: nextflow run ./software/samtools/sort/test/ -ansi-log false
diff --git a/.github/workflows/tcoffee.yml b/.github/workflows/tcoffee.yml
index ab235e1b..7ec3431e 100644
--- a/.github/workflows/tcoffee.yml
+++ b/.github/workflows/tcoffee.yml
@@ -2,7 +2,7 @@ name: tcoffee
 on:
   push: {}
   pull_request:
-    paths: tools/tcoffee/*
+    paths: software/tcoffee/*
 
 jobs:
   run_ci_test:
@@ -26,5 +26,5 @@ jobs:
 
     # Test the module
     - run: |
-        cd tools/tcoffee/test/
+        cd software/tcoffee/test/
         nextflow run . -ansi-log false
diff --git a/.github/workflows/trim_galore.yml b/.github/workflows/trim_galore.yml
index d914313e..ae823971 100644
--- a/.github/workflows/trim_galore.yml
+++ b/.github/workflows/trim_galore.yml
@@ -2,7 +2,7 @@ name: Trim Galore!
 on:
   push: {}
   pull_request:
-    paths: tools/trim_galore/*
+    paths: software/trim_galore/*
 
 jobs:
   run_ci_test:
@@ -20,4 +20,4 @@ jobs:
         sudo mv nextflow /usr/local/bin/
 
     # Test the module
-    - run: nextflow run ./tools/trim_galore/test/ -ansi-log false
+    - run: nextflow run ./software/trim_galore/test/ -ansi-log false