Merge pull request #85 from nf-core/pytest-workflow-refactor

Refactor all tests to use pytest-workflow

.github/workflows/bwa_index.yml

@@ -1,30 +1,36 @@
 name: bwa_index
 on:
-  push:
+    push:
-    paths:
+        paths:
-      - software/bwa/index/**
+            - software/bwa/index/**
-      - .github/workflows/bwa_index.yml
+            - .github/workflows/bwa_index.yml
-      - tests
+            - tests/software/bwa/**
-  pull_request:
+    pull_request:
-    paths:
+        paths:
-      - software/bwa/index/**
+            - software/bwa/index/**
-      - .github/workflows/bwa_index.yml
+            - .github/workflows/bwa_index.yml
-      - tests
+            - tests/software/bwa/**
 
 jobs:
-  ci_test:
+    ci_test:
-    runs-on: ubuntu-latest
+        runs-on: ubuntu-latest
-    env:
+        env:
-      NXF_ANSI_LOG: false
+            NXF_ANSI_LOG: false
-    steps:
+        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
+            - name: Set up Python
-      run: |
+              uses: actions/setup-python@v2
-        export NXF_VER="20.07.1"
+              with:
-        wget -qO- get.nextflow.io | bash
+                  python-version: "3.x"
-        sudo mv nextflow /usr/local/bin/
+            - name: Install dependencies
+              run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
+            # Test the module
-    - run: nextflow run ./software/bwa/index/test/ -profile docker
+            - run: pytest --tag bwa_index --symlink --wt 2

.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
+      - name: Set up Python
-      run: |
+        uses: actions/setup-python@v2
-        export NXF_VER="20.07.1"
+        with:
-        wget -qO- get.nextflow.io | bash
+          python-version: "3.x"
-        sudo mv nextflow /usr/local/bin/
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
+      # Test the module
-    - run: nextflow run ./software/bwa/mem/test/ -profile docker
+      - run: pytest --tag bwa_index --symlink --wt 2

.github/workflows/docker.yml

@@ -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;

.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
+      - name: Set up Python
-      run: |
+        uses: actions/setup-python@v2
-        export NXF_VER="20.07.1"
+        with:
-        wget -qO- get.nextflow.io | bash
+          python-version: "3.x"
-        sudo mv nextflow /usr/local/bin/
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    - name: Set up Python
+      # Test the module
-      uses: actions/setup-python@v2
+      - run: pytest --tag fastqc --symlink --wt 2
-      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

.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
+      - name: Set up Python
-      run: |
+        uses: actions/setup-python@v2
-        export NXF_VER="20.07.1"
+        with:
-        wget -qO- get.nextflow.io | bash
+          python-version: "3.x"
-        sudo mv nextflow /usr/local/bin/
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
+      # Test the module
-    - run: nextflow run ./software/picard/collectmultiplemetrics/test/ -profile docker
+      - run: pytest --tag picard_collectmultiplemetrics --symlink --wt 2

.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
+      - name: Set up Python
-      run: |
+        uses: actions/setup-python@v2
-        export NXF_VER="20.07.1"
+        with:
-        wget -qO- get.nextflow.io | bash
+          python-version: "3.x"
-        sudo mv nextflow /usr/local/bin/
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
+      # Test the module
-    - run: nextflow run ./software/picard/markduplicates/test/ -profile docker
+      - run: pytest --tag picard_markduplicates --symlink --wt 2

.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
+      - name: Set up Python
-      run: |
+        uses: actions/setup-python@v2
-        export NXF_VER="20.07.1"
+        with:
-        wget -qO- get.nextflow.io | bash
+          python-version: "3.x"
-        sudo mv nextflow /usr/local/bin/
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
+      # Test the module
-    - run: nextflow run ./software/picard/mergesamfiles/test/ -profile docker
+      - run: pytest --tag picard_mergesamfiles --symlink --wt 2

.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
+      - name: Set up Python
-      run: |
+        uses: actions/setup-python@v2
-        export NXF_VER="20.07.1"
+        with:
-        wget -qO- get.nextflow.io | bash
+          python-version: "3.x"
-        sudo mv nextflow /usr/local/bin/
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
+      # Test the module
-    - run: nextflow run ./software/samtools/flagstat/test/ -profile docker
+      - run: pytest --tag samtools_flagstat --symlink --wt 2

.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
+      - name: Set up Python
-      run: |
+        uses: actions/setup-python@v2
-        export NXF_VER="20.07.1"
+        with:
-        wget -qO- get.nextflow.io | bash
+          python-version: "3.x"
-        sudo mv nextflow /usr/local/bin/
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
+      # Test the module
-    - run: nextflow run ./software/samtools/idxstats/test/ -profile docker
+      - run: pytest --tag samtools_idxstats --symlink --wt 2

.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
+      - name: Set up Python
-      run: |
+        uses: actions/setup-python@v2
-        export NXF_VER="20.07.1"
+        with:
-        wget -qO- get.nextflow.io | bash
+          python-version: "3.x"
-        sudo mv nextflow /usr/local/bin/
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
+      # Test the module
-    - run: nextflow run ./software/samtools/index/test/ -profile docker
+      - run: pytest --tag samtools_index --symlink --wt 2

.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
+      - name: Set up Python
-      run: |
+        uses: actions/setup-python@v2
-        export NXF_VER="20.07.1"
+        with:
-        wget -qO- get.nextflow.io | bash
+          python-version: "3.x"
-        sudo mv nextflow /usr/local/bin/
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
+      # Test the module
-    - run: nextflow run ./software/samtools/sort/test/ -profile docker
+      - run: pytest --tag samtools_sort --symlink --wt 2

.github/workflows/samtools_stats.yml

@@ -3,13 +3,13 @@ on:
   push:
     paths:
       - software/samtools/stats/**
-      - .github/workflows/samtools_stats.yml
+      - .github/workflows/software/samtools_stats.yml
-      - tests
+      - tests/software/samtools/**
   pull_request:
     paths:
       - software/samtools/stats/**
-      - .github/workflows/samtools_stats.yml
+      - .github/workflows/software/samtools_stats.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
+      - name: Set up Python
-      run: |
+        uses: actions/setup-python@v2
-        export NXF_VER="20.07.1"
+        with:
-        wget -qO- get.nextflow.io | bash
+          python-version: "3.x"
-        sudo mv nextflow /usr/local/bin/
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
+      # Test the module
-    - run: nextflow run ./software/samtools/stats/test/ -profile docker
+      - run: pytest --tag samtools_stats --symlink --wt 2

.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
+      - name: Set up Python
-      run: |
+        uses: actions/setup-python@v2
-        export NXF_VER="20.07.1"
+        with:
-        wget -qO- get.nextflow.io | bash
+          python-version: "3.x"
-        sudo mv nextflow /usr/local/bin/
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
+      # Test the module
-    - run: nextflow run ./software/trimgalore/test/ -profile docker
+      - run: pytest --tag trimgalore --symlink --wt 2

software/SOFTWARE/TOOL/test/main.nf

@@ -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()
-}

software/SOFTWARE/TOOL/test/nextflow.config

@@ -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
-    }
-}

software/bwa/index/test/input/NC_010473.fa

@@ -1 +0,0 @@
-../../../../../tests/data/fasta/E_coli/NC_010473.fa

software/bwa/index/test/main.nf

@@ -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()
-}

software/bwa/index/test/nextflow.config

@@ -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
-    }
-}

software/bwa/index/test/output/bwa/NC_010473.fa.amb

@@ -1,3 +0,0 @@
-4686137 1 2
-20895 1 Y
-142347 1 R

software/bwa/index/test/output/bwa/NC_010473.fa.ann

@@ -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

software/bwa/mem/test/input/Ecoli_DNA_R1.fastq.gz

@@ -1 +0,0 @@
-../../../../../tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz

software/bwa/mem/test/input/Ecoli_DNA_R2.fastq.gz

@@ -1 +0,0 @@
-../../../../../tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz

software/bwa/mem/test/input/NC_010473.fa

@@ -1 +0,0 @@
-../../../../../tests/data/fasta/E_coli/NC_010473.fa

software/bwa/mem/test/input/index

@@ -1 +0,0 @@
-../../../../../tests/data/index/E_coli/bwa/

software/bwa/mem/test/main.nf

@@ -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()
-}

software/bwa/mem/test/nextflow.config

@@ -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
-    }
-}

software/picard/collectmultiplemetrics/test/input/NC_010473.fa

@@ -1 +0,0 @@
-../../../../../tests/data/fasta/E_coli/NC_010473.fa

software/picard/collectmultiplemetrics/test/input/test.paired_end.sorted.bam

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam

software/picard/collectmultiplemetrics/test/main.nf

@@ -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()
-}

software/picard/collectmultiplemetrics/test/nextflow.config

@@ -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
-    }
-}

software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.alignment_summary_metrics

@@ -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			
-
-

software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics

@@ -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
-
-

software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_metrics

@@ -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
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-182	31
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-186	24
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-201	26
-202	40
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-396	22
-397	36
-398	28
-404	1
-

software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics

@@ -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
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-50	40
-51	40
-52	40
-53	40
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-57	40
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-60	40
-61	40
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-63	40
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-67	40
-68	40
-69	40
-70	40
-71	40
-72	40
-73	40
-74	40
-75	40
-76	40
-77	40
-78	40
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-80	40
-81	40
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-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
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-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
-

software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution_metrics

@@ -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
-

software/picard/markduplicates/test/input/test.paired_end.sorted.bam

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam

software/picard/markduplicates/test/main.nf

@@ -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()
-}

software/picard/markduplicates/test/nextflow.config

@@ -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
-    }
-}

software/picard/markduplicates/test/output/picard/test.MarkDuplicates.metrics.txt

@@ -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
-

software/picard/mergesamfiles/test/input/test.paired_end.COPY.sorted.bam

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam

software/picard/mergesamfiles/test/input/test.paired_end.sorted.bam

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam

software/picard/mergesamfiles/test/main.nf

@@ -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()
-}

software/picard/mergesamfiles/test/nextflow.config

@@ -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
-    }
-}

software/samtools/flagstat/test/input/test.paired_end.sorted.bam

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam

software/samtools/flagstat/test/input/test.paired_end.sorted.bam.bai

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam.bai

software/samtools/flagstat/test/main.nf

@@ -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()
-}

software/samtools/flagstat/test/nextflow.config

@@ -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
-    }
-}

software/samtools/flagstat/test/output/samtools/test.paired_end.sorted.bam.flagstat

@@ -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)

software/samtools/idxstats/test/input/test.paired_end.sorted.bam

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam

software/samtools/idxstats/test/input/test.paired_end.sorted.bam.bai

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam.bai

software/samtools/idxstats/test/main.nf

@@ -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()
-}

software/samtools/idxstats/test/nextflow.config

@@ -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
-    }
-}

software/samtools/idxstats/test/output/samtools/test.paired_end.sorted.bam.idxstats

@@ -1,2 +0,0 @@
-gi|170079663|ref|NC_010473.1|	4686137	20000	0
-*	0	0	0

software/samtools/index/test/input/test.paired_end.sorted.bam

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam

software/samtools/index/test/main.nf

@@ -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()
-}

software/samtools/index/test/nextflow.config

@@ -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
-    }
-}

software/samtools/sort/test/input/test.paired_end.name.sorted.bam

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.name.sorted.bam

software/samtools/sort/test/main.nf

@@ -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()
-}

software/samtools/sort/test/nextflow.config

@@ -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
-    }
-}

software/samtools/stats/test/input/test.paired_end.sorted.bam

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam

software/samtools/stats/test/input/test.paired_end.sorted.bam.bai

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam.bai

software/samtools/stats/test/main.nf

@@ -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()
-}

software/samtools/stats/test/nextflow.config

@@ -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
-    }
-}

software/trimgalore/test/input/test_R1.fastq.gz

@@ -1 +0,0 @@
-../../../../tests/data/fastq/rna/test_R1.fastq.gz

software/trimgalore/test/input/test_R2.fastq.gz

@@ -1 +0,0 @@
-../../../../tests/data/fastq/rna/test_R2.fastq.gz

software/trimgalore/test/input/test_single_end.fastq.gz

@@ -1 +0,0 @@
-../../../../tests/data/fastq/rna/test_single_end.fastq.gz

software/trimgalore/test/main.nf

@@ -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()
-}

software/trimgalore/test/nextflow.config

@@ -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
-    }
-}

software/trimgalore/test/output/test_paired_end/test_1.fastq.gz_trimming_report.txt

@@ -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
-

software/trimgalore/test/output/test_paired_end/test_2.fastq.gz_trimming_report.txt

@@ -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%)

software/trimgalore/test/output/test_single_end/test.fastq.gz_trimming_report.txt

@@ -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%)
-

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)
+    )
+}

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

tests/software/fastqc/main.nf

@@ -29,3 +29,5 @@ workflow test_paired_end {
 
     FASTQC_PE ( input )
 }
+
+// TODO Test e2e

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

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 )
+}

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

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 )
+}

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

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 )
+}

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