diff --git a/.github/workflows/software/bwa_index.yml b/.github/workflows/software/bwa_index.yml
index c15c35c9..7a045703 100644
--- a/.github/workflows/software/bwa_index.yml
+++ b/.github/workflows/software/bwa_index.yml
@@ -17,14 +17,20 @@ jobs:
     env:
       NXF_ANSI_LOG: false
     steps:
+      - uses: actions/checkout@v2
 
-    - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER="20.07.1"
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
 
-    - name: Install Nextflow
-      run: |
-        export NXF_VER="20.07.1"
-        wget -qO- get.nextflow.io | bash
-        sudo mv nextflow /usr/local/bin/
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
-    - run: nextflow run ./software/bwa/index/test/ -profile docker
+      # Test the module
+      - run: pytest --tag bwa_index --symlink --wt 2
diff --git a/.github/workflows/software/bwa_mem.yml b/.github/workflows/software/bwa_mem.yml
index 7f463471..20c438f6 100644
--- a/.github/workflows/software/bwa_mem.yml
+++ b/.github/workflows/software/bwa_mem.yml
@@ -17,14 +17,20 @@ jobs:
     env:
       NXF_ANSI_LOG: false
     steps:
+      - uses: actions/checkout@v2
 
-    - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER="20.07.1"
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
 
-    - name: Install Nextflow
-      run: |
-        export NXF_VER="20.07.1"
-        wget -qO- get.nextflow.io | bash
-        sudo mv nextflow /usr/local/bin/
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
-    - run: nextflow run ./software/bwa/mem/test/ -profile docker
+      # Test the module
+      - run: pytest --tag bwa_index --symlink --wt 2
diff --git a/software/bwa/index/test/input/NC_010473.fa b/software/bwa/index/test/input/NC_010473.fa
deleted file mode 120000
index d2298ff8..00000000
--- a/software/bwa/index/test/input/NC_010473.fa
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/fasta/E_coli/NC_010473.fa
\ No newline at end of file
diff --git a/software/bwa/index/test/main.nf b/software/bwa/index/test/main.nf
deleted file mode 100644
index ef0db3ef..00000000
--- a/software/bwa/index/test/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWA_INDEX } from '../main.nf' addParams( options: [:] )
-
-workflow test {
-    BWA_INDEX ( file("${baseDir}/input/NC_010473.fa", checkIfExists: true) )
-}
-
-workflow {
-    test()
-}
diff --git a/software/bwa/index/test/nextflow.config b/software/bwa/index/test/nextflow.config
deleted file mode 100644
index 4149feea..00000000
--- a/software/bwa/index/test/nextflow.config
+++ /dev/null
@@ -1,20 +0,0 @@
-
-params {
-    outdir = "output/"
-    publish_dir_mode = "copy"
-    enable_conda = false
-}
-
-profiles {
-    conda  {
-        params.enable_conda = true
-    }
-    docker {
-        docker.enabled = true
-        docker.runOptions = '-u \$(id -u):\$(id -g)'
-    }
-    singularity {
-        singularity.enabled = true
-        singularity.autoMounts = true
-    }
-}
diff --git a/software/bwa/index/test/output/bwa/NC_010473.fa.amb b/software/bwa/index/test/output/bwa/NC_010473.fa.amb
deleted file mode 100644
index 7355c4ea..00000000
--- a/software/bwa/index/test/output/bwa/NC_010473.fa.amb
+++ /dev/null
@@ -1,3 +0,0 @@
-4686137 1 2
-20895 1 Y
-142347 1 R
diff --git a/software/bwa/index/test/output/bwa/NC_010473.fa.ann b/software/bwa/index/test/output/bwa/NC_010473.fa.ann
deleted file mode 100644
index ddfe94ec..00000000
--- a/software/bwa/index/test/output/bwa/NC_010473.fa.ann
+++ /dev/null
@@ -1,3 +0,0 @@
-4686137 1 11
-0 gi|170079663|ref|NC_010473.1| Escherichia coli str. K-12 substr. DH10B, complete genome
-0 4686137 2
diff --git a/software/bwa/index/test/output/bwa/NC_010473.fa.bwt b/software/bwa/index/test/output/bwa/NC_010473.fa.bwt
deleted file mode 100644
index 855b64ae..00000000
Binary files a/software/bwa/index/test/output/bwa/NC_010473.fa.bwt and /dev/null differ
diff --git a/software/bwa/index/test/output/bwa/NC_010473.fa.pac b/software/bwa/index/test/output/bwa/NC_010473.fa.pac
deleted file mode 100644
index 3aebd5a6..00000000
Binary files a/software/bwa/index/test/output/bwa/NC_010473.fa.pac and /dev/null differ
diff --git a/software/bwa/index/test/output/bwa/NC_010473.fa.sa b/software/bwa/index/test/output/bwa/NC_010473.fa.sa
deleted file mode 100644
index 3ad7129d..00000000
Binary files a/software/bwa/index/test/output/bwa/NC_010473.fa.sa and /dev/null differ
diff --git a/software/bwa/mem/test/input/Ecoli_DNA_R1.fastq.gz b/software/bwa/mem/test/input/Ecoli_DNA_R1.fastq.gz
deleted file mode 120000
index 8b5dcc03..00000000
--- a/software/bwa/mem/test/input/Ecoli_DNA_R1.fastq.gz
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz
\ No newline at end of file
diff --git a/software/bwa/mem/test/input/Ecoli_DNA_R2.fastq.gz b/software/bwa/mem/test/input/Ecoli_DNA_R2.fastq.gz
deleted file mode 120000
index 097c7dc9..00000000
--- a/software/bwa/mem/test/input/Ecoli_DNA_R2.fastq.gz
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz
\ No newline at end of file
diff --git a/software/bwa/mem/test/input/NC_010473.fa b/software/bwa/mem/test/input/NC_010473.fa
deleted file mode 120000
index d2298ff8..00000000
--- a/software/bwa/mem/test/input/NC_010473.fa
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/fasta/E_coli/NC_010473.fa
\ No newline at end of file
diff --git a/software/bwa/mem/test/input/index b/software/bwa/mem/test/input/index
deleted file mode 120000
index e269dc83..00000000
--- a/software/bwa/mem/test/input/index
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/index/E_coli/bwa/
\ No newline at end of file
diff --git a/software/bwa/mem/test/main.nf b/software/bwa/mem/test/main.nf
deleted file mode 100755
index 4d93e720..00000000
--- a/software/bwa/mem/test/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWA_MEM as BWA_MEM_SE } from '../main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
-include { BWA_MEM as BWA_MEM_PE } from '../main.nf'  addParams( options: [ publish_dir:'test_paired_end' ] )
-
-/*
- * Test with single-end data
- */
-workflow test_single_end {
-
-    def input = []
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
-
-    BWA_MEM_SE (
-        input,
-        file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
-        file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
-    )
-}
-
-/*
- * Test with paired-end data
- */
-workflow test_paired_end {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
-                file("${baseDir}/input/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
-
-    BWA_MEM_PE (
-        input,
-        file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
-        file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
-    )
-}
-
-workflow {
-    test_single_end()
-    test_paired_end()
-}
diff --git a/software/bwa/mem/test/nextflow.config b/software/bwa/mem/test/nextflow.config
deleted file mode 100644
index 4149feea..00000000
--- a/software/bwa/mem/test/nextflow.config
+++ /dev/null
@@ -1,20 +0,0 @@
-
-params {
-    outdir = "output/"
-    publish_dir_mode = "copy"
-    enable_conda = false
-}
-
-profiles {
-    conda  {
-        params.enable_conda = true
-    }
-    docker {
-        docker.enabled = true
-        docker.runOptions = '-u \$(id -u):\$(id -g)'
-    }
-    singularity {
-        singularity.enabled = true
-        singularity.autoMounts = true
-    }
-}
diff --git a/software/bwa/mem/test/output/test_paired_end/test.bam b/software/bwa/mem/test/output/test_paired_end/test.bam
deleted file mode 100644
index 75b56194..00000000
Binary files a/software/bwa/mem/test/output/test_paired_end/test.bam and /dev/null differ
diff --git a/software/bwa/mem/test/output/test_single_end/test.bam b/software/bwa/mem/test/output/test_single_end/test.bam
deleted file mode 100644
index 7bd8d461..00000000
Binary files a/software/bwa/mem/test/output/test_single_end/test.bam and /dev/null differ
diff --git a/tests/software/bwa/main.nf b/tests/software/bwa/main.nf
new file mode 100644
index 00000000..a4dcdbbf
--- /dev/null
+++ b/tests/software/bwa/main.nf
@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWA_INDEX } from '../../../software/bwa/index/main.nf' addParams( options: [:] )
+include { BWA_MEM as BWA_MEM_SE } from '../../../software/bwa/mem/main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
+include { BWA_MEM as BWA_MEM_PE } from '../../../software/bwa/mem/main.nf'  addParams( options: [ publish_dir:'test_paired_end' ] )
+
+workflow test_bwa_index {
+    BWA_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) )
+}
+
+/*
+ * Test with single-end data
+ */
+workflow test_bwa_mem_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
+
+    BWA_MEM_SE (
+        input,
+        file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
+        file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    )
+}
+
+/*
+ * Test with paired-end data
+ */
+workflow test_bwa_mem_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
+
+    BWA_MEM_PE (
+        input,
+        file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
+        file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    )
+}
diff --git a/tests/software/bwa/test.yml b/tests/software/bwa/test.yml
new file mode 100644
index 00000000..9efefa1d
--- /dev/null
+++ b/tests/software/bwa/test.yml
@@ -0,0 +1,32 @@
+- name: Run bwa index
+  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_index -c tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa_index
+  files:
+    - path: output/bwa/NC_010473.fa.amb
+      md5sum: 942a990ae872f1c0b8d72dda2db405d5
+    - path: output/bwa/NC_010473.fa.bwt
+      md5sum: 7301b52e2ecb893d429a49fa692447ae
+    - path: output/bwa/NC_010473.fa.pac
+      md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
+    - path: output/bwa/NC_010473.fa.sa
+      md5sum: a47dcc92e750e2f16fbd979b8ff9538e
+
+- name: Run bwa mem single-end
+  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_single_end -c tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa_mem
+  files:
+    - path: output/test_single_end/test.bam
+      md5sum: 3ee21210bac387e0335008146e4728bc
+
+- name: Run bwa mem paired-end
+  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa_mem
+  files:
+    - path: output/test_paired_end/test.bam
+      md5sum: 510d8acc6448c07cdacce8e64ec0904c
diff --git a/tests/software/fastqc/main.nf b/tests/software/fastqc/main.nf
index 597d56f6..629b4632 100644
--- a/tests/software/fastqc/main.nf
+++ b/tests/software/fastqc/main.nf
@@ -29,3 +29,5 @@ workflow test_paired_end {
 
     FASTQC_PE ( input )
 }
+
+// TODO Test e2e