diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
new file mode 100644
index 0000000..cbc909c
--- /dev/null
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,6 @@
+FOR CONTRIBUTOR:
+* [ ] - I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo.
+* [ ] - License permits unrestricted use (educational + commercial)
+* [ ] - This PR adds a new tool or tool collection
+* [ ] - This PR updates an existing tool or tool collection
+* [ ] - This PR does something else (explain below)
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
new file mode 100644
index 0000000..ff17786
--- /dev/null
+++ b/.github/workflows/pr.yaml
@@ -0,0 +1,437 @@
+name: Galaxy Tool Linting and Tests for push and PR
+on: [push, pull_request]
+env:
+  GALAXY_REPO: https://github.com/galaxyproject/galaxy
+  GALAXY_RELEASE: release_21.05
+  MAX_CHUNKS: 4
+jobs:
+  # the setup job does two things:
+  # 1. cache the pip cache and .planemo
+  # 2. determine the list of changed repositories
+  # it produces one artifact which contains
+  # - a file with the latest SHA from the chosen branch of the Galaxy repo
+  # - a file containing the list of changed repositories
+  # which are needed in subsequent steps.
+  setup:
+    name: Setup cache and determine changed repositories
+    runs-on: ubuntu-latest
+    outputs:
+      galaxy_head_sha: ${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }}
+      commit_range: ${{ steps.get-commit-range.outputs.commit_range }}
+      nchunks: ${{ steps.get-chunks.outputs.nchunks }}
+      chunk_list: ${{ steps.get-chunks.outputs.chunk_list }}
+    strategy:
+      matrix:
+        python-version: [3.7]
+    steps:
+    - name: Print github context properties
+      run: |
+        echo 'event: ${{ github.event_name }}'
+        echo 'sha: ${{ github.sha }}'
+        echo 'ref: ${{ github.ref }}'
+        echo 'head_ref: ${{ github.head_ref }}'
+        echo 'base_ref: ${{ github.base_ref }}'
+        echo 'event.before: ${{ github.event.before }}'
+        echo 'event.after: ${{ github.event.after }}'
+    - name: Determine latest commit in the Galaxy repo
+      id: get-galaxy-sha
+      run: echo "::set-output name=galaxy_head_sha::$(git ls-remote ${{ env.GALAXY_REPO }} refs/heads/${{ env.GALAXY_RELEASE }} | cut -f1)"
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }}
+    - name: Cache .planemo
+      uses: actions/cache@v2
+      id: cache-planemo
+      with:
+        path: ~/.planemo
+        key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }}
+    # Install the `wheel` package so that when installing other packages which
+    # are not available as wheels, pip will build a wheel for them, which can be cached.
+    - name: Install wheel
+      run: pip install wheel
+    - name: Install Planemo and flake8
+      run: pip install planemo flake8 flake8-import-order
+    - name: Fake a Planemo run to update cache
+      if: steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true'
+      run: |
+        touch tool.xml
+        PIP_QUIET=1 planemo test --galaxy_python_version ${{ matrix.python-version }} --no_conda_auto_init --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    # The range of commits to check for changes is:
+    # - `origin/master...` for all events happening on a feature branch
+    # - for events on the master branch we compare against the sha before the event
+    #   (note that this does not work for feature branch events since we want all
+    #   commits on the feature branch and not just the commits of the last event)
+    # - for pull requests we compare against the 1st ancestor, given the current
+    #   HEAD is the merge between the PR branch and the base branch
+    - name: Set commit range (push to the feature branch)
+      if: github.ref != 'refs/heads/master' && github.event_name == 'push'
+      run: |
+        git fetch origin master
+        echo "COMMIT_RANGE=origin/master..." >> $GITHUB_ENV
+    - name: Set commit range (push to the master branch, e.g. merge)
+      if: github.ref == 'refs/heads/master' && github.event_name == 'push'
+      run: echo "COMMIT_RANGE=${{ github.event.before }}.." >> $GITHUB_ENV
+    - name: Set commit range (pull request)
+      if: github.event_name == 'pull_request'
+      run: echo "COMMIT_RANGE=HEAD~.." >> $GITHUB_ENV
+    - id: get-commit-range
+      run: echo "::set-output name=commit_range::$COMMIT_RANGE"
+    - name: Planemo ci_find_repos for the commit range
+      run: planemo ci_find_repos --changed_in_commit_range $COMMIT_RANGE --exclude packages --exclude deprecated --exclude_from .tt_skip --output repository_list.txt
+    - name: Show repository list
+      run: cat repository_list.txt
+    - uses: actions/upload-artifact@v2
+      with:
+        name: Workflow artifacts
+        path: repository_list.txt
+    - name: Planemo ci_find_tools for the repository list
+      run: |
+        touch tool_list.txt
+        if [ -s repository_list.txt ]; then
+            planemo ci_find_tools --output tool_list.txt $(cat repository_list.txt)
+        fi
+    - name: Show tool list
+      run: cat tool_list.txt
+    - name: Compute chunks
+      id: get-chunks
+      run: |
+        nchunks=$(wc -l < tool_list.txt)
+        if [ "$nchunks" -gt "$MAX_CHUNKS" ]; then
+            nchunks=$MAX_CHUNKS
+        elif [ "$nchunks" -eq 0 ]; then
+            nchunks=1
+        fi
+        echo "::set-output name=nchunks::$nchunks"
+        echo "::set-output name=chunk_list::[$(seq -s ", " 0 $(($nchunks - 1)))]"
+    - name: Show chunks
+      run: |
+        echo 'Using ${{ steps.get-chunks.outputs.nchunks }} chunks (${{ steps.get-chunks.outputs.chunk_list }})'
+
+  # Planemo lint the changed repositories
+  lint:
+    name: Lint tools
+    needs: setup
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.7]
+    steps:
+    # checkout the repository
+    # and use it as the current working directory
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - uses: actions/download-artifact@v2
+      with:
+        name: Workflow artifacts
+        path: ../workflow_artifacts/
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Planemo lint
+      run: |
+        set -e
+        while read -r DIR; do
+            planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR";
+        done < ../workflow_artifacts/repository_list.txt
+    - name: Planemo ci_find_tools for the commit range
+      run: planemo ci_find_tools --changed_in_commit_range ${{ needs.setup.outputs.commit_range }} --exclude packages --exclude deprecated --exclude_from .tt_skip --output tool_list.txt
+    - name: Check if each changed tool is in the list of changed repositories
+      run: |
+        set -e
+        while read -r TOOL; do
+            # Check if any changed repo dir is a substring of $TOOL
+            if ! echo $TOOL | grep -qf ../workflow_artifacts/repository_list.txt; then
+                echo "Tool $TOOL not in changed repositories list: .shed.yml file missing" >&2
+                exit 1
+            fi
+        done < tool_list.txt
+
+  # flake8 of Python scripts in the changed repositories
+  flake8:
+    name: Lint Python scripts
+    needs: setup
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.7]
+    steps:
+    # checkout the repository to master
+    # and use it as the current working directory
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - uses: actions/download-artifact@v2
+      with:
+        name: Workflow artifacts
+        path: ../workflow_artifacts/
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
+    - name: Install flake8
+      run: pip install flake8 flake8-import-order
+    - name: Flake8
+      run: |
+        if [ -s ../workflow_artifacts/repository_list.txt ]; then
+            flake8 $(cat ../workflow_artifacts/repository_list.txt)
+        fi
+
+  lintr:
+    name: Lint R scripts
+    needs: setup
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        r-version: [4.0.1]
+    steps:
+    # checkout the repository to master
+    # and use it as the current working directory
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - uses: actions/download-artifact@v2
+      with:
+        name: Workflow artifacts
+        path: ../workflow_artifacts/
+    - uses: r-lib/actions/setup-r@master
+      with:
+        r-version: ${{ matrix.r-version }}
+    - name: Cache R packages
+      uses: actions/cache@v2
+      with:
+        path: ${{ env.R_LIBS_USER }}
+        key: r_cache_${{ matrix.r-version }}
+    - name: Install non-R lintr dependencies
+      run: sudo apt-get install libcurl4-openssl-dev
+    - name: Install lintr
+      run: |
+        install.packages('remotes')
+        remotes::install_cran("lintr")
+      shell: Rscript {0}
+    - name: lintr
+      run: |
+        library(lintr)
+        linters <- with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL,
+          object_name_linter = NULL, object_usage_linter=NULL)
+        con <- file("../workflow_artifacts/repository_list.txt", "r")
+        status <- 0
+        while (TRUE) {
+          repo <- readLines(con, n = 1)
+          if (length(repo) == 0) {
+             break
+          }
+          lnt <- lint_dir(repo, relative_path=T, linters=linters)
+          if (length(lnt) > 0) {
+            status <- 1
+            for (l in lnt) {
+              rel_path <- paste(repo, l$filename, sep="/")
+              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message), stderr())
+            }
+          }
+        }
+        quit(status = status)
+      shell: Rscript {0}
+
+  # Planemo test the changed repositories, each chunk creates an artifact
+  # containing HTML and JSON reports for the executed tests
+  test:
+    name: Test tools
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    needs: setup
+    strategy:
+      fail-fast: false
+      matrix:
+        chunk: ${{ fromJson(needs.setup.outputs.chunk_list) }}
+        python-version: [3.7]
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+    # checkout the repository
+    # and use it as the current working directory
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - uses: actions/download-artifact@v2
+      with:
+        name: Workflow artifacts
+        path: ../workflow_artifacts/
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
+    - name: Cache .planemo
+      uses: actions/cache@v2
+      id: cache-planemo
+      with:
+        path: ~/.planemo
+        key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Planemo ci_find_tools for the repository list, chunked
+      run: |
+        touch tool_list_chunk.txt
+        if [ -s ../workflow_artifacts/repository_list.txt ]; then
+          planemo ci_find_tools --chunk_count ${{ needs.setup.outputs.nchunks }} --chunk ${{ matrix.chunk }} --group_tools --output tool_list_chunk.txt $(cat ../workflow_artifacts/repository_list.txt)
+        fi
+    - name: Show tool list chunk
+      run: cat tool_list_chunk.txt
+    - name: Planemo test tools
+      run: |
+        mkdir json_output
+        while read -r TOOL_GROUP; do
+            # Check if any of the lines in .tt_biocontainer_skip is a substring of $TOOL_GROUP
+            if echo $TOOL_GROUP | grep -qf .tt_biocontainer_skip; then
+                PLANEMO_OPTIONS=""
+            else
+                PLANEMO_OPTIONS="--biocontainers --no_dependency_resolution --no_conda_auto_init"
+            fi
+            json=$(mktemp -u -p json_output --suff .json)
+            PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE --galaxy_python_version ${{ matrix.python-version }} --test_output_json "$json" $TOOL_GROUP || true
+            docker system prune --all --force --volumes || true
+        done < tool_list_chunk.txt
+        if [ ! -s tool_list_chunk.txt ]; then
+            echo '{"tests":[]}' > "$(mktemp -u -p json_output --suff .json)"
+        fi
+    - name: Merge tool_test_output.json files
+      run: planemo merge_test_reports json_output/*.json tool_test_output.json
+    - name: Create tool_test_output.html
+      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
+    - name: Copy artifacts into place
+      run: |
+        mkdir upload
+        mv tool_test_output.json tool_test_output.html upload/
+    - uses: actions/upload-artifact@v2
+      with:
+        name: 'Tool test output ${{ matrix.chunk }}'
+        path: upload
+
+  # - combine the results of the test chunks (which will never fail due
+  #   to `|| true`) and create a global test report as json and html which
+  #   is provided as artifact
+  # - check if any tool test actually failed (by lookup in the combined json)
+  #   and fail this step if this is the case
+  combine_outputs:
+    name: Combine chunked test results
+    needs: [setup, test]
+    strategy:
+      matrix:
+        python-version: [3.7]
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v2
+      with:
+        path: artifacts
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Install jq
+      run: sudo apt-get install jq
+    - name: Combine outputs
+      run: find artifacts/ -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
+    - name: Create tool_test_output.html
+      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
+    - name: Copy artifacts into place
+      run: |
+        mkdir upload
+        mv tool_test_output.json tool_test_output.html upload/
+    - uses: actions/upload-artifact@v2
+      with:
+        name: 'All tool test results'
+        path: upload
+    - name: Check status of combined outputs
+      run: |
+        if jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | grep -v "success"; then
+            echo "Unsuccessful tests found, inspect the 'All tool test results' artifact for details."
+            exit 1
+        fi
+
+  # deploy the tools to the toolsheds (first TTS for testing)
+  deploy:
+    name: Deploy
+    needs: [setup, lint, flake8, lintr, combine_outputs]
+    strategy:
+      matrix:
+        python-version: [3.7]
+    runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/master' && github.repository_owner == 'abims-sbr'
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - uses: actions/download-artifact@v2
+      with:
+        name: Workflow artifacts
+        path: ../workflow_artifacts/
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Deploy on testtoolshed
+      env:
+        SHED_KEY: ${{ secrets.TTS_API_KEY }}
+      run: |
+        while read -r DIR; do
+            planemo shed_update --shed_target testtoolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
+        done < ../workflow_artifacts/repository_list.txt
+      continue-on-error: true
+    - name: Deploy on toolshed
+      env:
+        SHED_KEY: ${{ secrets.TS_API_KEY }}
+      run: |
+        while read -r DIR; do
+            planemo shed_update --shed_target toolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
+        done < ../workflow_artifacts/repository_list.txt
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index ccf408b..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-# This is a special configuration file to run tests on Travis-CI via
-# GitHub notifications when changes are committed.
-#
-# See http://travis-ci.org/ for details
-language: python
-
-before_install:
- - sudo apt-get install -y python-virtualenv
- - virtualenv planemo-venv
- - . planemo-venv/bin/activate
- - pip install planemo
-
-script:
- - travis_wait 20
- - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/01_Filter_Assemblies > /dev/null 2>&1
- - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/02_Pairwise > /dev/null 2>&1
- - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/03_POGs  
- - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/03b_Orthogroups_Tool > /dev/null 2>&1
- - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/04_BlastAlign > /dev/null 2>&1
- - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/05_CDS_search
- - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/06_ConcatPhyl
- - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/07_MutCount
diff --git a/.tt_skip b/.tt_skip
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/.tt_skip
@@ -0,0 +1 @@
+