diff --git a/.github/workflows/bwa_index.yml b/.github/workflows/bwa_index.yml
index c15c35c9..609fde64 100644
--- a/.github/workflows/bwa_index.yml
+++ b/.github/workflows/bwa_index.yml
@@ -1,30 +1,36 @@
 name: bwa_index
 on:
-  push:
-    paths:
-      - software/bwa/index/**
-      - .github/workflows/bwa_index.yml
-      - tests
-  pull_request:
-    paths:
-      - software/bwa/index/**
-      - .github/workflows/bwa_index.yml
-      - tests
+    push:
+        paths:
+            - software/bwa/index/**
+            - .github/workflows/bwa_index.yml
+            - tests/software/bwa/**
+    pull_request:
+        paths:
+            - software/bwa/index/**
+            - .github/workflows/bwa_index.yml
+            - tests/software/bwa/**
 
 jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    env:
-      NXF_ANSI_LOG: false
-    steps:
+    ci_test:
+        runs-on: ubuntu-latest
+        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/bwa_mem.yml b/.github/workflows/bwa_mem.yml
index 7f463471..93f8ea07 100644
--- a/.github/workflows/bwa_mem.yml
+++ b/.github/workflows/bwa_mem.yml
@@ -4,12 +4,12 @@ on:
     paths:
       - software/bwa/mem/**
       - .github/workflows/bwa_mem.yml
-      - tests
+      - tests/software/bwa/**
   pull_request:
     paths:
       - software/bwa/mem/**
       - .github/workflows/bwa_mem.yml
-      - tests
+      - tests/software/bwa/**
 
 jobs:
   ci_test:
@@ -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/.github/workflows/docker.yml b/.github/workflows/docker.yml
deleted file mode 100644
index 35171a6f..00000000
--- a/.github/workflows/docker.yml
+++ /dev/null
@@ -1,54 +0,0 @@
-name: Build Docker Images
-on:
-  push:
-    # Only on pushes to master (after PRs are merged)
-    branches: master
-    # Only if a conda environment file or a docker build file has been updated
-    paths:
-      - software/*/environment.yml
-      - software/*/Dockerfile
-
-jobs:
-  build_docker:
-    runs-on: ubuntu-latest
-    steps:
-
-      # Check out the repo
-      - uses: actions/checkout@v2
-
-      # Find the tool wrappers that changed
-      # Annoyingly, matrix can't take dynamic variables
-      - name: Find changed tools
-        run: |
-          TOOLS=$( git diff --name-only HEAD~ | egrep -o 'tools\/[^\/]+\/' | sort | uniq | awk NF | tr '\r\n' ' ' )
-          # Save so that GitHub Actions can see this variable in the next step
-          echo "::set-env name=TOOLS::$TOOLS"
-          echo "Tools that appear to have been updated:"
-          echo $TOOLS
-
-
-      - name: Build images
-        run: |
-          echo "Tools that appear to have been updated:"
-          echo -e $TOOLS
-          echo '-----'
-          for TOOL in $TOOLS; do
-            echo $TOOL
-          done;
-          echo '-----'
-          for d in software/*; do
-            for TOOL in $TOOLS; do
-              echo "$d -- $TOOL"
-              if echo $d/ | grep -q "$TOOL"; then
-                cd "$GITHUB_WORKSPACE/$d"
-                TOOLNAME=$(basename `pwd`)
-                # IMGNAME=docker.pkg.github.com/${GITHUB_REPOSITORY,,}/${TOOLNAME,,}:$GITHUB_SHA
-                # TODO: How do we have a proper version tag here?
-                IMGNAME=docker.pkg.github.com/${GITHUB_REPOSITORY,,}/${TOOLNAME,,}:latest
-                echo "Image name is: $IMGNAME"
-                echo "${{ secrets.GITHUB_TOKEN }}" | docker login -u ${{ github.actor }} --password-stdin docker.pkg.github.com
-                docker build -t $IMGNAME  .
-                docker push $IMGNAME
-              fi;
-            done;
-          done;
diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml
index 1379b8bb..c668adb2 100644
--- a/.github/workflows/fastqc.yml
+++ b/.github/workflows/fastqc.yml
@@ -4,34 +4,37 @@ on:
     paths:
       - software/fastqc/**
       - .github/workflows/fastqc.yml
-      - tests
+      - tests/software/fastqc/**
   pull_request:
     paths:
       - software/fastqc/**
       - .github/workflows/fastqc.yml
-      - tests
+      - tests/software/fastqc/**
 
 jobs:
   ci_test:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.07.1, '']
     env:
       NXF_ANSI_LOG: false
     steps:
+      - uses: actions/checkout@v2
 
-    - uses: actions/checkout@v2
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          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
 
-    - 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: pytest --tag fastqc --symlink --wt 2
+      # Test the module
+      - run: pytest --tag fastqc --symlink --wt 2
diff --git a/.github/workflows/picard_collectmultiplemetrics.yml b/.github/workflows/picard_collectmultiplemetrics.yml
index 292d01f7..b9176d72 100644
--- a/.github/workflows/picard_collectmultiplemetrics.yml
+++ b/.github/workflows/picard_collectmultiplemetrics.yml
@@ -4,12 +4,12 @@ on:
     paths:
       - software/picard/collectmultiplemetrics/**
       - .github/workflows/picard_collectmultiplemetrics.yml
-      - tests
+      - tests/software/picard/**
   pull_request:
     paths:
       - software/picard/collectmultiplemetrics/**
       - .github/workflows/picard_collectmultiplemetrics.yml
-      - tests
+      - tests/software/picard/**
 
 jobs:
   ci_test:
@@ -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/picard/collectmultiplemetrics/test/ -profile docker
+      # Test the module
+      - run: pytest --tag picard_collectmultiplemetrics --symlink --wt 2
diff --git a/.github/workflows/picard_markduplicates.yml b/.github/workflows/picard_markduplicates.yml
index fb0674f8..b6374318 100644
--- a/.github/workflows/picard_markduplicates.yml
+++ b/.github/workflows/picard_markduplicates.yml
@@ -4,12 +4,12 @@ on:
     paths:
       - software/picard/markduplicates/**
       - .github/workflows/picard_markduplicates.yml
-      - tests
+      - tests/software/picard/**
   pull_request:
     paths:
       - software/picard/markduplicates/**
       - .github/workflows/picard_markduplicates.yml
-      - tests
+      - tests/software/picard/**
 
 jobs:
   ci_test:
@@ -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/picard/markduplicates/test/ -profile docker
+      # Test the module
+      - run: pytest --tag picard_markduplicates --symlink --wt 2
diff --git a/.github/workflows/picard_mergesamfiles.yml b/.github/workflows/picard_mergesamfiles.yml
index 8cbf3645..0d329d8a 100644
--- a/.github/workflows/picard_mergesamfiles.yml
+++ b/.github/workflows/picard_mergesamfiles.yml
@@ -4,12 +4,12 @@ on:
     paths:
       - software/picard/mergesamfiles/**
       - .github/workflows/picard_mergesamfiles.yml
-      - tests
+      - tests/software/picard/**
   pull_request:
     paths:
       - software/picard/mergesamfiles/**
       - .github/workflows/picard_mergesamfiles.yml
-      - tests
+      - tests/software/picard/**
 
 jobs:
   ci_test:
@@ -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/picard/mergesamfiles/test/ -profile docker
+      # Test the module
+      - run: pytest --tag picard_mergesamfiles --symlink --wt 2
diff --git a/.github/workflows/samtools_flagstat.yml b/.github/workflows/samtools_flagstat.yml
index 69267617..a35dd0ac 100644
--- a/.github/workflows/samtools_flagstat.yml
+++ b/.github/workflows/samtools_flagstat.yml
@@ -4,12 +4,12 @@ on:
     paths:
       - software/samtools/flagstat/**
       - .github/workflows/samtools_flagstat.yml
-      - tests
+      - tests/software/samtools/**
   pull_request:
     paths:
       - software/samtools/flagstat/**
       - .github/workflows/samtools_flagstat.yml
-      - tests
+      - tests/software/samtools/**
 
 jobs:
   ci_test:
@@ -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/samtools/flagstat/test/ -profile docker
+      # Test the module
+      - run: pytest --tag samtools_flagstat --symlink --wt 2
diff --git a/.github/workflows/samtools_idxstats.yml b/.github/workflows/samtools_idxstats.yml
index a3e64998..4c01046f 100644
--- a/.github/workflows/samtools_idxstats.yml
+++ b/.github/workflows/samtools_idxstats.yml
@@ -4,12 +4,12 @@ on:
     paths:
       - software/samtools/idxstats/**
       - .github/workflows/samtools_idxstats.yml
-      - tests
+      - tests/software/samtools/**
   pull_request:
     paths:
       - software/samtools/idxstats/**
       - .github/workflows/samtools_idxstats.yml
-      - tests
+      - tests/software/samtools/**
 
 jobs:
   ci_test:
@@ -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/samtools/idxstats/test/ -profile docker
+      # Test the module
+      - run: pytest --tag samtools_idxstats --symlink --wt 2
diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml
index 57ef33aa..2c680274 100644
--- a/.github/workflows/samtools_index.yml
+++ b/.github/workflows/samtools_index.yml
@@ -4,12 +4,12 @@ on:
     paths:
       - software/samtools/index/**
       - .github/workflows/samtools_index.yml
-      - tests
+      - tests/software/samtools/**
   pull_request:
     paths:
       - software/samtools/index/**
       - .github/workflows/samtools_index.yml
-      - tests
+      - tests/software/samtools/**
 
 jobs:
   ci_test:
@@ -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/samtools/index/test/ -profile docker
+      # Test the module
+      - run: pytest --tag samtools_index --symlink --wt 2
diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml
index 02affa2c..2198fac6 100644
--- a/.github/workflows/samtools_sort.yml
+++ b/.github/workflows/samtools_sort.yml
@@ -4,12 +4,12 @@ on:
     paths:
       - software/samtools/sort/**
       - .github/workflows/samtools_sort.yml
-      - tests
+      - tests/software/samtools/**
   pull_request:
     paths:
       - software/samtools/sort/**
       - .github/workflows/samtools_sort.yml
-      - tests
+      - tests/software/samtools/**
 
 jobs:
   ci_test:
@@ -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/samtools/sort/test/ -profile docker
+      # Test the module
+      - run: pytest --tag samtools_sort --symlink --wt 2
diff --git a/.github/workflows/samtools_stats.yml b/.github/workflows/samtools_stats.yml
index c5765235..f147e510 100644
--- a/.github/workflows/samtools_stats.yml
+++ b/.github/workflows/samtools_stats.yml
@@ -3,13 +3,13 @@ on:
   push:
     paths:
       - software/samtools/stats/**
-      - .github/workflows/samtools_stats.yml
-      - tests
+      - .github/workflows/software/samtools_stats.yml
+      - tests/software/samtools/**
   pull_request:
     paths:
       - software/samtools/stats/**
-      - .github/workflows/samtools_stats.yml
-      - tests
+      - .github/workflows/software/samtools_stats.yml
+      - tests/software/samtools/**
 
 jobs:
   ci_test:
@@ -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/samtools/stats/test/ -profile docker
+      # Test the module
+      - run: pytest --tag samtools_stats --symlink --wt 2
diff --git a/.github/workflows/trimgalore.yml b/.github/workflows/trimgalore.yml
index 689a0fa0..dfb081d0 100644
--- a/.github/workflows/trimgalore.yml
+++ b/.github/workflows/trimgalore.yml
@@ -4,12 +4,12 @@ on:
     paths:
       - software/trimgalore/**
       - .github/workflows/trimgalore.yml
-      - tests
+      - tests/software/trimgalore/**
   pull_request:
     paths:
       - software/trimgalore/**
       - .github/workflows/trimgalore.yml
-      - tests
+      - tests/software/trimgalore/**
 
 jobs:
   ci_test:
@@ -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/trimgalore/test/ -profile docker
+      # Test the module
+      - run: pytest --tag trimgalore --symlink --wt 2
diff --git a/software/SOFTWARE/TOOL/test/input/soflink_test_data_here b/software/SOFTWARE/TOOL/test/input/soflink_test_data_here
deleted file mode 100644
index e69de29b..00000000
diff --git a/software/SOFTWARE/TOOL/test/main.nf b/software/SOFTWARE/TOOL/test/main.nf
deleted file mode 100644
index e504e51e..00000000
--- a/software/SOFTWARE/TOOL/test/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTQC as FASTQC_SE } from '../main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
-include { FASTQC as FASTQC_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("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
-
-    FASTQC_SE ( input )
-}
-
-/*
- * Test with paired-end data
- */
-workflow test_paired_end {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
-                file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
-
-    FASTQC_PE ( input )
-}
-
-workflow {
-    test_single_end()
-    test_paired_end()
-}
diff --git a/software/SOFTWARE/TOOL/test/nextflow.config b/software/SOFTWARE/TOOL/test/nextflow.config
deleted file mode 100644
index 4149feea..00000000
--- a/software/SOFTWARE/TOOL/test/nextflow.config
+++ /dev/null
@@ -1,20 +0,0 @@
-
-params {
-    outdir = "output/"
-    publish_dir_mode = "copy"
-    enable_conda = false
-}
-
-profiles {
-    conda  {
-        params.enable_conda = true
-    }
-    docker {
-        docker.enabled = true
-        docker.runOptions = '-u \$(id -u):\$(id -g)'
-    }
-    singularity {
-        singularity.enabled = true
-        singularity.autoMounts = true
-    }
-}
diff --git a/software/SOFTWARE/TOOL/test/output/upload_test_data_output_here b/software/SOFTWARE/TOOL/test/output/upload_test_data_output_here
deleted file mode 100644
index e69de29b..00000000
diff --git a/software/bwa/index/test/input/NC_010473.fa b/software/bwa/index/test/input/NC_010473.fa
deleted file mode 120000
index d2298ff8..00000000
--- a/software/bwa/index/test/input/NC_010473.fa
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/fasta/E_coli/NC_010473.fa
\ No newline at end of file
diff --git a/software/bwa/index/test/main.nf b/software/bwa/index/test/main.nf
deleted file mode 100644
index ef0db3ef..00000000
--- a/software/bwa/index/test/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWA_INDEX } from '../main.nf' addParams( options: [:] )
-
-workflow test {
-    BWA_INDEX ( file("${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/software/picard/collectmultiplemetrics/test/input/NC_010473.fa b/software/picard/collectmultiplemetrics/test/input/NC_010473.fa
deleted file mode 120000
index d2298ff8..00000000
--- a/software/picard/collectmultiplemetrics/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/picard/collectmultiplemetrics/test/input/test.paired_end.sorted.bam b/software/picard/collectmultiplemetrics/test/input/test.paired_end.sorted.bam
deleted file mode 120000
index af606d91..00000000
--- a/software/picard/collectmultiplemetrics/test/input/test.paired_end.sorted.bam
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam
\ No newline at end of file
diff --git a/software/picard/collectmultiplemetrics/test/main.nf b/software/picard/collectmultiplemetrics/test/main.nf
deleted file mode 100755
index d52961d7..00000000
--- a/software/picard/collectmultiplemetrics/test/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_COLLECTMULTIPLEMETRICS } from '../main.nf' addParams( options: [:] )
-
-workflow test {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
-
-    PICARD_COLLECTMULTIPLEMETRICS (
-        input,
-        file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
-    )
-}
-
-workflow {
-    test()
-}
diff --git a/software/picard/collectmultiplemetrics/test/nextflow.config b/software/picard/collectmultiplemetrics/test/nextflow.config
deleted file mode 100644
index 4149feea..00000000
--- a/software/picard/collectmultiplemetrics/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/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.alignment_summary_metrics b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
deleted file mode 100644
index 8516e5b3..00000000
--- a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+++ /dev/null
@@ -1,12 +0,0 @@
-## htsjdk.samtools.metrics.StringHeader
-# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa    ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
-## htsjdk.samtools.metrics.StringHeader
-# Started on: Fri Aug 07 15:24:11 GMT 2020
-
-## METRICS CLASS	picard.analysis.AlignmentSummaryMetrics
-CATEGORY	TOTAL_READS	PF_READS	PCT_PF_READS	PF_NOISE_READS	PF_READS_ALIGNED	PCT_PF_READS_ALIGNED	PF_ALIGNED_BASES	PF_HQ_ALIGNED_READS	PF_HQ_ALIGNED_BASES	PF_HQ_ALIGNED_Q20_BASES	PF_HQ_MEDIAN_MISMATCHES	PF_MISMATCH_RATE	PF_HQ_ERROR_RATE	PF_INDEL_RATE	MEAN_READ_LENGTH	READS_ALIGNED_IN_PAIRS	PCT_READS_ALIGNED_IN_PAIRS	PF_READS_IMPROPER_PAIRS	PCT_PF_READS_IMPROPER_PAIRS	BAD_CYCLES	STRAND_BALANCE	PCT_CHIMERAS	PCT_ADAPTER	SAMPLE	LIBRARY	READ_GROUP
-FIRST_OF_PAIR	10000	10000	1	0	10000	1	1000000	9367	936700	936700	0	0	0	0	100	10000	1	0	0	0	0.5078	0	0			
-SECOND_OF_PAIR	10000	10000	1	0	10000	1	1000000	9366	936600	936600	0	0.000001	0.000001	0	100	10000	1	0	0	0	0.4922	0	0			
-PAIR	20000	20000	1	0	20000	1	2000000	18733	1873300	1873300	0	0.000001	0.000001	0	100	20000	1	0	0	0	0.5	0	0			
-
-
diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
deleted file mode 100644
index 45075c6b..00000000
Binary files a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf and /dev/null differ
diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
deleted file mode 100644
index 0a025994..00000000
--- a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+++ /dev/null
@@ -1,209 +0,0 @@
-## htsjdk.samtools.metrics.StringHeader
-# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa    ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
-## htsjdk.samtools.metrics.StringHeader
-# Started on: Fri Aug 07 15:24:11 GMT 2020
-
-## METRICS CLASS	picard.analysis.BaseDistributionByCycleMetrics
-READ_END	CYCLE	PCT_A	PCT_C	PCT_G	PCT_T	PCT_N
-1	1	24.74	25.02	25.61	24.63	0
-1	2	25.5	23.74	25.96	24.8	0
-1	3	24.91	25.4	24.96	24.73	0
-1	4	25.44	25.36	24.59	24.61	0
-1	5	25.33	25.28	25.04	24.35	0
-1	6	24.94	25.83	25.25	23.98	0
-1	7	24.26	25.58	26.45	23.71	0
-1	8	23.87	26.45	25.17	24.51	0
-1	9	24.03	26.08	25.7	24.19	0
-1	10	24.8	24.8	25.34	25.06	0
-1	11	25.03	25.07	24.86	25.04	0
-1	12	24.37	25.97	25.25	24.41	0
-1	13	25.16	24.85	25.59	24.4	0
-1	14	24.27	25.69	25.79	24.25	0
-1	15	24.69	25.93	25.62	23.76	0
-1	16	24.86	25.94	24.97	24.23	0
-1	17	24.38	25.68	25.18	24.76	0
-1	18	24.03	25.63	25.9	24.44	0
-1	19	24.48	24.89	25.72	24.91	0
-1	20	24.06	25.07	25.75	25.12	0
-1	21	24.76	25.39	24.4	25.45	0
-1	22	25.18	25.02	24.66	25.14	0
-1	23	24.54	25.44	25.83	24.19	0
-1	24	23.7	26.35	25.59	24.36	0
-1	25	23.81	24.86	25.83	25.5	0
-1	26	24.57	25.78	25.11	24.54	0
-1	27	24	25.53	25.8	24.67	0
-1	28	24.32	25.76	25.36	24.56	0
-1	29	24.57	25.03	26.21	24.19	0
-1	30	25.44	25.05	24.7	24.81	0
-1	31	24.16	25.28	25.86	24.7	0
-1	32	24.45	25.24	25.21	25.1	0
-1	33	24.47	26.17	24.98	24.38	0
-1	34	24.95	24.47	26.38	24.2	0
-1	35	24.46	26.59	24.82	24.13	0
-1	36	24.35	25.45	25.7	24.5	0
-1	37	24.54	25.05	25.9	24.51	0
-1	38	24.82	26.59	24.4	24.19	0
-1	39	24.37	25.48	25.59	24.56	0
-1	40	24.93	25.4	25.17	24.5	0
-1	41	24.6	25.51	24.78	25.11	0
-1	42	24.33	26.16	25.04	24.47	0
-1	43	25.01	25.57	25.51	23.91	0
-1	44	24.57	25.52	25.48	24.43	0
-1	45	24.62	25.32	25.59	24.47	0
-1	46	24.53	25.4	25.15	24.92	0
-1	47	24.59	25.66	24.94	24.81	0
-1	48	23.81	25.76	25.33	25.1	0
-1	49	25.35	25.7	23.8	25.15	0
-1	50	24.53	25.21	25.47	24.79	0
-1	51	24.03	25.69	25.92	24.36	0
-1	52	23.98	25.01	25.99	25.02	0
-1	53	24.46	25.5	25.59	24.45	0
-1	54	24.41	25.73	25.45	24.41	0
-1	55	25.18	25.19	25.45	24.18	0
-1	56	24.18	25.49	25.72	24.61	0
-1	57	24.08	25.49	25.41	25.02	0
-1	58	24.1	25.35	25.38	25.17	0
-1	59	24.58	25.58	25.39	24.45	0
-1	60	24.67	25.22	25.47	24.64	0
-1	61	24.09	25.56	25.36	24.99	0
-1	62	25.2	25.47	25.68	23.65	0
-1	63	24.47	25.4	25.28	24.85	0
-1	64	24.8	25.45	25.4	24.35	0
-1	65	25.08	26.2	24.91	23.81	0
-1	66	24.89	24.74	25.37	25	0
-1	67	25.1	25.13	25.01	24.76	0
-1	68	24.73	25.3	25.13	24.84	0
-1	69	24.94	25.18	25.2	24.68	0
-1	70	24.29	25.21	25.62	24.88	0
-1	71	24.21	26.3	25.72	23.77	0
-1	72	24.39	25.61	25.34	24.66	0
-1	73	25.29	24.55	25.67	24.49	0
-1	74	25.66	25.07	24.54	24.73	0
-1	75	24.26	26.19	24.81	24.74	0
-1	76	24.04	24.89	26.43	24.64	0
-1	77	25.01	25.04	25.04	24.91	0
-1	78	24.37	26.53	25.05	24.05	0
-1	79	24.6	25.35	25.69	24.36	0
-1	80	24.9	25.32	25.33	24.45	0
-1	81	25.1	26.14	24.64	24.12	0
-1	82	23.95	25.9	25.23	24.92	0
-1	83	24.73	25.25	25.41	24.61	0
-1	84	24.81	25.43	25.68	24.08	0
-1	85	24.73	24.72	25.57	24.98	0
-1	86	24.12	25.26	25.17	25.45	0
-1	87	24.68	25.94	25.17	24.21	0
-1	88	24.77	25.11	25.88	24.24	0
-1	89	24.09	25.62	25.34	24.95	0
-1	90	24.35	25.57	24.76	25.32	0
-1	91	25.17	25.07	25.31	24.45	0
-1	92	25.65	25.04	25	24.31	0
-1	93	25.04	25.51	25.04	24.41	0
-1	94	24.85	26.17	25.11	23.87	0
-1	95	24.81	25.37	25.5	24.32	0
-1	96	24.84	25.25	25.47	24.44	0
-1	97	24.61	25.47	25.27	24.65	0
-1	98	24.86	25	25.48	24.66	0
-1	99	23.74	25.3	25.96	25	0
-1	100	23.83	26.06	25.13	24.98	0
-2	101	24.05	25.38	26.27	24.3	0
-2	102	23.62	25.98	25.49	24.91	0
-2	103	23.93	25.62	26.32	24.13	0
-2	104	24.94	25.34	25.24	24.48	0
-2	105	24.69	25.34	25.35	24.62	0
-2	106	24.69	24.97	25.08	25.26	0
-2	107	24.1	25.17	26.68	24.05	0
-2	108	24.92	25.49	24.96	24.63	0
-2	109	24.23	25.94	24.81	25.02	0
-2	110	24.38	25.12	25.59	24.91	0
-2	111	24.42	25.6	25.75	24.23	0
-2	112	25.33	25.73	24.96	23.98	0
-2	113	25.35	24.51	26.17	23.97	0
-2	114	24.12	25.34	26.17	24.37	0
-2	115	24.77	25.23	25.13	24.87	0
-2	116	25.36	25.27	25.1	24.27	0
-2	117	24.88	24.93	25.68	24.51	0
-2	118	23.79	25.75	25.19	25.27	0
-2	119	24.43	25.82	24.93	24.82	0
-2	120	24.4	25.93	24.62	25.05	0
-2	121	25.88	24.75	25.12	24.25	0
-2	122	24.27	25.8	24.92	25.01	0
-2	123	24.61	25.95	25.28	24.16	0
-2	124	24.66	25.46	25.69	24.19	0
-2	125	24.09	25.61	25.73	24.57	0
-2	126	25.11	24.62	25.34	24.93	0
-2	127	24.51	26.23	24.74	24.52	0
-2	128	25.39	25.58	24.73	24.3	0
-2	129	24.85	25.62	24.9	24.63	0
-2	130	24.43	25.89	25.15	24.53	0
-2	131	24.7	25.53	25.58	24.19	0
-2	132	24.5	26.2	25.01	24.29	0
-2	133	23.88	25.74	25.43	24.95	0
-2	134	24.9	25.2	25.18	24.72	0
-2	135	24.16	25.63	25.75	24.46	0
-2	136	23.8	25.87	25.42	24.91	0
-2	137	24.96	25.03	26.27	23.74	0
-2	138	24.53	25.69	24.99	24.79	0
-2	139	23.96	25.89	24.7	25.45	0
-2	140	24.13	24.91	25.68	25.28	0
-2	141	24.32	25.44	25.03	25.21	0
-2	142	24.23	25.86	24.69	25.22	0
-2	143	24.44	25.74	24.6	25.22	0
-2	144	25.39	24.13	25.44	25.04	0
-2	145	24.68	25.9	25.28	24.14	0
-2	146	23.85	25.25	25.61	25.29	0
-2	147	25.2	23.57	26.09	25.14	0
-2	148	25.49	25.2	25.07	24.24	0
-2	149	25.12	25.47	25.15	24.26	0
-2	150	24.73	25.26	25.44	24.57	0
-2	151	25.43	25.54	24.96	24.07	0
-2	152	25.03	25.6	24.97	24.4	0
-2	153	25.63	25.45	24.67	24.25	0
-2	154	24.32	25.73	25.33	24.62	0
-2	155	23.73	25.22	25.57	25.48	0
-2	156	23.82	25.86	26.08	24.24	0
-2	157	24.82	24.65	25.22	25.31	0
-2	158	24.96	25.77	24.82	24.45	0
-2	159	24.16	26.01	25.42	24.41	0
-2	160	24.57	25.49	25.27	24.67	0
-2	161	24.56	25.46	25.66	24.32	0
-2	162	24.85	24.93	25.01	25.21	0
-2	163	24.54	24.82	25.87	24.77	0
-2	164	24.88	25.37	25.67	24.08	0
-2	165	24.49	25.02	26.39	24.1	0
-2	166	24.03	25.21	25.87	24.89	0
-2	167	24.37	24.94	25.79	24.9	0
-2	168	24.04	25.06	25.86	25.04	0
-2	169	24.44	25.11	25.49	24.95	0.01
-2	170	24.47	25.75	25.4	24.38	0
-2	171	24.31	25.94	25.55	24.2	0
-2	172	25.19	25.19	25.29	24.33	0
-2	173	24.78	25.82	25.31	24.09	0
-2	174	24.65	25.8	25.01	24.54	0
-2	175	24.7	25.09	25.57	24.64	0
-2	176	24.75	25	24.93	25.32	0
-2	177	24.61	25.39	25.07	24.93	0
-2	178	24.64	25.38	25.92	24.06	0
-2	179	25.21	25.97	24.86	23.96	0
-2	180	23.95	26.44	25.54	24.07	0
-2	181	25.06	25.25	26.07	23.62	0
-2	182	23.91	26.04	25.25	24.8	0
-2	183	25.01	25.52	25.44	24.03	0
-2	184	25.19	25.68	24.67	24.46	0
-2	185	24.81	25.27	24.82	25.1	0
-2	186	24.31	25.78	24.9	25.01	0
-2	187	24.94	24.98	25.55	24.53	0
-2	188	25.25	25.77	25.32	23.66	0
-2	189	25.07	25.91	24.94	24.08	0
-2	190	24.64	25.42	26.18	23.76	0
-2	191	24.92	25.38	25.24	24.46	0
-2	192	24.47	25.18	25.08	25.27	0
-2	193	25.02	25.58	24.58	24.82	0
-2	194	24.05	25.41	24.94	25.6	0
-2	195	24.91	25.05	25.08	24.96	0
-2	196	24.1	25.22	25.74	24.94	0
-2	197	24.56	24.56	25.68	25.2	0
-2	198	25.34	25.16	25.36	24.14	0
-2	199	24.8	25.47	25.7	24.03	0
-2	200	23.53	26.05	26.1	24.32	0
-
-
diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
deleted file mode 100644
index 038922f1..00000000
Binary files a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf and /dev/null differ
diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_metrics b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_metrics
deleted file mode 100644
index 1a19682b..00000000
--- a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_metrics
+++ /dev/null
@@ -1,343 +0,0 @@
-## htsjdk.samtools.metrics.StringHeader
-# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa    ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
-## htsjdk.samtools.metrics.StringHeader
-# Started on: Fri Aug 07 15:24:11 GMT 2020
-
-## METRICS CLASS	picard.analysis.InsertSizeMetrics
-MEDIAN_INSERT_SIZE	MODE_INSERT_SIZE	MEDIAN_ABSOLUTE_DEVIATION	MIN_INSERT_SIZE	MAX_INSERT_SIZE	MEAN_INSERT_SIZE	STANDARD_DEVIATION	READ_PAIRS	PAIR_ORIENTATION	WIDTH_OF_10_PERCENT	WIDTH_OF_20_PERCENT	WIDTH_OF_30_PERCENT	WIDTH_OF_40_PERCENT	WIDTH_OF_50_PERCENT	WIDTH_OF_60_PERCENT	WIDTH_OF_70_PERCENT	WIDTH_OF_80_PERCENT	WIDTH_OF_90_PERCENT	WIDTH_OF_95_PERCENT	WIDTH_OF_99_PERCENT	SAMPLE	LIBRARY	READ_GROUP
-236	117	82	69	404	234.8136	94.885497	10000	FR	35	67	99	133	165	199	231	263	295	313	329			
-
-## HISTOGRAM	java.lang.Integer
-insert_size	All_Reads.fr_count
-69	36
-70	11
-71	30
-72	24
-73	34
-74	25
-75	30
-76	22
-77	26
-78	24
-79	30
-80	25
-81	33
-82	33
-83	27
-84	26
-85	36
-86	26
-87	26
-88	34
-89	24
-90	33
-91	35
-92	40
-93	37
-94	20
-95	30
-96	26
-97	33
-98	29
-99	30
-100	33
-101	27
-102	29
-103	37
-104	32
-105	26
-106	38
-107	26
-108	32
-109	26
-110	29
-111	43
-112	26
-113	20
-114	34
-115	32
-116	32
-117	52
-118	30
-119	29
-120	28
-121	35
-122	25
-123	34
-124	22
-125	20
-126	38
-127	30
-128	32
-129	31
-130	33
-131	32
-132	22
-133	35
-134	30
-135	28
-136	33
-137	28
-138	29
-139	31
-140	34
-141	37
-142	30
-143	30
-144	27
-145	24
-146	26
-147	33
-148	33
-149	28
-150	25
-151	25
-152	24
-153	24
-154	33
-155	36
-156	21
-157	26
-158	26
-159	27
-160	27
-161	34
-162	28
-163	27
-164	28
-165	25
-166	34
-167	24
-168	41
-169	26
-170	34
-171	28
-172	30
-173	28
-174	26
-175	29
-176	37
-177	35
-178	28
-179	25
-180	25
-181	36
-182	31
-183	25
-184	29
-185	32
-186	24
-187	27
-188	31
-189	34
-190	45
-191	32
-192	20
-193	41
-194	30
-195	31
-196	24
-197	36
-198	27
-199	30
-200	30
-201	26
-202	40
-203	37
-204	37
-205	28
-206	33
-207	28
-208	31
-209	37
-210	28
-211	31
-212	32
-213	33
-214	33
-215	29
-216	28
-217	33
-218	27
-219	22
-220	31
-221	38
-222	29
-223	41
-224	22
-225	28
-226	29
-227	26
-228	26
-229	33
-230	21
-231	24
-232	31
-233	33
-234	23
-235	29
-236	30
-237	31
-238	33
-239	31
-240	25
-241	29
-242	40
-243	24
-244	29
-245	39
-246	32
-247	40
-248	30
-249	29
-250	32
-251	22
-252	33
-253	33
-254	27
-255	28
-256	19
-257	39
-258	27
-259	34
-260	30
-261	36
-262	34
-263	32
-264	34
-265	19
-266	45
-267	29
-268	38
-269	28
-270	27
-271	26
-272	35
-273	31
-274	31
-275	25
-276	23
-277	35
-278	31
-279	35
-280	27
-281	35
-282	28
-283	30
-284	19
-285	30
-286	31
-287	28
-288	28
-289	42
-290	34
-291	32
-292	36
-293	33
-294	34
-295	29
-296	26
-297	19
-298	37
-299	24
-300	29
-301	25
-302	26
-303	43
-304	31
-305	30
-306	28
-307	29
-308	35
-309	35
-310	29
-311	35
-312	30
-313	48
-314	17
-315	26
-316	25
-317	28
-318	31
-319	33
-320	36
-321	30
-322	34
-323	30
-324	38
-325	34
-326	23
-327	28
-328	37
-329	26
-330	30
-331	37
-332	33
-333	28
-334	28
-335	37
-336	42
-337	30
-338	33
-339	32
-340	37
-341	26
-342	37
-343	29
-344	23
-345	35
-346	25
-347	33
-348	34
-349	37
-350	30
-351	23
-352	30
-353	30
-354	35
-355	30
-356	28
-357	26
-358	31
-359	28
-360	27
-361	32
-362	30
-363	26
-364	29
-365	40
-366	33
-367	38
-368	27
-369	34
-370	43
-371	27
-372	35
-373	27
-374	24
-375	30
-376	36
-377	24
-378	30
-379	35
-380	26
-381	32
-382	34
-383	34
-384	34
-385	21
-386	34
-387	35
-388	29
-389	25
-390	24
-391	25
-392	29
-393	32
-394	33
-395	27
-396	22
-397	36
-398	28
-404	1
-
diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
deleted file mode 100644
index 5bea51f1..00000000
Binary files a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf and /dev/null differ
diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
deleted file mode 100644
index f78e7066..00000000
--- a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+++ /dev/null
@@ -1,209 +0,0 @@
-## htsjdk.samtools.metrics.StringHeader
-# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa    ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
-## htsjdk.samtools.metrics.StringHeader
-# Started on: Fri Aug 07 15:24:11 GMT 2020
-
-
-## HISTOGRAM	java.lang.Integer
-CYCLE	MEAN_QUALITY
-1	40
-2	40
-3	40
-4	40
-5	40
-6	40
-7	40
-8	40
-9	40
-10	40
-11	40
-12	40
-13	40
-14	40
-15	40
-16	40
-17	40
-18	40
-19	40
-20	40
-21	40
-22	40
-23	40
-24	40
-25	40
-26	40
-27	40
-28	40
-29	40
-30	40
-31	40
-32	40
-33	40
-34	40
-35	40
-36	40
-37	40
-38	40
-39	40
-40	40
-41	40
-42	40
-43	40
-44	40
-45	40
-46	40
-47	40
-48	40
-49	40
-50	40
-51	40
-52	40
-53	40
-54	40
-55	40
-56	40
-57	40
-58	40
-59	40
-60	40
-61	40
-62	40
-63	40
-64	40
-65	40
-66	40
-67	40
-68	40
-69	40
-70	40
-71	40
-72	40
-73	40
-74	40
-75	40
-76	40
-77	40
-78	40
-79	40
-80	40
-81	40
-82	40
-83	40
-84	40
-85	40
-86	40
-87	40
-88	40
-89	40
-90	40
-91	40
-92	40
-93	40
-94	40
-95	40
-96	40
-97	40
-98	40
-99	40
-100	40
-101	40
-102	40
-103	40
-104	40
-105	40
-106	40
-107	40
-108	40
-109	40
-110	40
-111	40
-112	40
-113	40
-114	40
-115	40
-116	40
-117	40
-118	40
-119	40
-120	40
-121	40
-122	40
-123	40
-124	40
-125	40
-126	40
-127	40
-128	40
-129	40
-130	40
-131	40
-132	40
-133	40
-134	40
-135	40
-136	40
-137	40
-138	40
-139	40
-140	40
-141	40
-142	40
-143	40
-144	40
-145	40
-146	40
-147	40
-148	40
-149	40
-150	40
-151	40
-152	40
-153	40
-154	40
-155	40
-156	40
-157	40
-158	40
-159	40
-160	40
-161	40
-162	40
-163	40
-164	40
-165	40
-166	40
-167	40
-168	40
-169	40
-170	40
-171	40
-172	40
-173	40
-174	40
-175	40
-176	40
-177	40
-178	40
-179	40
-180	40
-181	40
-182	40
-183	40
-184	40
-185	40
-186	40
-187	40
-188	40
-189	40
-190	40
-191	40
-192	40
-193	40
-194	40
-195	40
-196	40
-197	40
-198	40
-199	40
-200	40
-
diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution.pdf b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
deleted file mode 100644
index d51c4be3..00000000
Binary files a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution.pdf and /dev/null differ
diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution_metrics b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
deleted file mode 100644
index 0cba723c..00000000
--- a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+++ /dev/null
@@ -1,10 +0,0 @@
-## htsjdk.samtools.metrics.StringHeader
-# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa    ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
-## htsjdk.samtools.metrics.StringHeader
-# Started on: Fri Aug 07 15:24:11 GMT 2020
-
-
-## HISTOGRAM	java.lang.Byte
-QUALITY	COUNT_OF_Q
-40	1999999
-
diff --git a/software/picard/markduplicates/test/input/test.paired_end.sorted.bam b/software/picard/markduplicates/test/input/test.paired_end.sorted.bam
deleted file mode 120000
index af606d91..00000000
--- a/software/picard/markduplicates/test/input/test.paired_end.sorted.bam
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam
\ No newline at end of file
diff --git a/software/picard/markduplicates/test/main.nf b/software/picard/markduplicates/test/main.nf
deleted file mode 100755
index 300f8e4a..00000000
--- a/software/picard/markduplicates/test/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_MARKDUPLICATES } from '../main.nf' addParams( options: [:] )
-
-workflow test {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
-
-    PICARD_MARKDUPLICATES ( input )
-}
-
-workflow {
-    test()
-}
diff --git a/software/picard/markduplicates/test/nextflow.config b/software/picard/markduplicates/test/nextflow.config
deleted file mode 100644
index 4149feea..00000000
--- a/software/picard/markduplicates/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/picard/markduplicates/test/output/picard/test.MarkDuplicates.metrics.txt b/software/picard/markduplicates/test/output/picard/test.MarkDuplicates.metrics.txt
deleted file mode 100644
index 5227a218..00000000
--- a/software/picard/markduplicates/test/output/picard/test.MarkDuplicates.metrics.txt
+++ /dev/null
@@ -1,13 +0,0 @@
-## htsjdk.samtools.metrics.StringHeader
-# MarkDuplicates INPUT=[test.paired_end.sorted.bam] OUTPUT=test.bam METRICS_FILE=test.MarkDuplicates.metrics.txt    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
-## htsjdk.samtools.metrics.StringHeader
-# Started on: Fri Aug 07 15:11:32 GMT 2020
-
-## METRICS CLASS	picard.sam.DuplicationMetrics
-LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
-Unknown Library	0	10000	0	0	0	0	0	0	
-
-## HISTOGRAM	java.lang.Double
-set_size	all_sets	non_optical_sets
-1.0	10000	10000
-
diff --git a/software/picard/markduplicates/test/output/picard/test.bam b/software/picard/markduplicates/test/output/picard/test.bam
deleted file mode 100644
index 4d249ed8..00000000
Binary files a/software/picard/markduplicates/test/output/picard/test.bam and /dev/null differ
diff --git a/software/picard/mergesamfiles/test/input/test.paired_end.COPY.sorted.bam b/software/picard/mergesamfiles/test/input/test.paired_end.COPY.sorted.bam
deleted file mode 120000
index af606d91..00000000
--- a/software/picard/mergesamfiles/test/input/test.paired_end.COPY.sorted.bam
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam
\ No newline at end of file
diff --git a/software/picard/mergesamfiles/test/input/test.paired_end.sorted.bam b/software/picard/mergesamfiles/test/input/test.paired_end.sorted.bam
deleted file mode 120000
index af606d91..00000000
--- a/software/picard/mergesamfiles/test/input/test.paired_end.sorted.bam
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam
\ No newline at end of file
diff --git a/software/picard/mergesamfiles/test/main.nf b/software/picard/mergesamfiles/test/main.nf
deleted file mode 100755
index db93bb35..00000000
--- a/software/picard/mergesamfiles/test/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_MERGESAMFILES } from '../main.nf' addParams( options: [:] )
-
-workflow test {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
-                file("${baseDir}/input/test.paired_end.COPY.sorted.bam", checkIfExists: true), ] ]
-
-    PICARD_MERGESAMFILES ( input )
-}
-
-workflow {
-    test()
-}
diff --git a/software/picard/mergesamfiles/test/nextflow.config b/software/picard/mergesamfiles/test/nextflow.config
deleted file mode 100644
index 4149feea..00000000
--- a/software/picard/mergesamfiles/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/picard/mergesamfiles/test/output/picard/test.bam b/software/picard/mergesamfiles/test/output/picard/test.bam
deleted file mode 100644
index 10c16d25..00000000
Binary files a/software/picard/mergesamfiles/test/output/picard/test.bam and /dev/null differ
diff --git a/software/samtools/flagstat/test/input/test.paired_end.sorted.bam b/software/samtools/flagstat/test/input/test.paired_end.sorted.bam
deleted file mode 120000
index af606d91..00000000
--- a/software/samtools/flagstat/test/input/test.paired_end.sorted.bam
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam
\ No newline at end of file
diff --git a/software/samtools/flagstat/test/input/test.paired_end.sorted.bam.bai b/software/samtools/flagstat/test/input/test.paired_end.sorted.bam.bai
deleted file mode 120000
index 61a71557..00000000
--- a/software/samtools/flagstat/test/input/test.paired_end.sorted.bam.bai
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam.bai
\ No newline at end of file
diff --git a/software/samtools/flagstat/test/main.nf b/software/samtools/flagstat/test/main.nf
deleted file mode 100755
index 680f70dd..00000000
--- a/software/samtools/flagstat/test/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_FLAGSTAT } from '../main.nf' addParams( options: [:] )
-
-workflow test {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
-              file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
-
-    SAMTOOLS_FLAGSTAT ( input )
-}
-
-workflow {
-    test()
-}
diff --git a/software/samtools/flagstat/test/nextflow.config b/software/samtools/flagstat/test/nextflow.config
deleted file mode 100644
index 4149feea..00000000
--- a/software/samtools/flagstat/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/samtools/flagstat/test/output/samtools/test.paired_end.sorted.bam.flagstat b/software/samtools/flagstat/test/output/samtools/test.paired_end.sorted.bam.flagstat
deleted file mode 100644
index c25f585c..00000000
--- a/software/samtools/flagstat/test/output/samtools/test.paired_end.sorted.bam.flagstat
+++ /dev/null
@@ -1,13 +0,0 @@
-20000 + 0 in total (QC-passed reads + QC-failed reads)
-0 + 0 secondary
-0 + 0 supplementary
-0 + 0 duplicates
-20000 + 0 mapped (100.00% : N/A)
-20000 + 0 paired in sequencing
-10000 + 0 read1
-10000 + 0 read2
-20000 + 0 properly paired (100.00% : N/A)
-20000 + 0 with itself and mate mapped
-0 + 0 singletons (0.00% : N/A)
-0 + 0 with mate mapped to a different chr
-0 + 0 with mate mapped to a different chr (mapQ>=5)
diff --git a/software/samtools/idxstats/test/input/test.paired_end.sorted.bam b/software/samtools/idxstats/test/input/test.paired_end.sorted.bam
deleted file mode 120000
index af606d91..00000000
--- a/software/samtools/idxstats/test/input/test.paired_end.sorted.bam
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam
\ No newline at end of file
diff --git a/software/samtools/idxstats/test/input/test.paired_end.sorted.bam.bai b/software/samtools/idxstats/test/input/test.paired_end.sorted.bam.bai
deleted file mode 120000
index 61a71557..00000000
--- a/software/samtools/idxstats/test/input/test.paired_end.sorted.bam.bai
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam.bai
\ No newline at end of file
diff --git a/software/samtools/idxstats/test/main.nf b/software/samtools/idxstats/test/main.nf
deleted file mode 100755
index 61c05fb8..00000000
--- a/software/samtools/idxstats/test/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_IDXSTATS } from '../main.nf' addParams( options: [:] )
-
-workflow test {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
-              file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
-
-    SAMTOOLS_IDXSTATS ( input )
-}
-
-workflow {
-    test()
-}
diff --git a/software/samtools/idxstats/test/nextflow.config b/software/samtools/idxstats/test/nextflow.config
deleted file mode 100644
index 4149feea..00000000
--- a/software/samtools/idxstats/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/samtools/idxstats/test/output/samtools/test.paired_end.sorted.bam.idxstats b/software/samtools/idxstats/test/output/samtools/test.paired_end.sorted.bam.idxstats
deleted file mode 100644
index 13521d48..00000000
--- a/software/samtools/idxstats/test/output/samtools/test.paired_end.sorted.bam.idxstats
+++ /dev/null
@@ -1,2 +0,0 @@
-gi|170079663|ref|NC_010473.1|	4686137	20000	0
-*	0	0	0
diff --git a/software/samtools/index/test/input/test.paired_end.sorted.bam b/software/samtools/index/test/input/test.paired_end.sorted.bam
deleted file mode 120000
index af606d91..00000000
--- a/software/samtools/index/test/input/test.paired_end.sorted.bam
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam
\ No newline at end of file
diff --git a/software/samtools/index/test/main.nf b/software/samtools/index/test/main.nf
deleted file mode 100755
index 7d949828..00000000
--- a/software/samtools/index/test/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_INDEX } from '../main.nf' addParams( options: [:] )
-
-workflow test {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
-
-    SAMTOOLS_INDEX ( input )
-}
-
-workflow {
-    test()
-}
diff --git a/software/samtools/index/test/nextflow.config b/software/samtools/index/test/nextflow.config
deleted file mode 100644
index 4149feea..00000000
--- a/software/samtools/index/test/nextflow.config
+++ /dev/null
@@ -1,20 +0,0 @@
-
-params {
-    outdir = "output/"
-    publish_dir_mode = "copy"
-    enable_conda = false
-}
-
-profiles {
-    conda  {
-        params.enable_conda = true
-    }
-    docker {
-        docker.enabled = true
-        docker.runOptions = '-u \$(id -u):\$(id -g)'
-    }
-    singularity {
-        singularity.enabled = true
-        singularity.autoMounts = true
-    }
-}
diff --git a/software/samtools/index/test/output/samtools/test.paired_end.sorted.bam.bai b/software/samtools/index/test/output/samtools/test.paired_end.sorted.bam.bai
deleted file mode 100644
index 0d8e61e4..00000000
Binary files a/software/samtools/index/test/output/samtools/test.paired_end.sorted.bam.bai and /dev/null differ
diff --git a/software/samtools/sort/test/input/test.paired_end.name.sorted.bam b/software/samtools/sort/test/input/test.paired_end.name.sorted.bam
deleted file mode 120000
index 9edb0c38..00000000
--- a/software/samtools/sort/test/input/test.paired_end.name.sorted.bam
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.name.sorted.bam
\ No newline at end of file
diff --git a/software/samtools/sort/test/main.nf b/software/samtools/sort/test/main.nf
deleted file mode 100755
index 45a6d43f..00000000
--- a/software/samtools/sort/test/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_SORT } from '../main.nf' addParams( options: [:] )
-
-workflow test {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("${baseDir}/input/test.paired_end.name.sorted.bam", checkIfExists: true) ]
-
-    SAMTOOLS_SORT ( input )
-}
-
-workflow {
-    test()
-}
diff --git a/software/samtools/sort/test/nextflow.config b/software/samtools/sort/test/nextflow.config
deleted file mode 100644
index 4149feea..00000000
--- a/software/samtools/sort/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/samtools/sort/test/output/samtools/test.bam b/software/samtools/sort/test/output/samtools/test.bam
deleted file mode 100644
index 33c7cd98..00000000
Binary files a/software/samtools/sort/test/output/samtools/test.bam and /dev/null differ
diff --git a/software/samtools/stats/test/input/test.paired_end.sorted.bam b/software/samtools/stats/test/input/test.paired_end.sorted.bam
deleted file mode 120000
index af606d91..00000000
--- a/software/samtools/stats/test/input/test.paired_end.sorted.bam
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam
\ No newline at end of file
diff --git a/software/samtools/stats/test/input/test.paired_end.sorted.bam.bai b/software/samtools/stats/test/input/test.paired_end.sorted.bam.bai
deleted file mode 120000
index 61a71557..00000000
--- a/software/samtools/stats/test/input/test.paired_end.sorted.bam.bai
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam.bai
\ No newline at end of file
diff --git a/software/samtools/stats/test/main.nf b/software/samtools/stats/test/main.nf
deleted file mode 100755
index a3388303..00000000
--- a/software/samtools/stats/test/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_STATS } from '../main.nf' addParams( options: [:] )
-
-workflow test {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
-              file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
-
-    SAMTOOLS_STATS ( input )
-}
-
-workflow {
-    test()
-}
diff --git a/software/samtools/stats/test/nextflow.config b/software/samtools/stats/test/nextflow.config
deleted file mode 100644
index 4149feea..00000000
--- a/software/samtools/stats/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/samtools/stats/test/output/samtools/test.paired_end.sorted.bam.stats b/software/samtools/stats/test/output/samtools/test.paired_end.sorted.bam.stats
deleted file mode 100644
index 0de94d2f..00000000
--- a/software/samtools/stats/test/output/samtools/test.paired_end.sorted.bam.stats
+++ /dev/null
@@ -1,1105 +0,0 @@
-# This file was produced by samtools stats (1.10+htslib-1.10.2) and can be plotted using plot-bamstats
-# This file contains statistics for all reads.
-# The command line was:  stats test.paired_end.sorted.bam
-# CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
-# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
-CHK	8e5d2ba0	549f6ff5	2a9028a0
-# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	20000
-SN	filtered sequences:	0
-SN	sequences:	20000
-SN	is sorted:	1
-SN	1st fragments:	10000
-SN	last fragments:	10000
-SN	reads mapped:	20000
-SN	reads mapped and paired:	20000	# paired-end technology bit set + both mates mapped
-SN	reads unmapped:	0
-SN	reads properly paired:	20000	# proper-pair bit set
-SN	reads paired:	20000	# paired-end technology bit set
-SN	reads duplicated:	0	# PCR or optical duplicate bit set
-SN	reads MQ0:	1262	# mapped and MQ=0
-SN	reads QC failed:	0
-SN	non-primary alignments:	0
-SN	total length:	2000000	# ignores clipping
-SN	total first fragment length:	1000000	# ignores clipping
-SN	total last fragment length:	1000000	# ignores clipping
-SN	bases mapped:	2000000	# ignores clipping
-SN	bases mapped (cigar):	2000000	# more accurate
-SN	bases trimmed:	0
-SN	bases duplicated:	0
-SN	mismatches:	1	# from NM fields
-SN	error rate:	5.000000e-07	# mismatches / bases mapped (cigar)
-SN	average length:	100
-SN	average first fragment length:	100
-SN	average last fragment length:	100
-SN	maximum length:	100
-SN	maximum first fragment length:	100
-SN	maximum last fragment length:	100
-SN	average quality:	40.0
-SN	insert size average:	233.4
-SN	insert size standard deviation:	94.1
-SN	inward oriented pairs:	9087
-SN	outward oriented pairs:	913
-SN	pairs with other orientation:	0
-SN	pairs on different chromosomes:	0
-SN	percentage of properly paired reads (%):	100.0
-# First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part.
-# Columns correspond to qualities and rows to cycles. First column is the cycle number.
-FFQ	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-FFQ	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-FFQ	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-FFQ	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-FFQ	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-FFQ	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-FFQ	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
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-FFQ	98	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-FFQ	99	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-FFQ	100	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-# Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part.
-# Columns correspond to qualities and rows to cycles. First column is the cycle number.
-LFQ	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	20	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	23	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	24	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	25	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	26	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	28	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	29	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	30	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	31	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	32	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	33	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	34	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	35	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	36	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	37	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	38	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	39	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	40	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	41	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	42	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	43	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	44	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	45	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	46	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	47	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	48	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	49	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	50	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	51	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	52	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	53	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	54	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	55	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	56	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	57	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	58	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	59	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	60	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	61	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	62	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	63	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	64	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	65	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	66	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	67	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	68	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	69	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	70	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	71	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	72	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	73	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	74	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	75	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	76	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	77	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	78	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	79	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	80	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	81	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	82	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	83	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	84	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	85	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	86	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	87	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	88	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	89	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	90	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	91	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	92	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	93	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	94	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	95	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	96	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	97	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	98	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	99	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-LFQ	100	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10000	0
-# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part.
-GCF	7.29	0
-GCF	15.08	3
-GCF	16.58	0
-GCF	18.09	2
-GCF	19.60	1
-GCF	21.11	0
-GCF	22.11	5
-GCF	23.12	6
-GCF	24.12	7
-GCF	25.13	10
-GCF	26.13	14
-GCF	27.14	12
-GCF	28.14	24
-GCF	29.15	26
-GCF	30.65	36
-GCF	32.16	43
-GCF	33.17	53
-GCF	34.17	66
-GCF	35.18	57
-GCF	36.18	63
-GCF	37.19	76
-GCF	38.19	88
-GCF	39.20	108
-GCF	40.20	140
-GCF	41.21	160
-GCF	42.21	183
-GCF	43.22	214
-GCF	44.22	238
-GCF	45.23	297
-GCF	46.23	340
-GCF	47.24	387
-GCF	48.24	490
-GCF	49.25	538
-GCF	50.25	581
-GCF	51.26	597
-GCF	52.26	614
-GCF	53.27	669
-GCF	54.27	645
-GCF	55.28	576
-GCF	56.28	499
-GCF	57.29	488
-GCF	58.29	376
-GCF	59.30	340
-GCF	60.30	238
-GCF	61.31	192
-GCF	62.31	144
-GCF	63.32	102
-GCF	64.32	76
-GCF	65.33	62
-GCF	66.33	22
-GCF	67.34	26
-GCF	68.34	14
-GCF	69.35	6
-GCF	70.85	2
-GCF	72.86	1
-GCF	74.37	0
-GCF	75.88	1
-GCF	77.39	0
-GCF	78.39	1
-# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part.
-GCL	7.29	0
-GCL	15.08	1
-GCL	16.58	0
-GCL	18.59	1
-GCL	20.10	3
-GCL	21.61	4
-GCL	23.62	5
-GCL	25.13	9
-GCL	26.13	12
-GCL	27.14	15
-GCL	28.14	23
-GCL	29.15	31
-GCL	30.15	33
-GCL	31.16	39
-GCL	32.16	32
-GCL	33.17	59
-GCL	34.17	57
-GCL	35.18	76
-GCL	36.18	77
-GCL	37.19	83
-GCL	38.19	104
-GCL	39.20	117
-GCL	40.20	123
-GCL	41.21	148
-GCL	42.21	152
-GCL	43.22	208
-GCL	44.22	252
-GCL	45.23	280
-GCL	46.23	358
-GCL	47.24	406
-GCL	48.24	455
-GCL	49.25	571
-GCL	50.25	543
-GCL	51.26	623
-GCL	52.26	618
-GCL	53.27	639
-GCL	54.27	653
-GCL	55.28	557
-GCL	56.28	555
-GCL	57.29	458
-GCL	58.29	398
-GCL	59.30	313
-GCL	60.30	252
-GCL	61.31	199
-GCL	62.31	130
-GCL	63.32	98
-GCL	64.32	79
-GCL	65.33	56
-GCL	66.33	36
-GCL	67.34	24
-GCL	68.34	9
-GCL	69.35	8
-GCL	70.35	4
-GCL	71.36	1
-GCL	72.36	2
-GCL	73.37	1
-# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
-GCC	1	24.39	25.20	25.94	24.46	0.00	0.00
-GCC	2	24.56	24.86	25.73	24.86	0.00	0.00
-GCC	3	24.42	25.51	25.64	24.43	0.00	0.00
-GCC	4	25.19	25.35	24.91	24.55	0.00	0.00
-GCC	5	25.01	25.31	25.20	24.48	0.00	0.00
-GCC	6	24.82	25.40	25.16	24.62	0.00	0.00
-GCC	7	24.18	25.38	26.57	23.88	0.00	0.00
-GCC	8	24.39	25.97	25.07	24.57	0.00	0.00
-GCC	9	24.13	26.01	25.25	24.61	0.00	0.00
-GCC	10	24.59	24.96	25.46	24.98	0.00	0.00
-GCC	11	24.73	25.34	25.30	24.64	0.00	0.00
-GCC	12	24.85	25.85	25.11	24.20	0.00	0.00
-GCC	13	25.25	24.68	25.88	24.18	0.00	0.00
-GCC	14	24.20	25.52	25.98	24.31	0.00	0.00
-GCC	15	24.73	25.58	25.38	24.32	0.00	0.00
-GCC	16	25.11	25.61	25.04	24.25	0.00	0.00
-GCC	17	24.63	25.30	25.43	24.64	0.00	0.00
-GCC	18	23.91	25.69	25.55	24.86	0.00	0.00
-GCC	19	24.45	25.36	25.32	24.86	0.00	0.00
-GCC	20	24.23	25.50	25.18	25.09	0.00	0.00
-GCC	21	25.32	25.07	24.76	24.85	0.00	0.00
-GCC	22	24.73	25.41	24.79	25.07	0.00	0.00
-GCC	23	24.57	25.70	25.55	24.18	0.00	0.00
-GCC	24	24.18	25.91	25.64	24.27	0.00	0.00
-GCC	25	23.95	25.23	25.78	25.04	0.00	0.00
-GCC	26	24.84	25.20	25.23	24.73	0.00	0.00
-GCC	27	24.25	25.88	25.27	24.59	0.00	0.00
-GCC	28	24.86	25.67	25.05	24.43	0.00	0.00
-GCC	29	24.71	25.32	25.55	24.41	0.00	0.00
-GCC	30	24.93	25.47	24.93	24.67	0.00	0.00
-GCC	31	24.43	25.41	25.72	24.45	0.00	0.00
-GCC	32	24.48	25.72	25.11	24.70	0.00	0.00
-GCC	33	24.18	25.95	25.20	24.66	0.00	0.00
-GCC	34	24.93	24.84	25.78	24.46	0.00	0.00
-GCC	35	24.31	26.11	25.29	24.30	0.00	0.00
-GCC	36	24.07	25.66	25.56	24.70	0.00	0.00
-GCC	37	24.75	25.04	26.09	24.12	0.00	0.00
-GCC	38	24.68	26.14	24.70	24.49	0.00	0.00
-GCC	39	24.16	25.68	25.14	25.00	0.00	0.00
-GCC	40	24.53	25.16	25.43	24.89	0.00	0.00
-GCC	41	24.46	25.48	24.91	25.16	0.00	0.00
-GCC	42	24.28	26.01	24.86	24.84	0.00	0.00
-GCC	43	24.73	25.66	25.05	24.57	0.00	0.00
-GCC	44	24.98	24.82	25.46	24.73	0.00	0.00
-GCC	45	24.65	25.61	25.43	24.30	0.00	0.00
-GCC	46	24.19	25.32	25.38	25.11	0.00	0.00
-GCC	47	24.89	24.61	25.52	24.98	0.00	0.00
-GCC	48	24.65	25.48	25.20	24.67	0.00	0.00
-GCC	49	25.23	25.59	24.48	24.70	0.00	0.00
-GCC	50	24.63	25.23	25.45	24.68	0.00	0.00
-GCC	51	24.73	25.61	25.44	24.21	0.00	0.00
-GCC	52	24.50	25.30	25.48	24.71	0.00	0.00
-GCC	53	25.05	25.48	25.13	24.35	0.00	0.00
-GCC	54	24.36	25.73	25.39	24.52	0.00	0.00
-GCC	55	24.45	25.20	25.51	24.83	0.00	0.00
-GCC	56	24.00	25.68	25.90	24.43	0.00	0.00
-GCC	57	24.45	25.07	25.32	25.16	0.00	0.00
-GCC	58	24.53	25.56	25.10	24.81	0.00	0.00
-GCC	59	24.37	25.80	25.41	24.43	0.00	0.00
-GCC	60	24.62	25.36	25.37	24.66	0.00	0.00
-GCC	61	24.32	25.51	25.51	24.66	0.00	0.00
-GCC	62	25.02	25.20	25.34	24.43	0.00	0.00
-GCC	63	24.50	25.11	25.57	24.81	0.00	0.00
-GCC	64	24.84	25.41	25.54	24.21	0.00	0.00
-GCC	65	24.79	25.61	25.65	23.95	0.00	0.00
-GCC	66	24.46	24.98	25.62	24.95	0.00	0.00
-GCC	67	24.73	25.04	25.40	24.83	0.00	0.00
-GCC	68	24.39	25.18	25.50	24.94	0.00	0.00
-GCC	69	24.69	25.15	25.35	24.82	0.01	0.00
-GCC	70	24.38	25.48	25.51	24.63	0.00	0.00
-GCC	71	24.26	26.12	25.64	23.98	0.00	0.00
-GCC	72	24.79	25.40	25.32	24.50	0.00	0.00
-GCC	73	25.04	25.18	25.49	24.29	0.00	0.00
-GCC	74	25.16	25.43	24.77	24.64	0.00	0.00
-GCC	75	24.48	25.64	25.19	24.69	0.00	0.00
-GCC	76	24.39	24.95	25.68	24.98	0.00	0.00
-GCC	77	24.81	25.21	25.05	24.92	0.00	0.00
-GCC	78	24.50	25.95	25.48	24.05	0.00	0.00
-GCC	79	24.91	25.66	25.27	24.16	0.00	0.00
-GCC	80	24.43	25.88	25.43	24.26	0.00	0.00
-GCC	81	25.08	25.70	25.36	23.87	0.00	0.00
-GCC	82	23.93	25.97	25.24	24.86	0.00	0.00
-GCC	83	24.87	25.39	25.43	24.32	0.00	0.00
-GCC	84	25.00	25.55	25.18	24.27	0.00	0.00
-GCC	85	24.77	25.00	25.20	25.04	0.00	0.00
-GCC	86	24.21	25.52	25.04	25.23	0.00	0.00
-GCC	87	24.81	25.46	25.36	24.37	0.00	0.00
-GCC	88	25.01	25.44	25.60	23.95	0.00	0.00
-GCC	89	24.58	25.77	25.14	24.52	0.00	0.00
-GCC	90	24.50	25.50	25.47	24.54	0.00	0.00
-GCC	91	25.05	25.23	25.27	24.45	0.00	0.00
-GCC	92	25.06	25.11	25.04	24.79	0.00	0.00
-GCC	93	25.03	25.55	24.81	24.61	0.00	0.00
-GCC	94	24.45	25.79	25.02	24.73	0.00	0.00
-GCC	95	24.86	25.21	25.29	24.64	0.00	0.00
-GCC	96	24.47	25.23	25.61	24.69	0.00	0.00
-GCC	97	24.59	25.02	25.48	24.93	0.00	0.00
-GCC	98	25.10	25.08	25.42	24.40	0.00	0.00
-GCC	99	24.27	25.39	25.83	24.52	0.00	0.00
-GCC	100	23.68	26.05	25.61	24.65	0.00	0.00
-# ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
-FBC	1	24.74	25.02	25.61	24.63	0.00	0.00
-FBC	2	25.50	23.74	25.96	24.80	0.00	0.00
-FBC	3	24.91	25.40	24.96	24.73	0.00	0.00
-FBC	4	25.44	25.36	24.59	24.61	0.00	0.00
-FBC	5	25.33	25.28	25.04	24.35	0.00	0.00
-FBC	6	24.94	25.83	25.25	23.98	0.00	0.00
-FBC	7	24.26	25.58	26.45	23.71	0.00	0.00
-FBC	8	23.87	26.45	25.17	24.51	0.00	0.00
-FBC	9	24.03	26.08	25.70	24.19	0.00	0.00
-FBC	10	24.80	24.80	25.34	25.06	0.00	0.00
-FBC	11	25.03	25.07	24.86	25.04	0.00	0.00
-FBC	12	24.37	25.97	25.25	24.41	0.00	0.00
-FBC	13	25.16	24.85	25.59	24.40	0.00	0.00
-FBC	14	24.27	25.69	25.79	24.25	0.00	0.00
-FBC	15	24.69	25.93	25.62	23.76	0.00	0.00
-FBC	16	24.86	25.94	24.97	24.23	0.00	0.00
-FBC	17	24.38	25.68	25.18	24.76	0.00	0.00
-FBC	18	24.03	25.63	25.90	24.44	0.00	0.00
-FBC	19	24.48	24.89	25.72	24.91	0.00	0.00
-FBC	20	24.06	25.07	25.75	25.12	0.00	0.00
-FBC	21	24.76	25.39	24.40	25.45	0.00	0.00
-FBC	22	25.18	25.02	24.66	25.14	0.00	0.00
-FBC	23	24.54	25.44	25.83	24.19	0.00	0.00
-FBC	24	23.70	26.35	25.59	24.36	0.00	0.00
-FBC	25	23.81	24.86	25.83	25.50	0.00	0.00
-FBC	26	24.57	25.78	25.11	24.54	0.00	0.00
-FBC	27	24.00	25.53	25.80	24.67	0.00	0.00
-FBC	28	24.32	25.76	25.36	24.56	0.00	0.00
-FBC	29	24.57	25.03	26.21	24.19	0.00	0.00
-FBC	30	25.44	25.05	24.70	24.81	0.00	0.00
-FBC	31	24.16	25.28	25.86	24.70	0.00	0.00
-FBC	32	24.45	25.24	25.21	25.10	0.00	0.00
-FBC	33	24.47	26.17	24.98	24.38	0.00	0.00
-FBC	34	24.95	24.47	26.38	24.20	0.00	0.00
-FBC	35	24.46	26.59	24.82	24.13	0.00	0.00
-FBC	36	24.35	25.45	25.70	24.50	0.00	0.00
-FBC	37	24.54	25.05	25.90	24.51	0.00	0.00
-FBC	38	24.82	26.59	24.40	24.19	0.00	0.00
-FBC	39	24.37	25.48	25.59	24.56	0.00	0.00
-FBC	40	24.93	25.40	25.17	24.50	0.00	0.00
-FBC	41	24.60	25.51	24.78	25.11	0.00	0.00
-FBC	42	24.33	26.16	25.04	24.47	0.00	0.00
-FBC	43	25.01	25.57	25.51	23.91	0.00	0.00
-FBC	44	24.57	25.52	25.48	24.43	0.00	0.00
-FBC	45	24.62	25.32	25.59	24.47	0.00	0.00
-FBC	46	24.53	25.40	25.15	24.92	0.00	0.00
-FBC	47	24.59	25.66	24.94	24.81	0.00	0.00
-FBC	48	23.81	25.76	25.33	25.10	0.00	0.00
-FBC	49	25.35	25.70	23.80	25.15	0.00	0.00
-FBC	50	24.53	25.21	25.47	24.79	0.00	0.00
-FBC	51	24.03	25.69	25.92	24.36	0.00	0.00
-FBC	52	23.98	25.01	25.99	25.02	0.00	0.00
-FBC	53	24.46	25.50	25.59	24.45	0.00	0.00
-FBC	54	24.41	25.73	25.45	24.41	0.00	0.00
-FBC	55	25.18	25.19	25.45	24.18	0.00	0.00
-FBC	56	24.18	25.49	25.72	24.61	0.00	0.00
-FBC	57	24.08	25.49	25.41	25.02	0.00	0.00
-FBC	58	24.10	25.35	25.38	25.17	0.00	0.00
-FBC	59	24.58	25.58	25.39	24.45	0.00	0.00
-FBC	60	24.67	25.22	25.47	24.64	0.00	0.00
-FBC	61	24.09	25.56	25.36	24.99	0.00	0.00
-FBC	62	25.20	25.47	25.68	23.65	0.00	0.00
-FBC	63	24.47	25.40	25.28	24.85	0.00	0.00
-FBC	64	24.80	25.45	25.40	24.35	0.00	0.00
-FBC	65	25.08	26.20	24.91	23.81	0.00	0.00
-FBC	66	24.89	24.74	25.37	25.00	0.00	0.00
-FBC	67	25.10	25.13	25.01	24.76	0.00	0.00
-FBC	68	24.73	25.30	25.13	24.84	0.00	0.00
-FBC	69	24.94	25.18	25.20	24.68	0.00	0.00
-FBC	70	24.29	25.21	25.62	24.88	0.00	0.00
-FBC	71	24.21	26.30	25.72	23.77	0.00	0.00
-FBC	72	24.39	25.61	25.34	24.66	0.00	0.00
-FBC	73	25.29	24.55	25.67	24.49	0.00	0.00
-FBC	74	25.66	25.07	24.54	24.73	0.00	0.00
-FBC	75	24.26	26.19	24.81	24.74	0.00	0.00
-FBC	76	24.04	24.89	26.43	24.64	0.00	0.00
-FBC	77	25.01	25.04	25.04	24.91	0.00	0.00
-FBC	78	24.37	26.53	25.05	24.05	0.00	0.00
-FBC	79	24.60	25.35	25.69	24.36	0.00	0.00
-FBC	80	24.90	25.32	25.33	24.45	0.00	0.00
-FBC	81	25.10	26.14	24.64	24.12	0.00	0.00
-FBC	82	23.95	25.90	25.23	24.92	0.00	0.00
-FBC	83	24.73	25.25	25.41	24.61	0.00	0.00
-FBC	84	24.81	25.43	25.68	24.08	0.00	0.00
-FBC	85	24.73	24.72	25.57	24.98	0.00	0.00
-FBC	86	24.12	25.26	25.17	25.45	0.00	0.00
-FBC	87	24.68	25.94	25.17	24.21	0.00	0.00
-FBC	88	24.77	25.11	25.88	24.24	0.00	0.00
-FBC	89	24.09	25.62	25.34	24.95	0.00	0.00
-FBC	90	24.35	25.57	24.76	25.32	0.00	0.00
-FBC	91	25.17	25.07	25.31	24.45	0.00	0.00
-FBC	92	25.65	25.04	25.00	24.31	0.00	0.00
-FBC	93	25.04	25.51	25.04	24.41	0.00	0.00
-FBC	94	24.85	26.17	25.11	23.87	0.00	0.00
-FBC	95	24.81	25.37	25.50	24.32	0.00	0.00
-FBC	96	24.84	25.25	25.47	24.44	0.00	0.00
-FBC	97	24.61	25.47	25.27	24.65	0.00	0.00
-FBC	98	24.86	25.00	25.48	24.66	0.00	0.00
-FBC	99	23.74	25.30	25.96	25.00	0.00	0.00
-FBC	100	23.83	26.06	25.13	24.98	0.00	0.00
-# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
-FTC	246020	254592	253576	245812	0
-# ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
-LBC	1	24.05	25.38	26.27	24.30	0.00	0.00
-LBC	2	23.62	25.98	25.49	24.91	0.00	0.00
-LBC	3	23.93	25.62	26.32	24.13	0.00	0.00
-LBC	4	24.94	25.34	25.24	24.48	0.00	0.00
-LBC	5	24.69	25.34	25.35	24.62	0.00	0.00
-LBC	6	24.69	24.97	25.08	25.26	0.00	0.00
-LBC	7	24.10	25.17	26.68	24.05	0.00	0.00
-LBC	8	24.92	25.49	24.96	24.63	0.00	0.00
-LBC	9	24.23	25.94	24.81	25.02	0.00	0.00
-LBC	10	24.38	25.12	25.59	24.91	0.00	0.00
-LBC	11	24.42	25.60	25.75	24.23	0.00	0.00
-LBC	12	25.33	25.73	24.96	23.98	0.00	0.00
-LBC	13	25.35	24.51	26.17	23.97	0.00	0.00
-LBC	14	24.12	25.34	26.17	24.37	0.00	0.00
-LBC	15	24.77	25.23	25.13	24.87	0.00	0.00
-LBC	16	25.36	25.27	25.10	24.27	0.00	0.00
-LBC	17	24.88	24.93	25.68	24.51	0.00	0.00
-LBC	18	23.79	25.75	25.19	25.27	0.00	0.00
-LBC	19	24.43	25.82	24.93	24.82	0.00	0.00
-LBC	20	24.40	25.93	24.62	25.05	0.00	0.00
-LBC	21	25.88	24.75	25.12	24.25	0.00	0.00
-LBC	22	24.27	25.80	24.92	25.01	0.00	0.00
-LBC	23	24.61	25.95	25.28	24.16	0.00	0.00
-LBC	24	24.66	25.46	25.69	24.19	0.00	0.00
-LBC	25	24.09	25.61	25.73	24.57	0.00	0.00
-LBC	26	25.11	24.62	25.34	24.93	0.00	0.00
-LBC	27	24.51	26.23	24.74	24.52	0.00	0.00
-LBC	28	25.39	25.58	24.73	24.30	0.00	0.00
-LBC	29	24.85	25.62	24.90	24.63	0.00	0.00
-LBC	30	24.43	25.89	25.15	24.53	0.00	0.00
-LBC	31	24.70	25.53	25.58	24.19	0.00	0.00
-LBC	32	24.50	26.20	25.01	24.29	0.00	0.00
-LBC	33	23.88	25.74	25.43	24.95	0.00	0.00
-LBC	34	24.90	25.20	25.18	24.72	0.00	0.00
-LBC	35	24.16	25.63	25.75	24.46	0.00	0.00
-LBC	36	23.80	25.87	25.42	24.91	0.00	0.00
-LBC	37	24.96	25.03	26.27	23.74	0.00	0.00
-LBC	38	24.53	25.69	24.99	24.79	0.00	0.00
-LBC	39	23.96	25.89	24.70	25.45	0.00	0.00
-LBC	40	24.13	24.91	25.68	25.28	0.00	0.00
-LBC	41	24.32	25.44	25.03	25.21	0.00	0.00
-LBC	42	24.23	25.86	24.69	25.22	0.00	0.00
-LBC	43	24.44	25.74	24.60	25.22	0.00	0.00
-LBC	44	25.39	24.13	25.44	25.04	0.00	0.00
-LBC	45	24.68	25.90	25.28	24.14	0.00	0.00
-LBC	46	23.85	25.25	25.61	25.29	0.00	0.00
-LBC	47	25.20	23.57	26.09	25.14	0.00	0.00
-LBC	48	25.49	25.20	25.07	24.24	0.00	0.00
-LBC	49	25.12	25.47	25.15	24.26	0.00	0.00
-LBC	50	24.73	25.26	25.44	24.57	0.00	0.00
-LBC	51	25.43	25.54	24.96	24.07	0.00	0.00
-LBC	52	25.03	25.60	24.97	24.40	0.00	0.00
-LBC	53	25.63	25.45	24.67	24.25	0.00	0.00
-LBC	54	24.32	25.73	25.33	24.62	0.00	0.00
-LBC	55	23.73	25.22	25.57	25.48	0.00	0.00
-LBC	56	23.82	25.86	26.08	24.24	0.00	0.00
-LBC	57	24.82	24.65	25.22	25.31	0.00	0.00
-LBC	58	24.96	25.77	24.82	24.45	0.00	0.00
-LBC	59	24.16	26.01	25.42	24.41	0.00	0.00
-LBC	60	24.57	25.49	25.27	24.67	0.00	0.00
-LBC	61	24.56	25.46	25.66	24.32	0.00	0.00
-LBC	62	24.85	24.93	25.01	25.21	0.00	0.00
-LBC	63	24.54	24.82	25.87	24.77	0.00	0.00
-LBC	64	24.88	25.37	25.67	24.08	0.00	0.00
-LBC	65	24.49	25.02	26.39	24.10	0.00	0.00
-LBC	66	24.03	25.21	25.87	24.89	0.00	0.00
-LBC	67	24.37	24.94	25.79	24.90	0.00	0.00
-LBC	68	24.04	25.06	25.86	25.04	0.00	0.00
-LBC	69	24.44	25.11	25.49	24.95	0.01	0.00
-LBC	70	24.47	25.75	25.40	24.38	0.00	0.00
-LBC	71	24.31	25.94	25.55	24.20	0.00	0.00
-LBC	72	25.19	25.19	25.29	24.33	0.00	0.00
-LBC	73	24.78	25.82	25.31	24.09	0.00	0.00
-LBC	74	24.65	25.80	25.01	24.54	0.00	0.00
-LBC	75	24.70	25.09	25.57	24.64	0.00	0.00
-LBC	76	24.75	25.00	24.93	25.32	0.00	0.00
-LBC	77	24.61	25.39	25.07	24.93	0.00	0.00
-LBC	78	24.64	25.38	25.92	24.06	0.00	0.00
-LBC	79	25.21	25.97	24.86	23.96	0.00	0.00
-LBC	80	23.95	26.44	25.54	24.07	0.00	0.00
-LBC	81	25.06	25.25	26.07	23.62	0.00	0.00
-LBC	82	23.91	26.04	25.25	24.80	0.00	0.00
-LBC	83	25.01	25.52	25.44	24.03	0.00	0.00
-LBC	84	25.19	25.68	24.67	24.46	0.00	0.00
-LBC	85	24.81	25.27	24.82	25.10	0.00	0.00
-LBC	86	24.31	25.78	24.90	25.01	0.00	0.00
-LBC	87	24.94	24.98	25.55	24.53	0.00	0.00
-LBC	88	25.25	25.77	25.32	23.66	0.00	0.00
-LBC	89	25.07	25.91	24.94	24.08	0.00	0.00
-LBC	90	24.64	25.42	26.18	23.76	0.00	0.00
-LBC	91	24.92	25.38	25.24	24.46	0.00	0.00
-LBC	92	24.47	25.18	25.08	25.27	0.00	0.00
-LBC	93	25.02	25.58	24.58	24.82	0.00	0.00
-LBC	94	24.05	25.41	24.94	25.60	0.00	0.00
-LBC	95	24.91	25.05	25.08	24.96	0.00	0.00
-LBC	96	24.10	25.22	25.74	24.94	0.00	0.00
-LBC	97	24.56	24.56	25.68	25.20	0.00	0.00
-LBC	98	25.34	25.16	25.36	24.14	0.00	0.00
-LBC	99	24.80	25.47	25.70	24.03	0.00	0.00
-LBC	100	23.53	26.05	26.10	24.32	0.00	0.00
-# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
-LTC	246099	254317	253651	245932	1
-# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs
-IS	0	0	0	0	0
-IS	1	0	0	0	0
-IS	2	0	0	0	0
-IS	3	0	0	0	0
-IS	4	0	0	0	0
-IS	5	0	0	0	0
-IS	6	0	0	0	0
-IS	7	0	0	0	0
-IS	8	0	0	0	0
-IS	9	0	0	0	0
-IS	10	0	0	0	0
-IS	11	0	0	0	0
-IS	12	0	0	0	0
-IS	13	0	0	0	0
-IS	14	0	0	0	0
-IS	15	0	0	0	0
-IS	16	0	0	0	0
-IS	17	0	0	0	0
-IS	18	0	0	0	0
-IS	19	0	0	0	0
-IS	20	0	0	0	0
-IS	21	0	0	0	0
-IS	22	0	0	0	0
-IS	23	0	0	0	0
-IS	24	0	0	0	0
-IS	25	0	0	0	0
-IS	26	0	0	0	0
-IS	27	0	0	0	0
-IS	28	0	0	0	0
-IS	29	0	0	0	0
-IS	30	0	0	0	0
-IS	31	0	0	0	0
-IS	32	0	0	0	0
-IS	33	0	0	0	0
-IS	34	0	0	0	0
-IS	35	0	0	0	0
-IS	36	0	0	0	0
-IS	37	0	0	0	0
-IS	38	0	0	0	0
-IS	39	0	0	0	0
-IS	40	0	0	0	0
-IS	41	0	0	0	0
-IS	42	0	0	0	0
-IS	43	0	0	0	0
-IS	44	0	0	0	0
-IS	45	0	0	0	0
-IS	46	0	0	0	0
-IS	47	0	0	0	0
-IS	48	0	0	0	0
-IS	49	0	0	0	0
-IS	50	0	0	0	0
-IS	51	0	0	0	0
-IS	52	0	0	0	0
-IS	53	0	0	0	0
-IS	54	0	0	0	0
-IS	55	0	0	0	0
-IS	56	0	0	0	0
-IS	57	0	0	0	0
-IS	58	0	0	0	0
-IS	59	0	0	0	0
-IS	60	0	0	0	0
-IS	61	0	0	0	0
-IS	62	0	0	0	0
-IS	63	0	0	0	0
-IS	64	0	0	0	0
-IS	65	0	0	0	0
-IS	66	0	0	0	0
-IS	67	0	0	0	0
-IS	68	0	0	0	0
-IS	69	36	0	36	0
-IS	70	11	0	11	0
-IS	71	30	0	30	0
-IS	72	24	0	24	0
-IS	73	34	0	34	0
-IS	74	25	0	25	0
-IS	75	30	0	30	0
-IS	76	22	0	22	0
-IS	77	26	0	26	0
-IS	78	24	0	24	0
-IS	79	30	0	30	0
-IS	80	25	0	25	0
-IS	81	33	0	33	0
-IS	82	33	0	33	0
-IS	83	27	0	27	0
-IS	84	26	0	26	0
-IS	85	36	0	36	0
-IS	86	26	0	26	0
-IS	87	26	0	26	0
-IS	88	34	0	34	0
-IS	89	24	0	24	0
-IS	90	33	0	33	0
-IS	91	35	0	35	0
-IS	92	40	0	40	0
-IS	93	37	0	37	0
-IS	94	20	0	20	0
-IS	95	30	0	30	0
-IS	96	26	0	26	0
-IS	97	33	0	33	0
-IS	98	29	0	29	0
-IS	99	30	0	30	0
-IS	100	33	15	18	0
-IS	101	27	27	0	0
-IS	102	29	29	0	0
-IS	103	37	37	0	0
-IS	104	32	32	0	0
-IS	105	26	26	0	0
-IS	106	38	38	0	0
-IS	107	26	26	0	0
-IS	108	32	32	0	0
-IS	109	26	26	0	0
-IS	110	29	29	0	0
-IS	111	43	43	0	0
-IS	112	26	26	0	0
-IS	113	20	20	0	0
-IS	114	34	34	0	0
-IS	115	32	32	0	0
-IS	116	32	32	0	0
-IS	117	52	52	0	0
-IS	118	30	30	0	0
-IS	119	29	29	0	0
-IS	120	28	28	0	0
-IS	121	35	35	0	0
-IS	122	25	25	0	0
-IS	123	34	34	0	0
-IS	124	22	22	0	0
-IS	125	20	20	0	0
-IS	126	38	38	0	0
-IS	127	30	30	0	0
-IS	128	32	32	0	0
-IS	129	31	31	0	0
-IS	130	33	33	0	0
-IS	131	32	32	0	0
-IS	132	22	22	0	0
-IS	133	35	35	0	0
-IS	134	30	30	0	0
-IS	135	28	28	0	0
-IS	136	33	33	0	0
-IS	137	28	28	0	0
-IS	138	29	29	0	0
-IS	139	31	31	0	0
-IS	140	34	34	0	0
-IS	141	37	37	0	0
-IS	142	30	30	0	0
-IS	143	30	30	0	0
-IS	144	27	27	0	0
-IS	145	24	24	0	0
-IS	146	26	26	0	0
-IS	147	33	33	0	0
-IS	148	33	33	0	0
-IS	149	28	28	0	0
-IS	150	25	25	0	0
-IS	151	25	25	0	0
-IS	152	24	24	0	0
-IS	153	24	24	0	0
-IS	154	33	33	0	0
-IS	155	36	36	0	0
-IS	156	21	21	0	0
-IS	157	26	26	0	0
-IS	158	26	26	0	0
-IS	159	27	27	0	0
-IS	160	27	27	0	0
-IS	161	34	34	0	0
-IS	162	28	28	0	0
-IS	163	27	27	0	0
-IS	164	28	28	0	0
-IS	165	25	25	0	0
-IS	166	34	34	0	0
-IS	167	24	24	0	0
-IS	168	41	41	0	0
-IS	169	26	26	0	0
-IS	170	34	34	0	0
-IS	171	28	28	0	0
-IS	172	30	30	0	0
-IS	173	28	28	0	0
-IS	174	26	26	0	0
-IS	175	29	29	0	0
-IS	176	37	37	0	0
-IS	177	35	35	0	0
-IS	178	28	28	0	0
-IS	179	25	25	0	0
-IS	180	25	25	0	0
-IS	181	36	36	0	0
-IS	182	31	31	0	0
-IS	183	25	25	0	0
-IS	184	29	29	0	0
-IS	185	32	32	0	0
-IS	186	24	24	0	0
-IS	187	27	27	0	0
-IS	188	31	31	0	0
-IS	189	34	34	0	0
-IS	190	45	45	0	0
-IS	191	32	32	0	0
-IS	192	20	20	0	0
-IS	193	41	41	0	0
-IS	194	30	30	0	0
-IS	195	31	31	0	0
-IS	196	24	24	0	0
-IS	197	36	36	0	0
-IS	198	27	27	0	0
-IS	199	30	30	0	0
-IS	200	30	30	0	0
-IS	201	26	26	0	0
-IS	202	40	40	0	0
-IS	203	37	37	0	0
-IS	204	37	37	0	0
-IS	205	28	28	0	0
-IS	206	33	33	0	0
-IS	207	28	28	0	0
-IS	208	31	31	0	0
-IS	209	37	37	0	0
-IS	210	28	28	0	0
-IS	211	31	31	0	0
-IS	212	32	32	0	0
-IS	213	33	33	0	0
-IS	214	33	33	0	0
-IS	215	29	29	0	0
-IS	216	28	28	0	0
-IS	217	33	33	0	0
-IS	218	27	27	0	0
-IS	219	22	22	0	0
-IS	220	31	31	0	0
-IS	221	38	38	0	0
-IS	222	29	29	0	0
-IS	223	41	41	0	0
-IS	224	22	22	0	0
-IS	225	28	28	0	0
-IS	226	29	29	0	0
-IS	227	26	26	0	0
-IS	228	26	26	0	0
-IS	229	33	33	0	0
-IS	230	21	21	0	0
-IS	231	24	24	0	0
-IS	232	31	31	0	0
-IS	233	33	33	0	0
-IS	234	23	23	0	0
-IS	235	29	29	0	0
-IS	236	30	30	0	0
-IS	237	31	31	0	0
-IS	238	33	33	0	0
-IS	239	31	31	0	0
-IS	240	25	25	0	0
-IS	241	29	29	0	0
-IS	242	40	40	0	0
-IS	243	24	24	0	0
-IS	244	29	29	0	0
-IS	245	39	39	0	0
-IS	246	32	32	0	0
-IS	247	40	40	0	0
-IS	248	30	30	0	0
-IS	249	29	29	0	0
-IS	250	32	32	0	0
-IS	251	22	22	0	0
-IS	252	33	33	0	0
-IS	253	33	33	0	0
-IS	254	27	27	0	0
-IS	255	28	28	0	0
-IS	256	19	19	0	0
-IS	257	39	39	0	0
-IS	258	27	27	0	0
-IS	259	34	34	0	0
-IS	260	30	30	0	0
-IS	261	36	36	0	0
-IS	262	34	34	0	0
-IS	263	32	32	0	0
-IS	264	34	34	0	0
-IS	265	19	19	0	0
-IS	266	45	45	0	0
-IS	267	29	29	0	0
-IS	268	38	38	0	0
-IS	269	28	28	0	0
-IS	270	27	27	0	0
-IS	271	26	26	0	0
-IS	272	35	35	0	0
-IS	273	31	31	0	0
-IS	274	31	31	0	0
-IS	275	25	25	0	0
-IS	276	23	23	0	0
-IS	277	35	35	0	0
-IS	278	31	31	0	0
-IS	279	35	35	0	0
-IS	280	27	27	0	0
-IS	281	35	35	0	0
-IS	282	28	28	0	0
-IS	283	30	30	0	0
-IS	284	19	19	0	0
-IS	285	30	30	0	0
-IS	286	31	31	0	0
-IS	287	28	28	0	0
-IS	288	28	28	0	0
-IS	289	42	42	0	0
-IS	290	34	34	0	0
-IS	291	32	32	0	0
-IS	292	36	36	0	0
-IS	293	33	33	0	0
-IS	294	34	34	0	0
-IS	295	29	29	0	0
-IS	296	26	26	0	0
-IS	297	19	19	0	0
-IS	298	37	37	0	0
-IS	299	24	24	0	0
-IS	300	29	29	0	0
-IS	301	25	25	0	0
-IS	302	26	26	0	0
-IS	303	43	43	0	0
-IS	304	31	31	0	0
-IS	305	30	30	0	0
-IS	306	28	28	0	0
-IS	307	29	29	0	0
-IS	308	35	35	0	0
-IS	309	35	35	0	0
-IS	310	29	29	0	0
-IS	311	35	35	0	0
-IS	312	30	30	0	0
-IS	313	48	48	0	0
-IS	314	17	17	0	0
-IS	315	26	26	0	0
-IS	316	25	25	0	0
-IS	317	28	28	0	0
-IS	318	31	31	0	0
-IS	319	33	33	0	0
-IS	320	36	36	0	0
-IS	321	30	30	0	0
-IS	322	34	34	0	0
-IS	323	30	30	0	0
-IS	324	38	38	0	0
-IS	325	34	34	0	0
-IS	326	23	23	0	0
-IS	327	28	28	0	0
-IS	328	37	37	0	0
-IS	329	26	26	0	0
-IS	330	30	30	0	0
-IS	331	37	37	0	0
-IS	332	33	33	0	0
-IS	333	28	28	0	0
-IS	334	28	28	0	0
-IS	335	37	37	0	0
-IS	336	42	42	0	0
-IS	337	30	30	0	0
-IS	338	33	33	0	0
-IS	339	32	32	0	0
-IS	340	37	37	0	0
-IS	341	26	26	0	0
-IS	342	37	37	0	0
-IS	343	29	29	0	0
-IS	344	23	23	0	0
-IS	345	35	35	0	0
-IS	346	25	25	0	0
-IS	347	33	33	0	0
-IS	348	34	34	0	0
-IS	349	37	37	0	0
-IS	350	30	30	0	0
-IS	351	23	23	0	0
-IS	352	30	30	0	0
-IS	353	30	30	0	0
-IS	354	35	35	0	0
-IS	355	30	30	0	0
-IS	356	28	28	0	0
-IS	357	26	26	0	0
-IS	358	31	31	0	0
-IS	359	28	28	0	0
-IS	360	27	27	0	0
-IS	361	32	32	0	0
-IS	362	30	30	0	0
-IS	363	26	26	0	0
-IS	364	29	29	0	0
-IS	365	40	40	0	0
-IS	366	33	33	0	0
-IS	367	38	38	0	0
-IS	368	27	27	0	0
-IS	369	34	34	0	0
-IS	370	43	43	0	0
-IS	371	27	27	0	0
-IS	372	35	35	0	0
-IS	373	27	27	0	0
-IS	374	24	24	0	0
-IS	375	30	30	0	0
-IS	376	36	36	0	0
-IS	377	24	24	0	0
-IS	378	30	30	0	0
-IS	379	35	35	0	0
-IS	380	26	26	0	0
-IS	381	32	32	0	0
-IS	382	34	34	0	0
-IS	383	34	34	0	0
-IS	384	34	34	0	0
-IS	385	21	21	0	0
-IS	386	34	34	0	0
-IS	387	35	35	0	0
-IS	388	29	29	0	0
-IS	389	25	25	0	0
-IS	390	24	24	0	0
-IS	391	25	25	0	0
-IS	392	29	29	0	0
-IS	393	32	32	0	0
-IS	394	33	33	0	0
-IS	395	27	27	0	0
-# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
-RL	100	20000
-# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count
-FRL	100	10000
-# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count
-LRL	100	10000
-# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions
-# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)
-# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.
-COV	[1-1]	1	1059236
-COV	[2-2]	2	327748
-COV	[3-3]	3	71636
-COV	[4-4]	4	14151
-COV	[5-5]	5	2032
-COV	[6-6]	6	562
-COV	[7-7]	7	32
-# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile
-GCD	0.0	0.862	0.000	0.000	0.000	0.000	0.000
-GCD	1.6	1.293	0.020	0.020	0.020	0.020	0.020
-GCD	39.0	1.724	0.440	0.440	0.440	0.440	0.440
-GCD	41.0	2.155	0.290	0.290	0.290	0.290	0.290
-GCD	43.0	2.586	0.385	0.385	0.385	0.385	0.385
-GCD	44.0	3.448	0.415	0.415	0.425	0.435	0.435
-GCD	45.0	4.310	0.345	0.345	0.428	0.510	0.510
-GCD	46.0	5.603	0.395	0.395	0.405	0.535	0.535
-GCD	47.0	9.052	0.345	0.376	0.447	0.533	0.605
-GCD	48.0	15.948	0.344	0.387	0.442	0.490	0.512
-GCD	49.0	23.707	0.367	0.399	0.430	0.481	0.563
-GCD	50.0	38.362	0.357	0.374	0.407	0.440	0.480
-GCD	51.0	58.190	0.325	0.375	0.423	0.482	0.520
-GCD	52.0	78.879	0.380	0.415	0.440	0.474	0.525
-GCD	53.0	93.103	0.364	0.410	0.450	0.477	0.516
-GCD	54.0	98.707	0.346	0.395	0.430	0.450	0.549
-GCD	55.0	99.138	0.450	0.450	0.450	0.450	0.450
-GCD	56.0	100.000	0.410	0.410	0.412	0.415	0.415
diff --git a/software/trimgalore/test/input/test_R1.fastq.gz b/software/trimgalore/test/input/test_R1.fastq.gz
deleted file mode 120000
index e7b4b614..00000000
--- a/software/trimgalore/test/input/test_R1.fastq.gz
+++ /dev/null
@@ -1 +0,0 @@
-../../../../tests/data/fastq/rna/test_R1.fastq.gz
\ No newline at end of file
diff --git a/software/trimgalore/test/input/test_R2.fastq.gz b/software/trimgalore/test/input/test_R2.fastq.gz
deleted file mode 120000
index 5b7b57a3..00000000
--- a/software/trimgalore/test/input/test_R2.fastq.gz
+++ /dev/null
@@ -1 +0,0 @@
-../../../../tests/data/fastq/rna/test_R2.fastq.gz
\ No newline at end of file
diff --git a/software/trimgalore/test/input/test_single_end.fastq.gz b/software/trimgalore/test/input/test_single_end.fastq.gz
deleted file mode 120000
index b1f79001..00000000
--- a/software/trimgalore/test/input/test_single_end.fastq.gz
+++ /dev/null
@@ -1 +0,0 @@
-../../../../tests/data/fastq/rna/test_single_end.fastq.gz
\ No newline at end of file
diff --git a/software/trimgalore/test/main.nf b/software/trimgalore/test/main.nf
deleted file mode 100755
index 29754b9d..00000000
--- a/software/trimgalore/test/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { TRIMGALORE as TRIMGALORE_SE } from '../main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
-include { TRIMGALORE as TRIMGALORE_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("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
-
-    TRIMGALORE_SE ( input )
-}
-
-/*
- * Test with paired-end data
- */
-workflow test_paired_end {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
-                file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
-
-    TRIMGALORE_PE ( input )
-}
-
-workflow {
-    test_single_end()
-    test_paired_end()
-}
diff --git a/software/trimgalore/test/nextflow.config b/software/trimgalore/test/nextflow.config
deleted file mode 100644
index 6432ed7d..00000000
--- a/software/trimgalore/test/nextflow.config
+++ /dev/null
@@ -1,25 +0,0 @@
-
-params {
-    outdir = "output/"
-    publish_dir_mode = "copy"
-    enable_conda = false
-
-    clip_r1 = 0
-    clip_r2 = 0
-    three_prime_clip_r1 = 0
-    three_prime_clip_r2 = 0
-}
-
-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/trimgalore/test/output/test_paired_end/test_1.fastq.gz_trimming_report.txt b/software/trimgalore/test/output/test_paired_end/test_1.fastq.gz_trimming_report.txt
deleted file mode 100644
index 2a6191a5..00000000
--- a/software/trimgalore/test/output/test_paired_end/test_1.fastq.gz_trimming_report.txt
+++ /dev/null
@@ -1,97 +0,0 @@
-
-SUMMARISING RUN PARAMETERS
-==========================
-Input filename: test_1.fastq.gz
-Trimming mode: paired-end
-Trim Galore version: 0.6.4_dev
-Cutadapt version: 2.6
-Number of cores used for trimming: 1
-Quality Phred score cutoff: 20
-Quality encoding type selected: ASCII+33
-Using Nextera adapter for trimming (count: 83). Second best hit was Illumina (count: 0)
-Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
-Maximum trimming error rate: 0.1 (default)
-Minimum required adapter overlap (stringency): 1 bp
-Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
-Output file will be GZIP compressed
-
-
-This is cutadapt 2.6 with Python 3.7.3
-Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_1.fastq.gz
-Processing reads on 1 core in single-end mode ...
-Finished in 0.64 s (64 us/read; 0.94 M reads/minute).
-
-=== Summary ===
-
-Total reads processed:                  10,000
-Reads with adapters:                     3,225 (32.2%)
-Reads written (passing filters):        10,000 (100.0%)
-
-Total basepairs processed:       760,000 bp
-Quality-trimmed:                   4,492 bp (0.6%)
-Total written (filtered):        748,403 bp (98.5%)
-
-=== Adapter 1 ===
-
-Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 3225 times.
-
-No. of allowed errors:
-0-9 bp: 0; 10-12 bp: 1
-
-Bases preceding removed adapters:
-  A: 23.8%
-  C: 28.2%
-  G: 22.7%
-  T: 25.3%
-  none/other: 0.0%
-
-Overview of removed sequences
-length	count	expect	max.err	error counts
-1	2170	2500.0	0	2170
-2	622	625.0	0	622
-3	223	156.2	0	223
-4	64	39.1	0	64
-5	14	9.8	0	14
-6	9	2.4	0	9
-7	8	0.6	0	8
-8	5	0.2	0	5
-9	4	0.0	0	4
-10	8	0.0	1	7 1
-11	3	0.0	1	3
-12	4	0.0	1	4
-13	6	0.0	1	6
-14	5	0.0	1	4 1
-15	5	0.0	1	5
-16	6	0.0	1	5 1
-17	3	0.0	1	3
-18	3	0.0	1	3
-19	1	0.0	1	1
-20	3	0.0	1	3
-21	7	0.0	1	7
-22	7	0.0	1	7
-23	3	0.0	1	3
-24	6	0.0	1	6
-25	4	0.0	1	4
-26	2	0.0	1	2
-27	4	0.0	1	4
-28	1	0.0	1	1
-29	3	0.0	1	3
-30	4	0.0	1	4
-32	3	0.0	1	3
-33	2	0.0	1	1 1
-34	1	0.0	1	1
-35	1	0.0	1	1
-40	1	0.0	1	1
-42	1	0.0	1	0 1
-45	1	0.0	1	0 1
-49	1	0.0	1	0 1
-52	1	0.0	1	0 1
-56	2	0.0	1	0 2
-59	1	0.0	1	0 1
-67	1	0.0	1	0 1
-70	2	0.0	1	0 2
-
-RUN STATISTICS FOR INPUT FILE: test_1.fastq.gz
-=============================================
-10000 sequences processed in total
-
diff --git a/software/trimgalore/test/output/test_paired_end/test_1_val_1.fq.gz b/software/trimgalore/test/output/test_paired_end/test_1_val_1.fq.gz
deleted file mode 100644
index 5ed6d4d7..00000000
Binary files a/software/trimgalore/test/output/test_paired_end/test_1_val_1.fq.gz and /dev/null differ
diff --git a/software/trimgalore/test/output/test_paired_end/test_2.fastq.gz_trimming_report.txt b/software/trimgalore/test/output/test_paired_end/test_2.fastq.gz_trimming_report.txt
deleted file mode 100644
index bd436f10..00000000
--- a/software/trimgalore/test/output/test_paired_end/test_2.fastq.gz_trimming_report.txt
+++ /dev/null
@@ -1,100 +0,0 @@
-
-SUMMARISING RUN PARAMETERS
-==========================
-Input filename: test_2.fastq.gz
-Trimming mode: paired-end
-Trim Galore version: 0.6.4_dev
-Cutadapt version: 2.6
-Number of cores used for trimming: 1
-Quality Phred score cutoff: 20
-Quality encoding type selected: ASCII+33
-Using Nextera adapter for trimming (count: 83). Second best hit was Illumina (count: 0)
-Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
-Maximum trimming error rate: 0.1 (default)
-Minimum required adapter overlap (stringency): 1 bp
-Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
-Output file will be GZIP compressed
-
-
-This is cutadapt 2.6 with Python 3.7.3
-Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_2.fastq.gz
-Processing reads on 1 core in single-end mode ...
-Finished in 0.70 s (70 us/read; 0.86 M reads/minute).
-
-=== Summary ===
-
-Total reads processed:                  10,000
-Reads with adapters:                     3,295 (33.0%)
-Reads written (passing filters):        10,000 (100.0%)
-
-Total basepairs processed:       760,000 bp
-Quality-trimmed:                   7,096 bp (0.9%)
-Total written (filtered):        745,649 bp (98.1%)
-
-=== Adapter 1 ===
-
-Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 3295 times.
-
-No. of allowed errors:
-0-9 bp: 0; 10-12 bp: 1
-
-Bases preceding removed adapters:
-  A: 22.6%
-  C: 28.2%
-  G: 23.6%
-  T: 25.6%
-  none/other: 0.0%
-
-Overview of removed sequences
-length	count	expect	max.err	error counts
-1	2213	2500.0	0	2213
-2	647	625.0	0	647
-3	239	156.2	0	239
-4	53	39.1	0	53
-5	10	9.8	0	10
-6	7	2.4	0	7
-7	8	0.6	0	8
-8	5	0.2	0	5
-9	5	0.0	0	5
-10	10	0.0	1	8 2
-11	2	0.0	1	2
-12	4	0.0	1	4
-13	7	0.0	1	7
-14	3	0.0	1	3
-15	4	0.0	1	4
-16	5	0.0	1	5
-17	3	0.0	1	3
-18	5	0.0	1	4 1
-19	2	0.0	1	1 1
-20	3	0.0	1	3
-21	7	0.0	1	7
-22	6	0.0	1	6
-23	3	0.0	1	3
-24	7	0.0	1	7
-25	4	0.0	1	4
-26	2	0.0	1	2
-27	4	0.0	1	4
-28	1	0.0	1	1
-29	3	0.0	1	3
-30	4	0.0	1	4
-32	3	0.0	1	3
-33	1	0.0	1	1
-34	1	0.0	1	1
-35	2	0.0	1	1 1
-40	1	0.0	1	0 1
-41	1	0.0	1	1
-46	1	0.0	1	0 1
-48	1	0.0	1	0 1
-49	2	0.0	1	0 2
-56	2	0.0	1	0 2
-59	1	0.0	1	0 1
-70	1	0.0	1	0 1
-73	2	0.0	1	0 2
-
-RUN STATISTICS FOR INPUT FILE: test_2.fastq.gz
-=============================================
-10000 sequences processed in total
-
-Total number of sequences analysed for the sequence pair length validation: 10000
-
-Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21 (0.21%)
diff --git a/software/trimgalore/test/output/test_paired_end/test_2_val_2.fq.gz b/software/trimgalore/test/output/test_paired_end/test_2_val_2.fq.gz
deleted file mode 100644
index a3ae7c03..00000000
Binary files a/software/trimgalore/test/output/test_paired_end/test_2_val_2.fq.gz and /dev/null differ
diff --git a/software/trimgalore/test/output/test_single_end/test.fastq.gz_trimming_report.txt b/software/trimgalore/test/output/test_single_end/test.fastq.gz_trimming_report.txt
deleted file mode 100644
index 85c2b6c5..00000000
--- a/software/trimgalore/test/output/test_single_end/test.fastq.gz_trimming_report.txt
+++ /dev/null
@@ -1,61 +0,0 @@
-
-SUMMARISING RUN PARAMETERS
-==========================
-Input filename: test.fastq.gz
-Trimming mode: single-end
-Trim Galore version: 0.6.4_dev
-Cutadapt version: 2.6
-Number of cores used for trimming: 1
-Quality Phred score cutoff: 20
-Quality encoding type selected: ASCII+33
-Unable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count smallRNA: 0, count Nextera: 0)
-Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).
-Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
-Maximum trimming error rate: 0.1 (default)
-Minimum required adapter overlap (stringency): 1 bp
-Minimum required sequence length before a sequence gets removed: 20 bp
-Output file will be GZIP compressed
-
-
-This is cutadapt 2.6 with Python 3.7.3
-Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test.fastq.gz
-Processing reads on 1 core in single-end mode ...
-Finished in 0.06 s (28 us/read; 2.13 M reads/minute).
-
-=== Summary ===
-
-Total reads processed:                   2,052
-Reads with adapters:                       223 (10.9%)
-Reads written (passing filters):         2,052 (100.0%)
-
-Total basepairs processed:       103,432 bp
-Quality-trimmed:                      11 bp (0.0%)
-Total written (filtered):        103,117 bp (99.7%)
-
-=== Adapter 1 ===
-
-Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 223 times.
-
-No. of allowed errors:
-0-9 bp: 0; 10-13 bp: 1
-
-Bases preceding removed adapters:
-  A: 31.8%
-  C: 37.7%
-  G: 16.1%
-  T: 14.3%
-  none/other: 0.0%
-
-Overview of removed sequences
-length	count	expect	max.err	error counts
-1	190	513.0	0	190
-2	3	128.2	0	3
-3	16	32.1	0	16
-4	10	8.0	0	10
-5	4	2.0	0	4
-
-RUN STATISTICS FOR INPUT FILE: test.fastq.gz
-=============================================
-2052 sequences processed in total
-Sequences removed because they became shorter than the length cutoff of 20 bp:	0 (0.0%)
-
diff --git a/software/trimgalore/test/output/test_single_end/test_trimmed.fq.gz b/software/trimgalore/test/output/test_single_end/test_trimmed.fq.gz
deleted file mode 100644
index a1f8109c..00000000
Binary files a/software/trimgalore/test/output/test_single_end/test_trimmed.fq.gz 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
diff --git a/tests/software/fastqc/test.yml b/tests/software/fastqc/test.yml
index fe3cc275..f0f6b420 100644
--- a/tests/software/fastqc/test.yml
+++ b/tests/software/fastqc/test.yml
@@ -4,7 +4,6 @@
     - fastqc
   files:
     - path: output/test_single_end/test_fastqc.html
-      md5sum: 7027e72c3e55292c1567f12e02565e3b
     - path: output/test_single_end/test_fastqc.zip
 
 - name: Run fastqc paired-end test workflow
@@ -13,8 +12,6 @@
     - fastqc
   files:
     - path: output/test_paired_end/test_1_fastqc.html
-      md5sum: b3796b4323dc34970b7461f813135254
     - path: output/test_paired_end/test_2_fastqc.html
-      md5sum: 55182467f48ca5ed88a2608ea57a1afc
     - path: output/test_paired_end/test_1_fastqc.zip
     - path: output/test_paired_end/test_2_fastqc.zip
diff --git a/tests/software/picard/main.nf b/tests/software/picard/main.nf
new file mode 100644
index 00000000..d291de6d
--- /dev/null
+++ b/tests/software/picard/main.nf
@@ -0,0 +1,48 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_MERGESAMFILES } from '../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] )
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] )
+include { PICARD_MARKDUPLICATES } from '../../../software/picard/markduplicates/main.nf' addParams( options: [:] )
+
+workflow test_picard_mergesamfiles {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true), ] ]
+
+    PICARD_MERGESAMFILES ( input )
+}
+
+
+workflow test_picard_collectmultiplemetrics {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
+
+    PICARD_COLLECTMULTIPLEMETRICS (
+        input,
+        file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    )
+}
+
+workflow test_picard_markduplicates  {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+
+    PICARD_MARKDUPLICATES ( input )
+}
+
+workflow test_picard_markduplicates_not_sorted  {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
+
+    PICARD_MARKDUPLICATES ( input )
+}
diff --git a/tests/software/picard/test.yml b/tests/software/picard/test.yml
new file mode 100644
index 00000000..4a813f37
--- /dev/null
+++ b/tests/software/picard/test.yml
@@ -0,0 +1,43 @@
+- name: Run picard mergesamfiles
+  command: nextflow run ./tests/software/picard -profile docker -entry test_picard_mergesamfiles -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard_mergesamfiles
+  files:
+    - path: output/picard/test.bam
+      md5sum: a9c8a28d1aac362df5973ba2d9923f86
+
+- name: Run picard collectmultiplemetrics
+  command: nextflow run ./tests/software/picard -profile docker -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard_collectmultiplemetrics
+  files:
+    # These can't be md5'd consistently
+    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+
+- name: Run picard MarkDuplicates
+  command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard_markduplicates
+  files:
+    - path: output/picard/test.MarkDuplicates.metrics.txt
+    - path: output/picard/test.bam
+      md5sum: 50407a1ee722f2bf6a20471c8a7fd6b0
+
+- name: Run picard MarkDuplicates without a sorted bam file so it fails
+  command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard_markduplicates
+    - should fail
+  exit_code: 1
diff --git a/tests/software/samtools/main.nf b/tests/software/samtools/main.nf
new file mode 100644
index 00000000..747a1293
--- /dev/null
+++ b/tests/software/samtools/main.nf
@@ -0,0 +1,58 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] )
+include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] )
+include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addParams( options: [:] )
+include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] )
+include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] )
+
+workflow test_samtools_flagstat {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
+
+    SAMTOOLS_FLAGSTAT ( input )
+}
+
+workflow test_samtools_idxstats {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
+
+    SAMTOOLS_IDXSTATS ( input )
+}
+
+workflow test_samtools_index {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+
+    SAMTOOLS_INDEX ( input )
+}
+
+// FIXME Why is this passing it an already sorted bam?
+workflow test_samtools_sort  {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+
+    SAMTOOLS_SORT ( input )
+}
+
+workflow test_samtools_stats {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
+
+    SAMTOOLS_STATS ( input )
+}
diff --git a/tests/software/samtools/test.yml b/tests/software/samtools/test.yml
new file mode 100644
index 00000000..d4e61907
--- /dev/null
+++ b/tests/software/samtools/test.yml
@@ -0,0 +1,44 @@
+- name: Run samtools flagstat test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_flagstat -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_flagstat
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.flagstat
+      md5sum: 80590621c74f5ee43ada20d010a3837f
+
+- name: Run samtools idxstats test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_idxstats -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_idxstats
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.idxstats
+      md5sum: 3bee8b7d55e412da2b3816c5a18d60d5
+
+- name: Run samtools index test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_index -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_index
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.bai
+      md5sum: 67338c2995eae82c849830ca55aa7bd1
+
+- name: Run samtools sort test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_sort -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_sort
+  files:
+    - path: output/samtools/test.bam
+      md5sum: a41bfadacd2eeef1d31e05c135cc4f4e
+
+- name: Run samtools stats test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_stats -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_stats
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.stats
+      md5sum: 06c183864d6e47ab89b0650cae831a93
diff --git a/tests/software/trimgalore/main.nf b/tests/software/trimgalore/main.nf
new file mode 100644
index 00000000..0f03ee70
--- /dev/null
+++ b/tests/software/trimgalore/main.nf
@@ -0,0 +1,40 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { TRIMGALORE as TRIMGALORE_SE } from '../../../software/trimgalore/main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
+include { TRIMGALORE as TRIMGALORE_PE } from '../../../software/trimgalore/main.nf'  addParams( options: [ publish_dir:'test_paired_end' ] )
+
+/*
+ * Test with single-end data
+ */
+workflow test_trimgalore_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
+
+    TRIMGALORE_SE ( input )
+}
+
+// workflow test_trimgalore_single_end {
+
+//     def input = []
+//     input = [ [ id:'test', single_end:false ], // meta map
+//               [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
+
+//     TRIMGALORE_SE ( input )
+// }
+
+/*
+ * Test with paired-end data
+ */
+workflow test_trimgalore_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
+
+    TRIMGALORE_PE ( input )
+}
diff --git a/tests/software/trimgalore/test.yml b/tests/software/trimgalore/test.yml
new file mode 100644
index 00000000..9ba4dddf
--- /dev/null
+++ b/tests/software/trimgalore/test.yml
@@ -0,0 +1,21 @@
+- name: Run trimgalore single-end test workflow
+  command: nextflow run ./tests/software/trimgalore/ -profile docker -entry test_trimgalore_single_end -c tests/config/nextflow.config
+  tags:
+    - trimgalore
+  files:
+    # These can't be md5'd reliably
+    # TODO Test for includes
+    - path: output/test_single_end/test.fastq.gz_trimming_report.txt
+    - path: output/test_single_end/test_trimmed.fq.gz
+
+- name: Run trimgalore paired-end test workflow
+  command: nextflow run ./tests/software/trimgalore/ -profile docker -entry test_trimgalore_paired_end -c tests/config/nextflow.config
+  tags:
+    - trimgalore
+  files:
+    # These can't be md5'd reliably
+    # TODO Test for includes
+    - path: output/test_paired_end/test_1.fastq.gz_trimming_report.txt
+    - path: output/test_paired_end/test_1_val_1.fq.gz
+    - path: output/test_paired_end/test_2.fastq.gz_trimming_report.txt
+    - path: output/test_paired_end/test_2_val_2.fq.gz