Merge pull request #138 from nf-core/pytest-profiles

Pytest profiles

.github/filters.yml

@@ -1,10 +1,19 @@
+bowtie2_align:
+  - software/bowtie2/align/**
+  - software/bowtie2/build/**
+  - tests/software/bowtie2/**
+
+bowtie2_build:
+  - software/bowtie2/build/**
+  - tests/software/bowtie2/**
+
 bowtie_align:
   - software/bowtie/align/**
-  - software/bowtie/index/**
+  - software/bowtie/build/**
   - tests/software/bowtie/**
 
-bowtie_index:
-  - software/bowtie/index/**
+bowtie_build:
+  - software/bowtie/build/**
   - tests/software/bowtie/**
 
 bwa_index:
@@ -15,6 +24,22 @@ bwa_mem:
   - software/bwa/mem/**
   - tests/software/bwa/**
 
+cutadapt:
+  - software/cutadapt/**
+  - tests/software/cutadapt/**
+
+dsh_filterbed:
+  - software/dsh/filterbed/**
+  - tests/software/dsh/**
+
+dsh_splitbed:
+  - software/dsh/splitbed/**
+  - tests/software/dsh/**
+
+fastp:
+  - software/fastp/**
+  - tests/software/fastp/**
+
 fastqc:
   - software/fastqc/**
   - tests/software/fastqc/**
@@ -27,6 +52,10 @@ multiqc:
   - software/multiqc/**
   - tests/software/multiqc/**
 
+pangolin:
+  - software/pangolin/**
+  - tests/software/pangolin/**
+
 picard_collectmultiplemetrics:
   - software/picard/collectmultiplemetrics/**
   - tests/software/picard/**
@@ -43,6 +72,18 @@ preseq_lcextrap:
   - software/preseq/lcextrap/**
   - tests/software/preseq/**
 
+quast:
+  - software/quast/**
+  - tests/software/quast/**
+
+salmon_index:
+  - software/salmon/index/**
+  - tests/software/salmon/**
+
+salmon_quant:
+  - software/salmon/quant/**
+  - tests/software/salmon/**
+
 samtools_flagstat:
   - software/samtools/flagstat/**
   - tests/software/samtools/**
@@ -55,6 +96,10 @@ samtools_index:
   - software/samtools/index/**
   - tests/software/samtools/**
 
+samtools_mpileup:
+  - software/samtools/mpileup/**
+  - tests/software/samtools/**
+
 samtools_sort:
   - software/samtools/sort/**
   - tests/software/samtools/**
@@ -63,6 +108,23 @@ samtools_stats:
   - software/samtools/stats/**
   - tests/software/samtools/**
 
+samtools_view:
+  - software/samtools/view/**
+  - tests/software/samtools/**
+
+seacr_callpeak:
+  - software/seacr/callpeak/**
+  - tests/software/seacr/**
+
+star_align:
+  - software/star/align/**
+  - tests/software/star/**
+
+star_genomegenerate:
+  - software/star/genomegenerate/**
+  - tests/software/star/**
+
+
 stringtie:
       - software/stringtie/**
       - tests/software/stringtie/**

.github/workflows/bowtie2_align.yml

@@ -1,42 +0,0 @@
-name: bowtie2_align
-on:
-    push:
-        paths:
-            - software/bowtie2/align/**
-            - software/bowtie2/build/**
-            - .github/workflows/bowtie2_align.yml
-            - tests/software/bowtie2/**
-    pull_request:
-        paths:
-            - software/bowtie2/align/**
-            - software/bowtie2/build/**
-            - .github/workflows/bowtie2_align.yml
-            - tests/software/bowtie2/**
-
-jobs:
-    ci_test:
-        runs-on: ubuntu-latest
-        strategy:
-            matrix:
-                nxf_version: [20.11.0-edge]
-        env:
-            NXF_ANSI_LOG: false
-        steps:
-            - 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: 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 bowtie2_align --symlink --wt 2

.github/workflows/bowtie2_build.yml

@@ -1,40 +0,0 @@
-name: bowtie2_build
-on:
-  push:
-    paths:
-      - software/bowtie2/build/**
-      - .github/workflows/bowtie2_build.yml
-      - tests/software/bowtie2/**
-  pull_request:
-    paths:
-      - software/bowtie2/build/**
-      - .github/workflows/bowtie2_build.yml
-      - tests/software/bowtie2/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 bowtie2_build --symlink --wt 2

.github/workflows/bowtie_build.yml

@@ -1,40 +0,0 @@
-name: bowtie_build
-on:
-  push:
-    paths:
-      - software/bowtie/build/**
-      - .github/workflows/bowtie_build.yml
-      - tests/software/bowtie/**
-  pull_request:
-    paths:
-      - software/bowtie/build/**
-      - .github/workflows/bowtie_build.yml
-      - tests/software/bowtie/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 bowtie_build --symlink --wt 2

.github/workflows/cutadapt.yml

@@ -1,40 +0,0 @@
-name: cutadapt
-on:
-  push:
-    paths:
-      - software/cutadapt/**
-      - .github/workflows/cutadapt.yml
-      - tests/software/cutadapt/**
-  pull_request:
-    paths:
-      - software/cutadapt/**
-      - .github/workflows/cutadapt.yml
-      - tests/software/cutadapt/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 cutadapt --symlink --wt 2

.github/workflows/dsh_filterbed.yml

@@ -1,40 +0,0 @@
-name: dsh_filterbed
-on:
-  push:
-    paths:
-      - software/dsh/filterbed/**
-      - .github/workflows/dsh_filterbed.yml
-      - tests/software/dsh/**
-  pull_request:
-    paths:
-      - software/dsh/filterbed/**
-      - .github/workflows/dsh_filterbed.yml
-      - tests/software/dsh/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 dsh_filterbed --symlink --wt 2

.github/workflows/dsh_splitbed.yml

@@ -1,40 +0,0 @@
-name: dsh_splitbed
-on:
-  push:
-    paths:
-      - software/dsh/splitbed/**
-      - .github/workflows/dsh_splitbed.yml
-      - tests/software/dsh/**
-  pull_request:
-    paths:
-      - software/dsh/splitbed/**
-      - .github/workflows/dsh_splitbed.yml
-      - tests/software/dsh/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 dsh_splitbed --symlink --wt 2

.github/workflows/fastp.yml

@@ -1,40 +0,0 @@
-name: fastp
-on:
-  push:
-    paths:
-      - software/fastp/**
-      - .github/workflows/fastp.yml
-      - tests
-  pull_request:
-    paths:
-      - software/fastp/**
-      - .github/workflows/fastp.yml
-      - tests
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 fastp --symlink --wt 2

.github/workflows/pangolin.yml

@@ -1,40 +0,0 @@
-name: pangolin
-on:
-  push:
-    paths:
-      - software/pangolin/**
-      - .github/workflows/pangolin.yml
-      - tests
-  pull_request:
-    paths:
-      - software/pangolin/**
-      - .github/workflows/pangolin.yml
-      - tests
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 pangolin --symlink --wt 2

.github/workflows/pytest-workflow.yml

@@ -16,14 +16,16 @@ jobs:
           filters: '.github/filters.yml'
 
   test:
-    runs-on: ubuntu-latest
-    name: CI Test
+    runs-on: ubuntu-20.04
+    name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
     needs: changes
     if: needs.changes.outputs.modules != '[]'
     strategy:
+      fail-fast: false
       matrix:
         nxf_version: ['20.11.0-edge']
         tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
+        profile: ['docker', 'singularity', 'conda']
     env:
       NXF_ANSI_LOG: false
     steps:
@@ -59,15 +61,29 @@ jobs:
       - name: Install dependencies
         run: python -m pip install --upgrade pip pytest-workflow
 
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.5.3
+
+      - name: Setup miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: defaults, bioconda, conda-forge
+          python-version: ${{ matrix.python-version }}
+
       # Test the module
       - name: Run pytest-workflow
-        run: pytest --tag ${{ matrix.tags }} --symlink --wt 2
+        run: PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --wt 2 --kwdof
 
       - name: Upload logs on failure
-        if: ${{ failure() }}
+        if: failure()
         uses: actions/upload-artifact@v2
         with:
-          name: logs
+          name: logs-${{ matrix.tags }}-${{ matrix.profile }}-${{ matrix.nxf_version }}
           path: |
             /tmp/pytest_workflow_*/*/.nextflow.log
             /tmp/pytest_workflow_*/*/log.out

.github/workflows/quast.yml

@@ -1,40 +0,0 @@
-name: quast
-on:
-  push:
-    paths:
-      - software/quast/**
-      - .github/workflows/quast.yml
-      - tests
-  pull_request:
-    paths:
-      - software/pquast/**
-      - .github/workflows/quest.yml
-      - tests
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 quast --symlink --wt 2

.github/workflows/salmon_index.yml

@@ -1,40 +0,0 @@
-name: salmon_index
-on:
-  push:
-    paths:
-      - software/salmon/index/**
-      - .github/workflows/salmon_index.yml
-      - tests/software/salmon/**
-  pull_request:
-    paths:
-      - software/salmon/index/**
-      - .github/workflows/salmon_index.yml
-      - tests/software/salmon/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 salmon_index --symlink --wt 2

.github/workflows/salmon_quant.yml

@@ -1,40 +0,0 @@
-name: salmon_quant
-on:
-  push:
-    paths:
-      - software/salmon/quant/**
-      - .github/workflows/salmon_quant.yml
-      - tests/software/salmon/**
-  pull_request:
-    paths:
-      - software/salmon/quant/**
-      - .github/workflows/salmon_quant.yml
-      - tests/software/salmon/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 salmon_quant --symlink --wt 2

.github/workflows/samtools_mpileup.yml

@@ -1,40 +0,0 @@
-name: samtools_mpileup
-on:
-  push:
-    paths:
-      - software/samtools/mpileup/**
-      - .github/workflows/samtools_mpileup.yml
-      - tests/software/samtools/**
-  pull_request:
-    paths:
-      - software/samtools/mpileup/**
-      - .github/workflows/samtools_mpileup.yml
-      - tests/software/samtools/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 samtools_mpileup --symlink --wt 2

.github/workflows/samtools_view.yml

@@ -1,40 +0,0 @@
-name: samtools_view
-on:
-  push:
-    paths:
-      - software/samtools/view/**
-      - .github/workflows/samtools_view.yml
-      - tests/software/samtools/**
-  pull_request:
-    paths:
-      - software/samtools/view/**
-      - .github/workflows/samtools_view.yml
-      - tests/software/samtools/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 samtools_view --symlink --wt 2

.github/workflows/seacr_callpeak.yml

@@ -1,40 +0,0 @@
-name: seacr_callpeak
-on:
-  push:
-    paths:
-      - software/seacr/callpeak/**
-      - .github/workflows/seacr_callpeak.yml
-      - tests/software/seacr/**
-  pull_request:
-    paths:
-      - software/seacr/callpeak/**
-      - .github/workflows/seacr_callpeak.yml
-      - tests/software/seacr/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 seacr_callpeak --symlink --wt 2

.github/workflows/star_align.yml

@@ -1,40 +0,0 @@
-name: star_genomegenerate
-on:
-  push:
-    paths:
-      - software/star/align/**
-      - .github/workflows/star_align.yml
-      - tests/software/star/**
-  pull_request:
-    paths:
-      - software/star/align/**
-      - .github/workflows/star_align.yml
-      - tests/software/star/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 star_align --symlink --wt 2

.github/workflows/star_genomegenerate.yml

@@ -1,40 +0,0 @@
-name: star_genomegenerate
-on:
-  push:
-    paths:
-      - software/star/genomegenerate/**
-      - .github/workflows/star_genomegenerate.yml
-      - tests/software/star/**
-  pull_request:
-    paths:
-      - software/star/genomegenerate/**
-      - .github/workflows/star_genomegenerate.yml
-      - tests/software/star/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.11.0-edge]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - 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: 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 star_genomegenerate --symlink --wt 2

tests/config/nextflow.config

@@ -1,20 +1,17 @@
-
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
     enable_conda = false
+    singularity_pull_docker_container = true
 }
 
-profiles {
-    conda  {
-        params.enable_conda = true
-    }
-    docker {
-        docker.enabled = true
-        docker.runOptions = '-u \$(id -u):\$(id -g)'
-    }
-    singularity {
+if ("$PROFILE" == "singularity") {
     singularity.enabled = true
     singularity.autoMounts = true
-    }
+    singularity.runOptions = '-B /tmp/'
+} else if ("$PROFILE" == "conda") {
+    params.enable_conda = true
+} else {
+    docker.enabled = true
+    docker.runOptions = '-u \$(id -u):\$(id -g)'
 }

tests/software/bowtie/test.yml

@@ -1,5 +1,5 @@
 - name: Run bowtie build
-  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_build -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie -entry test_bowtie_build -c tests/config/nextflow.config
   tags:
     - bowtie
     - bowtie_build
@@ -18,7 +18,7 @@
       md5sum: f3c398bba5158f4039334a932d79c051
 
 - name: Run bowtie build and align single-end
-  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
   tags:
     - bowtie
     - bowtie_align
@@ -41,7 +41,7 @@
       md5sum: 9feed8a55d4b5e600dcc577768ef07fc
 
 - name: Run bowtie index and align paired-end
-  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
   tags:
     - bowtie
     - bowtie_align

tests/software/bowtie2/test.yml

@@ -1,5 +1,5 @@
 - name: Run bowtie2 build
-  command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_build -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_build -c tests/config/nextflow.config
   tags:
     - bowtie2
     - bowtie2_build
@@ -18,7 +18,7 @@
       md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
 
 - name: Run bowtie2 index and align single-end
-  command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_alignment_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_alignment_single_end -c tests/config/nextflow.config
   tags:
     - bowtie2
     - bowtie2_align
@@ -41,7 +41,7 @@
       md5sum: 906102f401d8234b6473790988fb09cf
 
 - name: Run bowtie2 index and align paired-end
-  command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_alignment_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_alignment_paired_end -c tests/config/nextflow.config
   tags:
     - bowtie2
     - bowtie2_align

tests/software/bwa/test.yml

@@ -1,5 +1,5 @@
 - name: Run bwa index
-  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_index -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bwa -entry test_bwa_index -c tests/config/nextflow.config
   tags:
     - bwa
     - bwa_index
@@ -14,7 +14,7 @@
       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
+  command: nextflow run ./tests/software/bwa -entry test_bwa_mem_single_end -c tests/config/nextflow.config
   tags:
     - bwa
     - bwa_mem
@@ -23,7 +23,7 @@
       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
+  command: nextflow run ./tests/software/bwa -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
   tags:
     - bwa
     - bwa_mem

tests/software/cutadapt/test.yml

@@ -1,5 +1,5 @@
 - name: Run cutadapt single-end test workflow
-  command: nextflow run ./tests/software/cutadapt -profile docker -entry test_cutadapt_se -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_se -c tests/config/nextflow.config
   tags:
     - cutadapt
     - cutadapt_se
@@ -8,7 +8,7 @@
     - path: ./output/cutadapt/test.trim.fastq.gz
 
 - name: Run cutadapt paired-end test workflow
-  command: nextflow run ./tests/software/cutadapt -profile docker -entry test_cutadapt_pe -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_pe -c tests/config/nextflow.config
   tags:
     - cutadapt
     - cutadapt_pe

tests/software/dsh/test.yml

@@ -1,5 +1,5 @@
 - name: Run dsh filterbed
-  command: nextflow run ./tests/software/dsh -profile docker -entry test_dsh_filterbed -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/dsh -entry test_dsh_filterbed -c tests/config/nextflow.config
   tags:
     - dsh
     - dsh_filterbed
@@ -8,7 +8,7 @@
       md5sum: 91cee4392d6034793f99f6c53891d866
 
 - name: Run dsh splitbed
-  command: nextflow run ./tests/software/dsh -profile docker -entry test_dsh_splitbed -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/dsh -entry test_dsh_splitbed -c tests/config/nextflow.config
   tags:
     - dsh
     - dsh_splitbed

tests/software/fastp/test.yml

@@ -1,5 +1,5 @@
 - name: fastp_se
-  command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_se -c ./tests/config/nextflow.config
+  command: nextflow run ./tests/software/fastp -entry test_fastp_se -c ./tests/config/nextflow.config
   tags:
     - fastp
     - fastp_se
@@ -12,7 +12,7 @@
     - path: ./output/fastp/test.fastp.html
 
 - name: fastp_pe
-  command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_pe -c ./tests/config/nextflow.config
+  command: nextflow run ./tests/software/fastp -entry test_fastp_pe -c ./tests/config/nextflow.config
   tags:
     - fastp
     - fastp_pe

tests/software/fastqc/test.yml

@@ -1,5 +1,5 @@
 - name: Run fastqc single-end test workflow
-  command: nextflow run ./tests/software/fastqc/ -profile docker -entry test_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/fastqc/ -entry test_single_end -c tests/config/nextflow.config
   tags:
     - fastqc
   files:
@@ -7,7 +7,7 @@
     - path: output/test_single_end/test_fastqc.zip
 
 - name: Run fastqc paired-end test workflow
-  command: nextflow run ./tests/software/fastqc/ -profile docker -entry test_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/fastqc/ -entry test_paired_end -c tests/config/nextflow.config
   tags:
     - fastqc
   files:

tests/software/gffread/test.yml

@@ -1,5 +1,5 @@
 - name: Run gffread  test workflow
-  command: nextflow run ./tests/software/gffread/ -profile docker -entry test_gffread -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/gffread/ -entry test_gffread -c tests/config/nextflow.config
   tags:
     - gffread
   files:

tests/software/multiqc/test.yml

@@ -1,5 +1,5 @@
 - name: Run multiqc test workflow
-  command: nextflow run ./tests/software/multiqc/ -profile docker -entry test_multiqc -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/multiqc/ -entry test_multiqc -c tests/config/nextflow.config
   tags:
     - multiqc
   files:

tests/software/pangolin/test.yml

@@ -1,5 +1,5 @@
 - name: pangolin
-  command: nextflow run ./tests/software/pangolin -profile docker -entry test_pangolin -c ./tests/config/nextflow.config
+  command: nextflow run ./tests/software/pangolin -entry test_pangolin -c ./tests/config/nextflow.config
   tags:
     - pangolin
   files:

tests/software/picard/test.yml

@@ -1,5 +1,5 @@
 - name: Run picard mergesamfiles
-  command: nextflow run ./tests/software/picard -profile docker -entry test_picard_mergesamfiles -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/picard -entry test_picard_mergesamfiles -c tests/config/nextflow.config
   tags:
     - picard
     - picard_mergesamfiles
@@ -8,7 +8,7 @@
       md5sum: a9c8a28d1aac362df5973ba2d9923f86
 
 - name: Run picard collectmultiplemetrics
-  command: nextflow run ./tests/software/picard -profile docker -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/picard -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
   tags:
     - picard
     - picard_collectmultiplemetrics
@@ -25,7 +25,7 @@
     - 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
+  command: nextflow run ./tests/software/picard -entry test_picard_markduplicates -c tests/config/nextflow.config
   tags:
     - picard
     - picard_markduplicates
@@ -35,7 +35,7 @@
       md5sum: 0ed0bfc94069380334ccd595f6d8207c
 
 - 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
+  command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config
   tags:
     - picard
     - picard_markduplicates

tests/software/preseq/test.yml

@@ -1,5 +1,5 @@
 - name: Run preseq single-end lcextrap
-  command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/preseq -entry test_preseq_single_end -c tests/config/nextflow.config
   tags:
     - preseq
     - preseq_lcextrap
@@ -10,7 +10,7 @@
     - path: output/test_preseq_single_end/test.command.log
 
 - name: Run preseq paired-end lcextrap
-  command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/preseq -entry test_preseq_paired_end -c tests/config/nextflow.config
   tags:
     - preseq
     - preseq_lcextrap

tests/software/quast/test.yml

@@ -1,5 +1,5 @@
 - name: quast_ref
-  command: nextflow run ./tests/software/quast -profile docker -entry test_quast_ref -c ./tests/config/nextflow.config
+  command: nextflow run ./tests/software/quast -entry test_quast_ref -c ./tests/config/nextflow.config
   tags:
     - quast
     - quast_reference
@@ -88,7 +88,7 @@
     - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
 
 - name: quast_noref
-  command: nextflow run ./tests/software/quast -profile docker -entry test_quast_noref -c ./tests/config/nextflow.config
+  command: nextflow run ./tests/software/quast -entry test_quast_noref -c ./tests/config/nextflow.config
   tags:
     - quast
     - quast_no_reference

tests/software/salmon/test.yml

@@ -1,5 +1,5 @@
 - name: salmon index
-  command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_index -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/salmon -entry test_salmon_index -c tests/config/nextflow.config
   tags:
     - salmon
     - salmon_index
@@ -31,7 +31,7 @@
       md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
 
 - name: salmon quant paired end
-  command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_quant_pe -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/salmon -entry test_salmon_quant_pe -c tests/config/nextflow.config
   tags:
     - salmon
     - salmon_quant
@@ -85,7 +85,7 @@
       md5sum: 27a76542337df436436e66017f66dd25
 
 - name: salmon quant single-end
-  command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_quant_se -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/salmon -entry test_salmon_quant_se -c tests/config/nextflow.config
   tags:
     - salmon
     - salmon_quant

tests/software/samtools/test.yml

@@ -1,5 +1,5 @@
 - name: Run samtools flagstat test workflow
-  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_flagstat -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_flagstat -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_flagstat
@@ -8,7 +8,7 @@
       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
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_idxstats -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_idxstats
@@ -17,7 +17,7 @@
       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
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_index -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_index
@@ -26,7 +26,7 @@
       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
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_sort -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_sort
@@ -35,7 +35,7 @@
       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
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_stats -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_stats
@@ -44,7 +44,7 @@
       md5sum: 06c183864d6e47ab89b0650cae831a93
 
 - name: Run samtools view test workflow
-  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_view -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_view -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_view
@@ -53,7 +53,7 @@
       md5sum: 7ea2c325e2249ed7ef44e1d9fdc4f8ff
 
 - name: Run samtools mpileup test workflow
-  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_mpileup -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_mpileup -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_mpileup

tests/software/seacr/test.yml

@@ -1,5 +1,5 @@
 - name: Run seacr call peak test workflow
-  command: nextflow run ./tests/software/seacr/ -profile docker -entry test_seacr_callpeak -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/seacr/ -entry test_seacr_callpeak -c tests/config/nextflow.config
   tags:
     - seacr
     - seacr_callpeak

tests/software/star/test.yml

@@ -1,5 +1,5 @@
 - name: Run star genomegenerate
-  command: nextflow run ./tests/software/star -profile docker -entry test_star_genomegenerate -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/star -entry test_star_genomegenerate -c tests/config/nextflow.config
   tags:
     - star
     - star_genomegenerate
@@ -32,7 +32,7 @@
       md5sum: 8fbe69abbbef4f89da3854873984dbac
 
 - name: Run star single-end alignment
-  command: nextflow run ./tests/software/star -profile docker -entry test_star_alignment_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/star -entry test_star_alignment_single_end -c tests/config/nextflow.config
   tags:
     - star
     - star_align
@@ -70,7 +70,7 @@
       md5sum: d41d8cd98f00b204e9800998ecf8427e
 
 - name: Run star paired-end alignment
-  command: nextflow run ./tests/software/star -profile docker -entry test_star_alignment_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/star -entry test_star_alignment_paired_end -c tests/config/nextflow.config
   tags:
     - star
     - star_align

tests/software/stringtie/test.yml

@@ -1,5 +1,5 @@
 - name: Run stringtie forward strand test workflow
-  command: nextflow run ./tests/software/stringtie/ -profile docker -entry test_stringtie_forward -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/stringtie/ -entry test_stringtie_forward -c tests/config/nextflow.config
   tags:
     - stringtie
   files:
@@ -21,7 +21,7 @@
       md5sum: 0106f70121a8b520d98b8739aed92915
 
 - name: Run stringtie reverse strand test workflow
-  command: nextflow run ./tests/software/stringtie/ -profile docker -entry test_stringtie_reverse -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/stringtie/ -entry test_stringtie_reverse -c tests/config/nextflow.config
   tags:
     - stringtie
   files:

tests/software/trimgalore/test.yml

@@ -1,5 +1,5 @@
 - 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
+  command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_single_end -c tests/config/nextflow.config
   tags:
     - trimgalore
   files:
@@ -9,7 +9,7 @@
     - 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
+  command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_paired_end -c tests/config/nextflow.config
   tags:
     - trimgalore
   files:

tests/software/ucsc/test.yml

@@ -1,5 +1,5 @@
 - name: Run bedgraphtobigwig  test workflow
-  command: nextflow run ./tests/software/ucsc/ -profile docker -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/ucsc/ -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
   tags:
     - ucsc_bedgraphtobigwig
   files: