From 23295ac46bc65ea2c2c9381e6f6617bb3161b305 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?=
 <mashehu@users.noreply.github.com>
Date: Thu, 30 Nov 2023 15:25:00 +0100
Subject: [PATCH 001/117] Parallelize pytest (#1)

---
 .github/workflows/create-lint-wf.yml     |  2 +-
 .github/workflows/lint-code.yml          | 10 +--
 .github/workflows/push_dockerhub_dev.yml |  2 +-
 .github/workflows/pytest.yml             | 84 ++++++++++++++++++------
 .github/workflows/tools-api-docs-dev.yml |  2 +-
 5 files changed, 71 insertions(+), 29 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index a3941f3ce1..152421b827 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -17,7 +17,7 @@ env:
 
 jobs:
   MakeTestWorkflow:
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     env:
       NXF_ANSI_LOG: false
     strategy:
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 168fac653c..5f053eb007 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -14,7 +14,7 @@ concurrency:
 
 jobs:
   EditorConfig:
-    runs-on: ["self-hosted"]
+    runs-on: ["ubuntu-latest"]
     steps:
       - uses: actions/checkout@v4
 
@@ -30,7 +30,7 @@ jobs:
         run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile')
 
   Prettier:
-    runs-on: ["self-hosted"]
+    runs-on: ["ubuntu-latest"]
     steps:
       - uses: actions/checkout@v4
 
@@ -45,7 +45,7 @@ jobs:
         run: prettier --check ${GITHUB_WORKSPACE}
 
   PythonBlack:
-    runs-on: ["self-hosted"]
+    runs-on: ["ubuntu-latest"]
     steps:
       - uses: actions/checkout@v4
 
@@ -75,7 +75,7 @@ jobs:
           allow-repeats: false
 
   isort:
-    runs-on: ["self-hosted"]
+    runs-on: ["ubuntu-latest"]
     steps:
       - name: Check out source-code repository
         uses: actions/checkout@v4
@@ -91,7 +91,7 @@ jobs:
           requirementsFiles: "requirements.txt requirements-dev.txt"
 
   static-type-check:
-    runs-on: ["self-hosted"]
+    runs-on: ["ubuntu-latest"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index 1230bfc9d3..169a917d83 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -13,7 +13,7 @@ concurrency:
 jobs:
   push_dockerhub:
     name: Push new Docker image to Docker Hub (dev)
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     # Only run for the nf-core repo, for releases and merged PRs
     if: ${{ github.repository == 'nf-core/tools' }}
     env:
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 9f8172a3be..3abbf8ef29 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -14,8 +14,9 @@ on:
       - "CHANGELOG.md"
   release:
     types: [published]
+  workflow_dispatch:
 
-# Cancel if a newer run is started
+# Cancel if a newer run with the same workflow name is queued
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
@@ -39,32 +40,42 @@ jobs:
         id: conditions
         run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> $GITHUB_ENV
 
-      - name: Check out source-code repository
-        uses: actions/checkout@v4
-        if: ${{ env.run-tests == 'true' }}
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
-        if: ${{ env.run-tests == 'true' }}
     outputs:
       python-version: ${{ matrix.python-version }}
       runner: ${{ matrix.runner }}
       run-tests: ${{ env.run-tests }}
 
+  # create a test matrix based on all python files in /tests
+  list_tests:
+    name: Get test file matrix
+    needs: setup
+    if: ${{ needs.setup.outputs.run-tests == 'true' }}
+    runs-on: ${{ needs.setup.outputs.runner }}
+    outputs:
+      tests: ${{ env.tests }}
+    steps:
+      - uses: actions/checkout@v4
+        name: Check out source-code repository
+
+      - name: List tests
+        id: list_tests
+        run:
+          | # get all python files in /tests except __init__.py and also all subdirectories and remove trailing commas
+          echo "tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
+
   test:
     name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
-    needs: setup
+    needs: [setup, list_tests]
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
     runs-on: ${{ needs.setup.outputs.runner }}
+    strategy:
+      matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
@@ -87,8 +98,6 @@ jobs:
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
-        with:
-          version: "latest-everything"
 
       - name: Cache nf-test installation
         id: cache-software
@@ -106,10 +115,43 @@ jobs:
           sudo mv nf-test /usr/local/bin/
 
       - name: Test with pytest
-        run: python3 -m pytest tests/ --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core
+        run: |
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core || exit_code=$?
+          # don't fail if no tests were collected, e.g. for test_licence.py
+          if [ "${exit_code}" -eq 5 ]; then
+            echo "No tests were collected"
+            exit 0
+          elif [ "${exit_code}" -ne 0 ]; then
+            echo "Tests failed with exit code ${exit_code}"
+            exit 1
+          fi
+
+      - name: Upload coverage
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage${{ matrix.test }}
+          path: .coverage
 
-      - uses: codecov/codecov-action@v1
-        name: Upload code coverage report
+  coverage:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v4
         with:
-          if: success()
-          token: ${{ secrets.CODECOV_TOKEN }}
+          python-version: 3.12
+          cache: "pip"
+      - name: Install deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+      - name: Download all artifacts
+        # Downloads coverage1, coverage2, etc.
+        uses: actions/download-artifact@v3
+      - name: Run coverage
+        run: |
+          coverage combine coverage*/.coverage*
+          coverage report
+          coverage xml
+      - uses: codecov/codecov-action@v3
diff --git a/.github/workflows/tools-api-docs-dev.yml b/.github/workflows/tools-api-docs-dev.yml
index f6106bd8b5..7de8913e03 100644
--- a/.github/workflows/tools-api-docs-dev.yml
+++ b/.github/workflows/tools-api-docs-dev.yml
@@ -20,7 +20,7 @@ concurrency:
 jobs:
   api-docs:
     name: Build & push Sphinx API docs
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
 
     steps:
       - name: Check out source-code repository

From 34285cf8903eb20ac7a1346ad6a93cb42037a992 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 30 Nov 2023 16:20:05 +0100
Subject: [PATCH 002/117] use PR to test aws runners

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 3abbf8ef29..d48cc381cc 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -26,7 +26,7 @@ env:
 
 jobs:
   setup:
-    runs-on: ["ubuntu-latest"]
+    runs-on: ["self-hosted"]
     strategy:
       matrix:
         python-version: ["3.8", "3.12"]

From 7cfb0ae4e8a924aa8ac15aa83e1d73ed69c177f8 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 30 Nov 2023 17:42:48 +0100
Subject: [PATCH 003/117] fix coverage step

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index d48cc381cc..12647f1bc5 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -145,7 +145,7 @@ jobs:
       - name: Install deps
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
+          pip install -r requirements-dev.txt
       - name: Download all artifacts
         # Downloads coverage1, coverage2, etc.
         uses: actions/download-artifact@v3

From 1a8d7f6d747c64910adf3522c3c8f16745175ac3 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 30 Nov 2023 18:51:31 +0100
Subject: [PATCH 004/117] try self-hosted again

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 12647f1bc5..46385cfd29 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -67,7 +67,7 @@ jobs:
     name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: [setup, list_tests]
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
-    runs-on: ${{ needs.setup.outputs.runner }}
+    runs-on: "self-hosted"
     strategy:
       matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
     steps:

From 8e4554d28f8238cbb947c1480aa0b83c165dc016 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 1 Dec 2023 07:28:40 +0100
Subject: [PATCH 005/117] smaller naming changes

---
 .github/workflows/pytest.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 46385cfd29..d5b89cd238 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -32,8 +32,8 @@ jobs:
         python-version: ["3.8", "3.12"]
         runner: ["ubuntu-latest"]
         include:
-          - runner: "ubuntu-20.04"
-            python-version: "3.8"
+          - python-version: "3.8"
+            runner: "ubuntu-20.04"
 
     steps:
       - name: Check conditions
@@ -64,7 +64,7 @@ jobs:
           echo "tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
 
   test:
-    name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
+    name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: [setup, list_tests]
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
     runs-on: "self-hosted"

From 3b6909493c8c97652547248caadcf79bd64fc394 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 1 Dec 2023 09:48:11 +0100
Subject: [PATCH 006/117] try to use github runner when available

---
 .github/workflows/pytest.yml | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 12647f1bc5..088a3d3b7a 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -40,9 +40,29 @@ jobs:
         id: conditions
         run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> $GITHUB_ENV
 
+      - name: Check queue size
+        id: queue
+        uses: actions/github-script@v4
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            const { data: { workflow_runs: runs } } = await github.actions.listWorkflowRuns({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              workflow_id: context.workflow,
+              branch: context.ref.replace('refs/heads/', ''),
+              status: 'queued',
+            });
+            const count = runs.length;
+            return {
+              'queue-size-exceeded': count > 30,
+              'queue-size': count,
+            };
+
     outputs:
       python-version: ${{ matrix.python-version }}
-      runner: ${{ matrix.runner }}
+      # set runner to self-hosted if queue size is exceeded
+      runner: ${{ steps.queue.outputs['queue-size-exceeded'] == 'true' && 'self-hosted' || matrix.runner }}
       run-tests: ${{ env.run-tests }}
 
   # create a test matrix based on all python files in /tests

From 6ea28b77dc596fee663b86c6bc8cd08a5168cfa5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 1 Dec 2023 09:57:49 +0100
Subject: [PATCH 007/117] Revert "try to use github runner when available"

This reverts commit 3b6909493c8c97652547248caadcf79bd64fc394.
---
 .github/workflows/pytest.yml | 22 +---------------------
 1 file changed, 1 insertion(+), 21 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 2f54ba578c..d5b89cd238 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -40,29 +40,9 @@ jobs:
         id: conditions
         run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> $GITHUB_ENV
 
-      - name: Check queue size
-        id: queue
-        uses: actions/github-script@v4
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          script: |
-            const { data: { workflow_runs: runs } } = await github.actions.listWorkflowRuns({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              workflow_id: context.workflow,
-              branch: context.ref.replace('refs/heads/', ''),
-              status: 'queued',
-            });
-            const count = runs.length;
-            return {
-              'queue-size-exceeded': count > 30,
-              'queue-size': count,
-            };
-
     outputs:
       python-version: ${{ matrix.python-version }}
-      # set runner to self-hosted if queue size is exceeded
-      runner: ${{ steps.queue.outputs['queue-size-exceeded'] == 'true' && 'self-hosted' || matrix.runner }}
+      runner: ${{ matrix.runner }}
       run-tests: ${{ env.run-tests }}
 
   # create a test matrix based on all python files in /tests

From 5c866c6c24fd3b8382a1d7a52efb595570f7c6dd Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 1 Dec 2023 10:23:48 +0100
Subject: [PATCH 008/117] run all tests even if one fails

---
 .github/workflows/pytest.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index d5b89cd238..3de1922670 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -70,6 +70,7 @@ jobs:
     runs-on: "self-hosted"
     strategy:
       matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
+      fail-fast: false # run all tests even if one fails
     steps:
       - uses: actions/checkout@v4
         name: Check out source-code repository

From 5bb519f2289d31f6a1889f17d1d6f4962804d1a9 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 1 Dec 2023 10:52:50 +0100
Subject: [PATCH 009/117] print nextflow config

---
 .github/workflows/pytest.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 3de1922670..82260e31ac 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -114,7 +114,8 @@ jobs:
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
-
+      - name: print nextflow.config
+        run: cat nextflow.config
       - name: Test with pytest
         run: |
           python3 -m pytest tests/${{matrix.test}} --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core || exit_code=$?

From 4f2b42de028c49ef649d1de6b795707c2d54880a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 1 Dec 2023 12:28:16 +0100
Subject: [PATCH 010/117] use full path for nextflow.config

---
 .github/workflows/pytest.yml | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 82260e31ac..e82f00967a 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -35,15 +35,10 @@ jobs:
           - python-version: "3.8"
             runner: "ubuntu-20.04"
 
-    steps:
-      - name: Check conditions
-        id: conditions
-        run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> $GITHUB_ENV
-
     outputs:
       python-version: ${{ matrix.python-version }}
       runner: ${{ matrix.runner }}
-      run-tests: ${{ env.run-tests }}
+      run-tests: ${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}"
 
   # create a test matrix based on all python files in /tests
   list_tests:
@@ -115,7 +110,8 @@ jobs:
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
       - name: print nextflow.config
-        run: cat nextflow.config
+        run: cat /opt/actions-runner/nextflow.config
+
       - name: Test with pytest
         run: |
           python3 -m pytest tests/${{matrix.test}} --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core || exit_code=$?

From 5f79510482c945cfafde6ae0bca4a7a1e380c7e0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 1 Dec 2023 12:39:16 +0100
Subject: [PATCH 011/117] fix workflow

---
 .github/workflows/pytest.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index e82f00967a..a7387129f5 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -35,6 +35,11 @@ jobs:
           - python-version: "3.8"
             runner: "ubuntu-20.04"
 
+    steps:
+      - name: Check conditions
+        id: conditions
+        run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> $GITHUB_ENV
+
     outputs:
       python-version: ${{ matrix.python-version }}
       runner: ${{ matrix.runner }}

From 498fca283da2c6d395d8437629a8afd7ba344db9 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 1 Dec 2023 12:43:28 +0100
Subject: [PATCH 012/117] use different logic

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index a7387129f5..5bb8df85ac 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -43,7 +43,7 @@ jobs:
     outputs:
       python-version: ${{ matrix.python-version }}
       runner: ${{ matrix.runner }}
-      run-tests: ${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}"
+      run-tests: ${{ steps.conditions.outputs.run-tests }}
 
   # create a test matrix based on all python files in /tests
   list_tests:

From b0ef65a760b0c5b7fb76c130f684662d17c40300 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 1 Dec 2023 12:47:12 +0100
Subject: [PATCH 013/117] revert

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 5bb8df85ac..f3bb4121e3 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -43,7 +43,7 @@ jobs:
     outputs:
       python-version: ${{ matrix.python-version }}
       runner: ${{ matrix.runner }}
-      run-tests: ${{ steps.conditions.outputs.run-tests }}
+      run-tests: ${{ env.run-tests }}
 
   # create a test matrix based on all python files in /tests
   list_tests:

From 7a1e09539d081c797e9a6d692d5fd39e7e9dca86 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 1 Dec 2023 14:33:24 +0100
Subject: [PATCH 014/117] try more self-hosted

---
 .github/workflows/create-lint-wf.yml               |  2 +-
 .github/workflows/create-test-lint-wf-template.yml |  2 +-
 .github/workflows/create-test-wf.yml               |  2 +-
 .github/workflows/fix-linting.yml                  |  2 +-
 .github/workflows/lint-code.yml                    | 10 +++++-----
 .github/workflows/sync.yml                         |  4 ++--
 6 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 152421b827..a3941f3ce1 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -17,7 +17,7 @@ env:
 
 jobs:
   MakeTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       NXF_ANSI_LOG: false
     strategy:
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 4be3098629..b14a0fac52 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -20,7 +20,7 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       NXF_ANSI_LOG: false
     strategy:
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 4f66adae6b..7b6a868f9e 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -17,7 +17,7 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       NXF_ANSI_LOG: false
     strategy:
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index d846151205..00a52583ec 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -10,7 +10,7 @@ jobs:
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
       github.repository == 'nf-core/tools'
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     steps:
       # Use the @nf-core-bot token to check out so we can push later
       - uses: actions/checkout@v4
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 5f053eb007..168fac653c 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -14,7 +14,7 @@ concurrency:
 
 jobs:
   EditorConfig:
-    runs-on: ["ubuntu-latest"]
+    runs-on: ["self-hosted"]
     steps:
       - uses: actions/checkout@v4
 
@@ -30,7 +30,7 @@ jobs:
         run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile')
 
   Prettier:
-    runs-on: ["ubuntu-latest"]
+    runs-on: ["self-hosted"]
     steps:
       - uses: actions/checkout@v4
 
@@ -45,7 +45,7 @@ jobs:
         run: prettier --check ${GITHUB_WORKSPACE}
 
   PythonBlack:
-    runs-on: ["ubuntu-latest"]
+    runs-on: ["self-hosted"]
     steps:
       - uses: actions/checkout@v4
 
@@ -75,7 +75,7 @@ jobs:
           allow-repeats: false
 
   isort:
-    runs-on: ["ubuntu-latest"]
+    runs-on: ["self-hosted"]
     steps:
       - name: Check out source-code repository
         uses: actions/checkout@v4
@@ -91,7 +91,7 @@ jobs:
           requirementsFiles: "requirements.txt requirements-dev.txt"
 
   static-type-check:
-    runs-on: ["ubuntu-latest"]
+    runs-on: ["self-hosted"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index b8fb287944..8351778dfa 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -16,7 +16,7 @@ concurrency:
 
 jobs:
   get-pipelines:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     outputs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
@@ -31,7 +31,7 @@ jobs:
 
   sync:
     needs: get-pipelines
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     strategy:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false

From 4b0b238b399ac20e845d7efd712a7e74b6705066 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 1 Dec 2023 15:05:30 +0100
Subject: [PATCH 015/117] remove config options

---
 nf_core/pipeline-template/nextflow.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 31917a3e31..6a6bee6a83 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -121,7 +121,6 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
         apptainer.enabled      = false
-        runOptions             = '-u $(id -u):$(id -g)'
     }
     arm {
         docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'

From 28a2a5858871b4c1986d673d986b26d428996ce3 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 4 Dec 2023 10:26:10 +0100
Subject: [PATCH 016/117] switch to new profile

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 .github/workflows/create-test-wf.yml               | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 4be3098629..2a4273ee37 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -91,7 +91,7 @@ jobs:
 
       - name: run the pipeline
         run: |
-          nextflow run my-prefix-testpipeline -profile test,docker --outdir ./results
+          nextflow run my-prefix-testpipeline -profile test,self_hosted_runner --outdir ./results
 
       # Remove results folder before linting
       - name: remove results folder
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 4f66adae6b..ddae4ef2d9 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -47,7 +47,7 @@ jobs:
       - name: Run nf-core/tools
         run: |
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
-          nextflow run nf-core-testpipeline -profile test,docker --outdir ./results
+          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
 
       - name: Upload log file artifact
         if: ${{ always() }}

From 6022a1d68c7ed1a65d61dbaae8a3cc1d8a4bbe6f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 4 Dec 2023 11:09:53 +0100
Subject: [PATCH 017/117] print config files, try fix for coverage creation

---
 .github/workflows/create-test-lint-wf-template.yml | 3 +++
 .github/workflows/pytest.yml                       | 9 ++++++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 8509ce6e8e..1a217fbd56 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -89,6 +89,9 @@ jobs:
         run: |
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
 
+      - name: print configs
+        run: nextflow config
+
       - name: run the pipeline
         run: |
           nextflow run my-prefix-testpipeline -profile test,self_hosted_runner --outdir ./results
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index f3bb4121e3..2e0c38b922 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -60,8 +60,9 @@ jobs:
       - name: List tests
         id: list_tests
         run:
-          | # get all python files in /tests except __init__.py and also all subdirectories and remove trailing commas
-          echo "tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
+          | # get all python files in /tests strting with test_ excluding test_modules, test_subworkflows and test_components
+          echo "tests=$(find tests/test_* -not -name test_modules.py -not -name test_subworkflows.py -not -name test_components.py -name  | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
+          #
 
   test:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
@@ -149,12 +150,14 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements-dev.txt
+
       - name: Download all artifacts
         # Downloads coverage1, coverage2, etc.
         uses: actions/download-artifact@v3
+
       - name: Run coverage
         run: |
-          coverage combine coverage*/.coverage*
+          coverage combine coverage*/.coverage* --sources=nf_core
           coverage report
           coverage xml
       - uses: codecov/codecov-action@v3

From 08f4d2832a35a5451aaa48ec0d109e0113dc2592 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 4 Dec 2023 11:29:10 +0100
Subject: [PATCH 018/117] print configs with profiles

---
 .github/workflows/create-test-lint-wf-template.yml | 3 ++-
 .github/workflows/pytest.yml                       | 9 +++++----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 1a217fbd56..5247bd71d3 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -90,7 +90,8 @@ jobs:
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
 
       - name: print configs
-        run: nextflow config
+        run: |
+          echo "Configs: $(nextflow config -flat -profile test,self_hosted_runner)"
 
       - name: run the pipeline
         run: |
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 2e0c38b922..b0b3ebbd1b 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -49,20 +49,21 @@ jobs:
   list_tests:
     name: Get test file matrix
     needs: setup
-    if: ${{ needs.setup.outputs.run-tests == 'true' }}
+
     runs-on: ${{ needs.setup.outputs.runner }}
     outputs:
       tests: ${{ env.tests }}
     steps:
       - uses: actions/checkout@v4
         name: Check out source-code repository
-
+      - name: Print conditions
+        run: echo "run-tests=${{ needs.setup.outputs.run-tests }}" >> $GITHUB_ENV
       - name: List tests
         id: list_tests
         run:
           | # get all python files in /tests strting with test_ excluding test_modules, test_subworkflows and test_components
-          echo "tests=$(find tests/test_* -not -name test_modules.py -not -name test_subworkflows.py -not -name test_components.py -name  | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
-          #
+          echo "tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
+        if: ${{ needs.setup.outputs.run-tests == 'true' }}
 
   test:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}

From 35cb092c780ca0271467fa3d98f03979cf377a79 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 4 Dec 2023 12:43:35 +0100
Subject: [PATCH 019/117] fix config command

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 5247bd71d3..448666ad3a 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -91,7 +91,7 @@ jobs:
 
       - name: print configs
         run: |
-          echo "Configs: $(nextflow config -flat -profile test,self_hosted_runner)"
+          echo "Configs: $(nextflow config -flat -profile test,self_hosted_runner my-prefix-testpipeline)"
 
       - name: run the pipeline
         run: |

From ac2acfc32f827c5842d7f05c63e18a0a3eb6c5ac Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 4 Dec 2023 12:55:06 +0100
Subject: [PATCH 020/117] simply list_tests

---
 .github/workflows/pytest.yml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index b0b3ebbd1b..b5fc199507 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -48,22 +48,17 @@ jobs:
   # create a test matrix based on all python files in /tests
   list_tests:
     name: Get test file matrix
-    needs: setup
-
-    runs-on: ${{ needs.setup.outputs.runner }}
+    runs-on: ["self-hosted"]
     outputs:
       tests: ${{ env.tests }}
     steps:
       - uses: actions/checkout@v4
         name: Check out source-code repository
-      - name: Print conditions
-        run: echo "run-tests=${{ needs.setup.outputs.run-tests }}" >> $GITHUB_ENV
       - name: List tests
         id: list_tests
         run:
           | # get all python files in /tests strting with test_ excluding test_modules, test_subworkflows and test_components
           echo "tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
-        if: ${{ needs.setup.outputs.run-tests == 'true' }}
 
   test:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}

From cd7fac24d1c94ab8c222a0c69cc2896aef142614 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 4 Dec 2023 13:38:41 +0100
Subject: [PATCH 021/117] print more configs

---
 .github/workflows/create-test-wf.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index f20696cb9f..9b44138bd7 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -44,6 +44,10 @@ jobs:
         with:
           version: ${{ matrix.NXF_VER }}
 
+      - name: print configs
+        run: |
+          echo "Configs: $(nextflow config -flat -profile test,self_hosted_runner my-prefix-testpipeline)"
+
       - name: Run nf-core/tools
         run: |
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain

From 1e5c2d73315e513d94c007c23d839bcb7e9c665c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 4 Dec 2023 13:55:49 +0100
Subject: [PATCH 022/117] don't print configs in this step

---
 .github/workflows/create-test-wf.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 9b44138bd7..f20696cb9f 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -44,10 +44,6 @@ jobs:
         with:
           version: ${{ matrix.NXF_VER }}
 
-      - name: print configs
-        run: |
-          echo "Configs: $(nextflow config -flat -profile test,self_hosted_runner my-prefix-testpipeline)"
-
       - name: Run nf-core/tools
         run: |
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain

From 0084d1567b9578f5baf54d83862029201aa5fd2b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 4 Dec 2023 16:20:38 +0100
Subject: [PATCH 023/117] exclude some template settings to be able to use
 nf-core configs

---
 .github/workflows/create-test-lint-wf-template.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 448666ad3a..f67c7f7d1a 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -26,11 +26,11 @@ jobs:
     strategy:
       matrix:
         TEMPLATE:
-          - "template_skip_all.yml"
+          # - "template_skip_all.yml"
           - "template_skip_github_badges.yml"
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
-          - "template_skip_nf_core_configs.yml"
+          # - "template_skip_nf_core_configs.yml"
 
     steps:
       - uses: actions/checkout@v4

From dddf94432c322ce144cdd195bfb33e2f8d7cba0b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 5 Dec 2023 08:43:15 +0100
Subject: [PATCH 024/117] try to fix coverage upload

---
 .github/workflows/pytest.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index b5fc199507..8722f1a90e 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -153,7 +153,7 @@ jobs:
 
       - name: Run coverage
         run: |
-          coverage combine coverage*/.coverage* --sources=nf_core
-          coverage report
+          coverage combine coverage*/.coverage*
           coverage xml
-      - uses: codecov/codecov-action@v3
+
+          - uses: codecov/codecov-action@v3

From 1423218cc97a45e613b8941d34004fe2767186d2 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 5 Dec 2023 11:22:30 +0100
Subject: [PATCH 025/117] debugging coverage step

---
 .github/workflows/pytest.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 8722f1a90e..60c0139be1 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -58,7 +58,7 @@ jobs:
         id: list_tests
         run:
           | # get all python files in /tests strting with test_ excluding test_modules, test_subworkflows and test_components
-          echo "tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
+          echo "tests=$(find tests/test_cli* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
 
   test:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
@@ -151,6 +151,11 @@ jobs:
         # Downloads coverage1, coverage2, etc.
         uses: actions/download-artifact@v3
 
+      - name: Print working directory and list files
+        run: |
+          pwd
+          ls -l
+
       - name: Run coverage
         run: |
           coverage combine coverage*/.coverage*

From c997ab2062b5bccbd6722c4315173fa92d278559 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 5 Dec 2023 12:38:43 +0100
Subject: [PATCH 026/117] ignore coverage errors for now

---
 .github/workflows/pytest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 60c0139be1..e4158c3e73 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -58,7 +58,7 @@ jobs:
         id: list_tests
         run:
           | # get all python files in /tests strting with test_ excluding test_modules, test_subworkflows and test_components
-          echo "tests=$(find tests/test_cli* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
+          echo "tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
 
   test:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
@@ -159,6 +159,6 @@ jobs:
       - name: Run coverage
         run: |
           coverage combine coverage*/.coverage*
-          coverage xml
+          coverage xml -i
 
           - uses: codecov/codecov-action@v3

From d84a86f4f4677820ef98f68d801de81284d00c2f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 5 Dec 2023 15:10:48 +0100
Subject: [PATCH 027/117] seems to work now?

---
 .github/workflows/pytest.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index e4158c3e73..7de17cb327 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -32,8 +32,8 @@ jobs:
         python-version: ["3.8", "3.12"]
         runner: ["ubuntu-latest"]
         include:
-          - python-version: "3.8"
-            runner: "ubuntu-20.04"
+          - runner: "ubuntu-20.04"
+            python-version: "3.8"
 
     steps:
       - name: Check conditions
@@ -161,4 +161,4 @@ jobs:
           coverage combine coverage*/.coverage*
           coverage xml -i
 
-          - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v3

From e23e6118a86bc189d849c7c0d7be0a080d328ba1 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 5 Dec 2023 16:23:59 +0100
Subject: [PATCH 028/117] add codecov token

---
 .github/workflows/pytest.yml | 3 +++
 codecov.yml                  | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 7de17cb327..ce9c69bc32 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -54,6 +54,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         name: Check out source-code repository
+
       - name: List tests
         id: list_tests
         run:
@@ -162,3 +163,5 @@ jobs:
           coverage xml -i
 
       - uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/codecov.yml b/codecov.yml
index 1ecf8960c0..23d09247bc 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -4,3 +4,6 @@ coverage:
       default:
         threshold: 5%
     patch: off
+comment:
+  layout: "condensed_header, condensed_files, condensed_footer" # add "condensed_" to "header", "files" and "footer"
+  hide_project_coverage: TRUE # set to true

From 9547c66ae7eac61ad9c6c1ce8fabde8ec875075d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 5 Dec 2023 16:36:07 +0100
Subject: [PATCH 029/117] try to fix name collisions

---
 .github/workflows/pytest.yml | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index ce9c69bc32..08ba463e8d 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -54,11 +54,14 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         name: Check out source-code repository
+        with:
+          path: "nf-core_tools"
 
       - name: List tests
         id: list_tests
-        run:
-          | # get all python files in /tests strting with test_ excluding test_modules, test_subworkflows and test_components
+        run: |
+          # get all python files in /tests strting with test_ excluding test_modules, test_subworkflows and test_components
+          cd nf-core_tools
           echo "tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
 
   test:
@@ -72,6 +75,11 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         name: Check out source-code repository
+        with:
+          path: "nf-core_tools"
+
+      - name: change to nf-core_tools directory
+        run: cd nf-core_tools
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
         uses: actions/setup-python@v4

From 96b3152bcae2f997244e7843ce16c56bb31d22e4 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 5 Dec 2023 16:46:12 +0100
Subject: [PATCH 030/117] add github token to editorconfig step

---
 .github/workflows/lint-code.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 168fac653c..b5e0feab60 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -15,6 +15,8 @@ concurrency:
 jobs:
   EditorConfig:
     runs-on: ["self-hosted"]
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v4
 

From 02fa592383c4fb4c429e462c233665bc387f9365 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 5 Dec 2023 18:53:34 +0100
Subject: [PATCH 031/117] debug changed directory

---
 .github/workflows/pytest.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 08ba463e8d..78fa114d94 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -79,7 +79,7 @@ jobs:
           path: "nf-core_tools"
 
       - name: change to nf-core_tools directory
-        run: cd nf-core_tools
+        run: cd nf-core_tools && pwd
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
         uses: actions/setup-python@v4
@@ -151,6 +151,10 @@ jobs:
         with:
           python-version: 3.12
           cache: "pip"
+
+      - name: change to nf-core_tools directory
+        run: cd nf-core_tools
+
       - name: Install deps
         run: |
           python -m pip install --upgrade pip

From a9981c5ac83a2162e915ed174fbee11e5d302414 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 5 Dec 2023 22:32:12 +0100
Subject: [PATCH 032/117] don't change path

---
 .github/workflows/pytest.yml | 18 +-----------------
 1 file changed, 1 insertion(+), 17 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 78fa114d94..b878020513 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -54,14 +54,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         name: Check out source-code repository
-        with:
-          path: "nf-core_tools"
 
       - name: List tests
         id: list_tests
         run: |
-          # get all python files in /tests strting with test_ excluding test_modules, test_subworkflows and test_components
-          cd nf-core_tools
           echo "tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
 
   test:
@@ -75,11 +71,6 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         name: Check out source-code repository
-        with:
-          path: "nf-core_tools"
-
-      - name: change to nf-core_tools directory
-        run: cd nf-core_tools && pwd
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
         uses: actions/setup-python@v4
@@ -99,6 +90,7 @@ jobs:
           sudo apt remove -y git git-man
           sudo add-apt-repository --remove ppa:git-core/ppa
           sudo apt install -y git
+
       - name: Get current date
         id: date
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
@@ -152,9 +144,6 @@ jobs:
           python-version: 3.12
           cache: "pip"
 
-      - name: change to nf-core_tools directory
-        run: cd nf-core_tools
-
       - name: Install deps
         run: |
           python -m pip install --upgrade pip
@@ -164,11 +153,6 @@ jobs:
         # Downloads coverage1, coverage2, etc.
         uses: actions/download-artifact@v3
 
-      - name: Print working directory and list files
-        run: |
-          pwd
-          ls -l
-
       - name: Run coverage
         run: |
           coverage combine coverage*/.coverage*

From 6b97c77af6a49bbb992fc2bab50047a908a9aeb0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 6 Dec 2023 09:55:32 +0100
Subject: [PATCH 033/117] more codecov debuggin

---
 .github/workflows/pytest.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index b878020513..9cfd7b26bf 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -158,6 +158,9 @@ jobs:
           coverage combine coverage*/.coverage*
           coverage xml -i
 
+      - name: show directory
+        run: ls -la
+
       - uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

From d0715e9f9a8e58a6bf20709dfc602893dad9e1e6 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 6 Dec 2023 11:02:41 +0100
Subject: [PATCH 034/117] specify codecov file

---
 .github/workflows/pytest.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 9cfd7b26bf..cdca23c959 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -164,3 +164,4 @@ jobs:
       - uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
+          file: coverage.xml

From 3edb3db98eef9e61f1daff0a961dd428fad4be97 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 7 Dec 2023 10:24:08 +0100
Subject: [PATCH 035/117] test on github runners, to see speed differences

---
 .github/workflows/pytest.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index cdca23c959..4564b1af26 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -58,13 +58,16 @@ jobs:
       - name: List tests
         id: list_tests
         run: |
-          echo "tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
+          tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')
+          # reverse list to run slowest tests first
+          tests=$(echo $tests | jq '.test | reverse')
+          echo "tests" >> $GITHUB_ENV
 
   test:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: [setup, list_tests]
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
-    runs-on: "self-hosted"
+    runs-on: ${{ needs.setup.outputs.runner }}
     strategy:
       matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
       fail-fast: false # run all tests even if one fails

From e107adab923c7df25d6f4e7e4bc39593bf561525 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 7 Dec 2023 10:29:17 +0100
Subject: [PATCH 036/117] run also list_test in github

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 4564b1af26..97f001c26c 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -48,7 +48,7 @@ jobs:
   # create a test matrix based on all python files in /tests
   list_tests:
     name: Get test file matrix
-    runs-on: ["self-hosted"]
+    runs-on: "ubuntu-latest"
     outputs:
       tests: ${{ env.tests }}
     steps:

From e3fa536d58a6603df3af1e59ee28127938793b0d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 7 Dec 2023 10:37:46 +0100
Subject: [PATCH 037/117] don't reverse for now

---
 .github/workflows/pytest.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 97f001c26c..20c6e22055 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -59,9 +59,7 @@ jobs:
         id: list_tests
         run: |
           tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')
-          # reverse list to run slowest tests first
-          tests=$(echo $tests | jq '.test | reverse')
-          echo "tests" >> $GITHUB_ENV
+          echo $tests >> $GITHUB_ENV
 
   test:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}

From d3ae3faf99ab5ffba4728f3b7d98c07e08d4d2e1 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 7 Dec 2023 10:39:25 +0100
Subject: [PATCH 038/117] more reversion

---
 .github/workflows/pytest.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 20c6e22055..12063c6df4 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -58,8 +58,7 @@ jobs:
       - name: List tests
         id: list_tests
         run: |
-          tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')
-          echo $tests >> $GITHUB_ENV
+          echo "tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
 
   test:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}

From db88a83fa0e61cabd72ecf139c3b2bbdc4eeaa41 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 7 Dec 2023 10:41:30 +0100
Subject: [PATCH 039/117] remove debugging

---
 .github/workflows/pytest.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 12063c6df4..dee5ba89a0 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -112,8 +112,6 @@ jobs:
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
-      - name: print nextflow.config
-        run: cat /opt/actions-runner/nextflow.config
 
       - name: Test with pytest
         run: |

From b34f99f01afdbccbfd2522686f57eb8075528a7d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 7 Dec 2023 13:53:51 +0100
Subject: [PATCH 040/117] cleanup work directory

---
 .github/workflows/pytest.yml | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 4564b1af26..e02017492a 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -58,10 +58,7 @@ jobs:
       - name: List tests
         id: list_tests
         run: |
-          tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')
-          # reverse list to run slowest tests first
-          tests=$(echo $tests | jq '.test | reverse')
-          echo "tests" >> $GITHUB_ENV
+          echo "tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
 
   test:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
@@ -115,8 +112,6 @@ jobs:
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
-      - name: print nextflow.config
-        run: cat /opt/actions-runner/nextflow.config
 
       - name: Test with pytest
         run: |
@@ -136,6 +131,10 @@ jobs:
           name: coverage${{ matrix.test }}
           path: .coverage
 
+      - name: Cleanup work directory
+        run: |
+          rm -rf work
+
   coverage:
     needs: test
     runs-on: ubuntu-latest
@@ -158,7 +157,9 @@ jobs:
 
       - name: Run coverage
         run: |
+          rm -f .coverage
           coverage combine coverage*/.coverage*
+          coverage report
           coverage xml -i
 
       - name: show directory

From 50814d1028ab5cd3788d1b14e0ebb8340f441b51 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 7 Dec 2023 14:00:12 +0100
Subject: [PATCH 041/117] switch to self-hosted again

---
 .github/workflows/pytest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 0e7cb6e92e..7de9749206 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -48,7 +48,7 @@ jobs:
   # create a test matrix based on all python files in /tests
   list_tests:
     name: Get test file matrix
-    runs-on: "ubuntu-latest"
+    runs-on: "self-hosted"
     outputs:
       tests: ${{ env.tests }}
     steps:
@@ -64,7 +64,7 @@ jobs:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: [setup, list_tests]
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
-    runs-on: ${{ needs.setup.outputs.runner }}
+    runs-on: self-hosted
     strategy:
       matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
       fail-fast: false # run all tests even if one fails

From c4fa3458a2013469bde927595b475aad4a54dadf Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 7 Dec 2023 14:12:49 +0100
Subject: [PATCH 042/117] don't need to install everything for coverage

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 7de9749206..ee0b4e2ae1 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -149,7 +149,7 @@ jobs:
       - name: Install deps
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements-dev.txt
+          pip install coverage
 
       - name: Download all artifacts
         # Downloads coverage1, coverage2, etc.

From fb8e644d5766c21ab643875098ba7f8ac135b5fd Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 7 Dec 2023 15:27:03 +0100
Subject: [PATCH 043/117] always cleanup work directory

---
 .github/workflows/pytest.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index ee0b4e2ae1..a8d8bfe52e 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -58,7 +58,7 @@ jobs:
       - name: List tests
         id: list_tests
         run: |
-          echo "tests=$(find tests/test_* | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
+          echo "tests=$(find tests/test_* | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_ENV
 
   test:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
@@ -134,6 +134,7 @@ jobs:
       - name: Cleanup work directory
         run: |
           rm -rf work
+        if: always()
 
   coverage:
     needs: test
@@ -155,6 +156,9 @@ jobs:
         # Downloads coverage1, coverage2, etc.
         uses: actions/download-artifact@v3
 
+      - name: show directory
+        run: tree
+
       - name: Run coverage
         run: |
           rm -f .coverage

From 82791ac59015bc129f18b7db6ae6a6024ecac65c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 7 Dec 2023 16:31:27 +0100
Subject: [PATCH 044/117] debug coverage

---
 .github/workflows/pytest.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index a8d8bfe52e..74c66626c1 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -163,8 +163,7 @@ jobs:
         run: |
           rm -f .coverage
           coverage combine coverage*/.coverage*
-          coverage report
-          coverage xml -i
+          coverage report -m
 
       - name: show directory
         run: ls -la

From 72b6553c3f0b4ce4f06fcaa3e1052172a5b4266f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 8 Dec 2023 10:05:12 +0100
Subject: [PATCH 045/117] cleanup everything

---
 .github/workflows/create-lint-wf.yml               | 4 ++++
 .github/workflows/create-test-lint-wf-template.yml | 4 ++++
 .github/workflows/create-test-wf.yml               | 4 ++++
 .github/workflows/pytest.yml                       | 3 +--
 4 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index a3941f3ce1..4911124acc 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -131,3 +131,7 @@ jobs:
         with:
           name: nf-core-log-file
           path: log.txt
+
+      - name: Cleanup work directory
+        run: rm -rf work
+        if: always()
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index f67c7f7d1a..0ea2fff272 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -142,3 +142,7 @@ jobs:
         with:
           name: nf-core-log-file
           path: artifact_files.tar
+
+      - name: Cleanup work directory
+        run: rm -rf work
+        if: always()
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index f20696cb9f..0247604396 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -55,3 +55,7 @@ jobs:
         with:
           name: nf-core-log-file
           path: log.txt
+
+      - name: Cleanup work directory
+        run: rm -rf work
+        if: always()
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 74c66626c1..5be9434ac2 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -132,8 +132,7 @@ jobs:
           path: .coverage
 
       - name: Cleanup work directory
-        run: |
-          rm -rf work
+        run: rm -rf work
         if: always()
 
   coverage:

From a1901f7e035a76742bf02559744a8f0e21289d62 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 8 Dec 2023 10:59:21 +0100
Subject: [PATCH 046/117] debugging coverage

---
 .github/workflows/pytest.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 5be9434ac2..b1c6852e6d 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -115,7 +115,7 @@ jobs:
 
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core || exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core -s || exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"
@@ -156,13 +156,14 @@ jobs:
         uses: actions/download-artifact@v3
 
       - name: show directory
-        run: tree
+        run: |
+          pwd
+          tree
 
       - name: Run coverage
         run: |
           rm -f .coverage
           coverage combine coverage*/.coverage*
-          coverage report -m
 
       - name: show directory
         run: ls -la

From 9528d2854c5dd37cad0c1c8c954a6077b5dd8a66 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 8 Dec 2023 11:15:09 +0100
Subject: [PATCH 047/117] fail gracefully during cleanup

---
 .github/workflows/create-lint-wf.yml               | 2 +-
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 .github/workflows/create-test-wf.yml               | 3 ++-
 .github/workflows/pytest.yml                       | 2 +-
 4 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 4911124acc..04548e0d76 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -133,5 +133,5 @@ jobs:
           path: log.txt
 
       - name: Cleanup work directory
-        run: rm -rf work
+        run: rm -rf work || true
         if: always()
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 0ea2fff272..e2a48152b5 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -144,5 +144,5 @@ jobs:
           path: artifact_files.tar
 
       - name: Cleanup work directory
-        run: rm -rf work
+        run: rm -rf work || true
         if: always()
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 0247604396..5b7e991998 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -57,5 +57,6 @@ jobs:
           path: log.txt
 
       - name: Cleanup work directory
-        run: rm -rf work
+        # cleanup and fail gracefully if I get a permission error
+        run: rm -rf work || true
         if: always()
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index b1c6852e6d..92b1fdb256 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -132,7 +132,7 @@ jobs:
           path: .coverage
 
       - name: Cleanup work directory
-        run: rm -rf work
+        run: rm -rf work || true
         if: always()
 
   coverage:

From 5c34797f2b40b8395a8dac7d35912b13c2b86334 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 8 Dec 2023 13:56:07 +0100
Subject: [PATCH 048/117] debug no cleaned up paths

---
 .github/workflows/create-lint-wf.yml               | 5 +++++
 .github/workflows/create-test-lint-wf-template.yml | 5 +++++
 .github/workflows/create-test-wf.yml               | 5 +++++
 .github/workflows/pytest.yml                       | 5 +++++
 4 files changed, 20 insertions(+)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 04548e0d76..558939da20 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -26,6 +26,11 @@ jobs:
           - "23.04.0"
           - "latest-everything"
     steps:
+      - name: go to working directory
+        run: |
+          mkdir -p create-lint-wf
+          cd create-lint-wf
+
       # Get the repo code
       - uses: actions/checkout@v4
         name: Check out source-code repository
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index e2a48152b5..5a94d8a2d7 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -33,6 +33,11 @@ jobs:
           # - "template_skip_nf_core_configs.yml"
 
     steps:
+      - name: go to working directory
+        run: |
+          mkdir -p create-test-lint-wf-template
+          cd create-test-lint-wf-template
+
       - uses: actions/checkout@v4
         name: Check out source-code repository
 
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 5b7e991998..e0836582e1 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -26,6 +26,11 @@ jobs:
           - "23.04.0"
           - "latest-everything"
     steps:
+      - name: go to working directory
+        run: |
+          mkdir -p create-test-wf
+          cd create-test-wf
+
       - uses: actions/checkout@v4
         name: Check out source-code repository
 
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 92b1fdb256..8c420cbeb8 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -69,6 +69,11 @@ jobs:
       matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
       fail-fast: false # run all tests even if one fails
     steps:
+      - name: go to working directory
+        run: |
+          mkdir -p pytest
+          cd pytest
+
       - uses: actions/checkout@v4
         name: Check out source-code repository
 

From c9510e254a82a3c0128529cd57a53e28044a525a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 8 Dec 2023 14:14:22 +0100
Subject: [PATCH 049/117] install tools also in coverage job

---
 .github/workflows/pytest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 8c420cbeb8..5c29423895 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -153,8 +153,8 @@ jobs:
 
       - name: Install deps
         run: |
-          python -m pip install --upgrade pip
-          pip install coverage
+          python -m pip install --upgrade pip -r requirements-dev.txt
+          pip install -e .
 
       - name: Download all artifacts
         # Downloads coverage1, coverage2, etc.

From 05bbc2f74062d130ddb9d3d6ac9f05d5acd7db37 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 8 Dec 2023 14:22:01 +0100
Subject: [PATCH 050/117] add coverage report back in

---
 .github/workflows/pytest.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 5c29423895..32f035fff1 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -169,6 +169,8 @@ jobs:
         run: |
           rm -f .coverage
           coverage combine coverage*/.coverage*
+          coverage report
+          coverage xml
 
       - name: show directory
         run: ls -la

From fc967132b3df0304aee6285e4daff8af39c2ad6c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 8 Dec 2023 16:00:25 +0100
Subject: [PATCH 051/117] coverage debugging...

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 32f035fff1..e439efb734 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -163,7 +163,7 @@ jobs:
       - name: show directory
         run: |
           pwd
-          tree
+          ls -la /opt/actions-runner/_work/tools/tools
 
       - name: Run coverage
         run: |

From 21b6c784618242731e528eb1e25afe3a4896f672 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 8 Dec 2023 16:22:03 +0100
Subject: [PATCH 052/117] change nextflow working dir

---
 .github/workflows/create-lint-wf.yml               | 3 ++-
 .github/workflows/create-test-lint-wf-template.yml | 5 +++--
 .github/workflows/create-test-wf.yml               | 1 +
 .github/workflows/pytest.yml                       | 3 ++-
 4 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 558939da20..57ae6b7592 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -26,10 +26,11 @@ jobs:
           - "23.04.0"
           - "latest-everything"
     steps:
-      - name: go to working directory
+      - name: go to subdirectory and change nextflow workdir
         run: |
           mkdir -p create-lint-wf
           cd create-lint-wf
+          export NXF_WORK=$(pwd)
 
       # Get the repo code
       - uses: actions/checkout@v4
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 5a94d8a2d7..c22721c5a3 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -35,8 +35,9 @@ jobs:
     steps:
       - name: go to working directory
         run: |
-          mkdir -p create-test-lint-wf-template
-          cd create-test-lint-wf-template
+          mkdir -p create-lint-wf-template
+          cd create-lint-wf-template
+          export NXF_WORK=$(pwd)
 
       - uses: actions/checkout@v4
         name: Check out source-code repository
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index e0836582e1..91d63c4ea5 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -30,6 +30,7 @@ jobs:
         run: |
           mkdir -p create-test-wf
           cd create-test-wf
+          export NXF_WORK=$(pwd)
 
       - uses: actions/checkout@v4
         name: Check out source-code repository
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index e439efb734..a9a22dd388 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -69,10 +69,11 @@ jobs:
       matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
       fail-fast: false # run all tests even if one fails
     steps:
-      - name: go to working directory
+      - name: go to subdirectory and change nextflow workdir
         run: |
           mkdir -p pytest
           cd pytest
+          export NXF_WORK=$(pwd)
 
       - uses: actions/checkout@v4
         name: Check out source-code repository

From 7a2188df2ad618de8eb1ca65e68bebf351553eae Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 8 Dec 2023 16:31:36 +0100
Subject: [PATCH 053/117] kick off tests

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index a9a22dd388..ab3d13675f 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -170,7 +170,7 @@ jobs:
         run: |
           rm -f .coverage
           coverage combine coverage*/.coverage*
-          coverage report
+          coverage report --debug=coverage
           coverage xml
 
       - name: show directory

From d14c02fc38a6499e56bdbea3df2d48c627e26e5b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 11 Dec 2023 14:18:27 +0100
Subject: [PATCH 054/117] add debugger ssh

---
 .github/workflows/pytest.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index ab3d13675f..5dd8ca8871 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -165,6 +165,8 @@ jobs:
         run: |
           pwd
           ls -la /opt/actions-runner/_work/tools/tools
+      - name: Setup ssh session
+        uses: Warpbuilds/action-debugger@v1.3
 
       - name: Run coverage
         run: |

From 86d4ae2f5b28eaa2cc9440231da70e02be1e80a5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 11 Dec 2023 15:35:30 +0100
Subject: [PATCH 055/117] more debugging

---
 .github/workflows/pytest.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 5dd8ca8871..b588854daa 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -121,7 +121,7 @@ jobs:
 
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core -s || exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core -s --durations=0 || exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"
@@ -161,10 +161,6 @@ jobs:
         # Downloads coverage1, coverage2, etc.
         uses: actions/download-artifact@v3
 
-      - name: show directory
-        run: |
-          pwd
-          ls -la /opt/actions-runner/_work/tools/tools
       - name: Setup ssh session
         uses: Warpbuilds/action-debugger@v1.3
 

From 49827b816b5961ca31c37c12c25817c6c8a42c9c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 11 Dec 2023 16:49:55 +0100
Subject: [PATCH 056/117] try non-cached python

---
 .github/workflows/pytest.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index b588854daa..38d8c7c666 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -150,7 +150,6 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.12
-          cache: "pip"
 
       - name: Install deps
         run: |

From 187a5b1db2c5db1a93059b1b7a984319e2d81346 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 11 Dec 2023 17:48:53 +0100
Subject: [PATCH 057/117] figure out differences in paths

---
 .github/workflows/pytest.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 38d8c7c666..53ca54e03d 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -74,6 +74,7 @@ jobs:
           mkdir -p pytest
           cd pytest
           export NXF_WORK=$(pwd)
+          echo $"which python: $(which python)"
 
       - uses: actions/checkout@v4
         name: Check out source-code repository
@@ -121,6 +122,7 @@ jobs:
 
       - name: Test with pytest
         run: |
+          echo "Which nf-core: $(which nf-core)"
           python3 -m pytest tests/${{matrix.test}} --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core -s --durations=0 || exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
@@ -160,11 +162,13 @@ jobs:
         # Downloads coverage1, coverage2, etc.
         uses: actions/download-artifact@v3
 
-      - name: Setup ssh session
-        uses: Warpbuilds/action-debugger@v1.3
+      # - name: Setup ssh session
+      #   uses: Warpbuilds/action-debugger@v1.3
 
       - name: Run coverage
         run: |
+          echo "Which nf-core: $(which nf-core)"
+          echo "Which python: $(which python)"
           rm -f .coverage
           coverage combine coverage*/.coverage*
           coverage report --debug=coverage

From 4674b3f3b4ab7a692e6d169ac2e1a9e2508755f8 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 12 Dec 2023 15:42:48 +0100
Subject: [PATCH 058/117] trying to set the python directory manually

---
 .github/workflows/pytest.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 53ca54e03d..7143b65a7a 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -150,6 +150,8 @@ jobs:
       - uses: actions/checkout@v4
       - name: Set up Python 3.9
         uses: actions/setup-python@v4
+        env:
+          AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
           python-version: 3.12
 

From f262b79a2bfc908c13bc0e849ed3533d434c98ff Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 13 Dec 2023 09:39:51 +0100
Subject: [PATCH 059/117] hopefully harmonizing python paths

---
 .github/workflows/pytest.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 7143b65a7a..f2f7147c0a 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -81,6 +81,8 @@ jobs:
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
         uses: actions/setup-python@v4
+        env:
+          AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
@@ -157,6 +159,7 @@ jobs:
 
       - name: Install deps
         run: |
+          cd pytest
           python -m pip install --upgrade pip -r requirements-dev.txt
           pip install -e .
 

From cd4ae58c0dc548d02b539e6a323ad3939b54884d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 13 Dec 2023 10:13:58 +0100
Subject: [PATCH 060/117] fix coverage step

---
 .github/workflows/pytest.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index f2f7147c0a..73b340f552 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -159,7 +159,6 @@ jobs:
 
       - name: Install deps
         run: |
-          cd pytest
           python -m pip install --upgrade pip -r requirements-dev.txt
           pip install -e .
 

From 4e1029c2838364259eb2d9da2eba8bf75c6a98e7 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 13 Dec 2023 11:37:11 +0100
Subject: [PATCH 061/117] trying to fix the source error

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 73b340f552..24bf99d9b8 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -125,7 +125,7 @@ jobs:
       - name: Test with pytest
         run: |
           echo "Which nf-core: $(which nf-core)"
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core -s --durations=0 || exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov-report=xml --cov-config=.github/.coveragerc -s --durations=0 || exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"

From 86a771db23a028dbd6196ba027742c27abf31322 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 13 Dec 2023 15:22:03 +0100
Subject: [PATCH 062/117] specify full path for coverage

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 24bf99d9b8..70eb9ce2e9 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -125,7 +125,7 @@ jobs:
       - name: Test with pytest
         run: |
           echo "Which nf-core: $(which nf-core)"
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov-report=xml --cov-config=.github/.coveragerc -s --durations=0 || exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov=$(realpath nf_core) --cov-report=xml --cov-config=.github/.coveragerc -s --durations=0 || exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"

From e7bea3492dd5efba6ebb57861462ccf96d5ef099 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 14 Dec 2023 08:05:06 +0100
Subject: [PATCH 063/117] copy more settings from pytest-split

---
 .github/.coveragerc          | 3 +++
 .github/workflows/pytest.yml | 3 +--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/.coveragerc b/.github/.coveragerc
index 522a29eb62..a13b37c38f 100644
--- a/.github/.coveragerc
+++ b/.github/.coveragerc
@@ -1,2 +1,5 @@
 [run]
 omit = nf_core/pipeline-template/*
+source = nf_core
+relative_files = True
+
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 70eb9ce2e9..6724348961 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -124,8 +124,7 @@ jobs:
 
       - name: Test with pytest
         run: |
-          echo "Which nf-core: $(which nf-core)"
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov=$(realpath nf_core) --cov-report=xml --cov-config=.github/.coveragerc -s --durations=0 || exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-report=xml --cov-config=.github/.coveragerc -s --durations=0 || exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"

From 5dfd403d3acc8a21916cd7232e3d2242e92d0a6b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 14 Dec 2023 08:29:20 +0100
Subject: [PATCH 064/117] handle exit code better

---
 .github/workflows/pytest.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 6724348961..d525a36c61 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -122,9 +122,14 @@ jobs:
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
 
+      - name: export workdir
+        run: |
+          export NXF_WORK=$(pwd)
+
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-report=xml --cov-config=.github/.coveragerc -s --durations=0 || exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-report=xml --cov-config=.github/.coveragerc -s --durations=0
+          exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"

From 08d7a62e6a0c1d4cd33708240be2df1fd56489ad Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 14 Dec 2023 09:21:38 +0100
Subject: [PATCH 065/117] didn't work

---
 .github/workflows/pytest.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index d525a36c61..c042416f44 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -128,8 +128,7 @@ jobs:
 
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-report=xml --cov-config=.github/.coveragerc -s --durations=0
-          exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-report=xml --cov-config=.github/.coveragerc -s --durations=0 && exit_code=0 || exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"

From 4fafbef13cc72579c1fcf5b39d5827318787986e Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 14 Dec 2023 09:32:09 +0100
Subject: [PATCH 066/117] switch to new gitlab branch

---
 tests/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/utils.py b/tests/utils.py
index 198ac3d583..148912fe64 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -27,7 +27,7 @@
 GITLAB_BRANCH_ORG_PATH_BRANCH = "org-path"
 GITLAB_BRANCH_TEST_OLD_SHA = "e772abc22c1ff26afdf377845c323172fb3c19ca"
 GITLAB_BRANCH_TEST_NEW_SHA = "7d73e21f30041297ea44367f2b4fd4e045c0b991"
-GITLAB_NFTEST_BRANCH = "nf-test-tests"
+GITLAB_NFTEST_BRANCH = "nf-test-tests-self-hosted-runners"
 
 
 def with_temporary_folder(func: Callable[..., Any]) -> Callable[..., Any]:

From b2a9458a38d0ddff6b033263df7d7e956feb4e79 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 14 Dec 2023 15:42:20 +0100
Subject: [PATCH 067/117] remove coverage output specification

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index c042416f44..f6d65bce1b 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -128,7 +128,7 @@ jobs:
 
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-report=xml --cov-config=.github/.coveragerc -s --durations=0 && exit_code=0 || exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-config=.github/.coveragerc --durations=0 && exit_code=0 || exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"

From 51bc286ed8f5ad40c228abc73a107e02407c8855 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 14 Dec 2023 15:43:48 +0100
Subject: [PATCH 068/117] omit all template files in coverage

---
 .github/.coveragerc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/.coveragerc b/.github/.coveragerc
index a13b37c38f..24a419ae07 100644
--- a/.github/.coveragerc
+++ b/.github/.coveragerc
@@ -1,5 +1,5 @@
 [run]
-omit = nf_core/pipeline-template/*
+omit = nf_core/*-template/*
 source = nf_core
 relative_files = True
 

From d376adea1e18e87b3f181138bf565c81b1867664 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 14 Dec 2023 18:02:55 +0100
Subject: [PATCH 069/117] try different coverage_config path

---
 .github/workflows/pytest.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index c31082722c..83519a8e36 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -128,7 +128,7 @@ jobs:
 
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-config=.github/.coveragerc --durations=0 && exit_code=0 || exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-config=./.github/.coveragerc --durations=0 && exit_code=0 || exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"
@@ -141,8 +141,8 @@ jobs:
       - name: Upload coverage
         uses: actions/upload-artifact@v3
         with:
-          name: coverage${{ matrix.test }}
-          path: .coverage
+          name: coverage_${{ matrix.test }}
+          path: coverage
 
       - name: Cleanup work directory
         run: rm -rf work || true
@@ -186,5 +186,6 @@ jobs:
 
       - uses: codecov/codecov-action@v3
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
           file: coverage.xml
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

From 704e348fc21ba2aa88144b531c694f39f65189c5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 14 Dec 2023 19:09:37 +0100
Subject: [PATCH 070/117] fix coverage artifact upload

---
 .github/workflows/pytest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 83519a8e36..cd7e05cd66 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -139,10 +139,10 @@ jobs:
           fi
 
       - name: Upload coverage
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage_${{ matrix.test }}
-          path: coverage
+          path: .coverage
 
       - name: Cleanup work directory
         run: rm -rf work || true

From e2b846e8d22a822d5d53ed79526f9fccae6ed46f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 14 Dec 2023 19:11:07 +0100
Subject: [PATCH 071/117] upgrade artifact download

---
 .github/workflows/pytest.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index cd7e05cd66..9953b9ad8c 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -166,8 +166,7 @@ jobs:
           pip install -e .
 
       - name: Download all artifacts
-        # Downloads coverage1, coverage2, etc.
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
 
       # - name: Setup ssh session
       #   uses: Warpbuilds/action-debugger@v1.3

From 4fa2825db8a5990cc61c9e042baa4d21746dc308 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 14 Dec 2023 20:32:01 +0100
Subject: [PATCH 072/117] run coverage step explicetly

---
 .github/workflows/pytest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 9953b9ad8c..6cb3ecb363 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -137,6 +137,8 @@ jobs:
             echo "Tests failed with exit code ${exit_code}"
             exit 1
           fi
+      - name: Report coverage
+        run: coverage report
 
       - name: Upload coverage
         uses: actions/upload-artifact@v4
@@ -173,8 +175,6 @@ jobs:
 
       - name: Run coverage
         run: |
-          echo "Which nf-core: $(which nf-core)"
-          echo "Which python: $(which python)"
           rm -f .coverage
           coverage combine coverage*/.coverage*
           coverage report --debug=coverage

From 2ab397402fba31d74cafab8f1eacf2a566a9022c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 14 Dec 2023 20:43:56 +0100
Subject: [PATCH 073/117] change location of coverage config

---
 .github/workflows/pytest.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 6cb3ecb363..d312354b27 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -122,13 +122,14 @@ jobs:
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
 
-      - name: export workdir
+      - name: export workdir & move coveragerc file up
         run: |
           export NXF_WORK=$(pwd)
+          mv .github/.coveragerc .
 
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-config=./.github/.coveragerc --durations=0 && exit_code=0 || exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0 || exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"

From 2031d069d6f480683e1b24954744ed349c6580ea Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 15 Dec 2023 07:29:49 +0100
Subject: [PATCH 074/117] add ssh debugger

---
 .github/workflows/pytest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index d312354b27..2d4dcd7c05 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -171,8 +171,8 @@ jobs:
       - name: Download all artifacts
         uses: actions/download-artifact@v4
 
-      # - name: Setup ssh session
-      #   uses: Warpbuilds/action-debugger@v1.3
+      - name: Setup ssh session
+        uses: Warpbuilds/action-debugger@v1.3
 
       - name: Run coverage
         run: |

From 3d2009d06edeec4648a0a32acc23049894b7c5d7 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 15 Dec 2023 09:41:03 +0100
Subject: [PATCH 075/117] use old version of artifact upload

---
 .github/workflows/pytest.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 2d4dcd7c05..4373873eba 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -142,7 +142,7 @@ jobs:
         run: coverage report
 
       - name: Upload coverage
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v3
         with:
           name: coverage_${{ matrix.test }}
           path: .coverage
@@ -156,7 +156,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.9
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
@@ -169,14 +169,13 @@ jobs:
           pip install -e .
 
       - name: Download all artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v3
 
       - name: Setup ssh session
         uses: Warpbuilds/action-debugger@v1.3
 
       - name: Run coverage
         run: |
-          rm -f .coverage
           coverage combine coverage*/.coverage*
           coverage report --debug=coverage
           coverage xml

From 2bbb40a9d2986b2598946fa0d2cf7329599cfbc0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 15 Dec 2023 13:50:04 +0100
Subject: [PATCH 076/117] debug artifact upload

---
 .github/workflows/pytest.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 4373873eba..c48bc74a3f 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -139,7 +139,9 @@ jobs:
             exit 1
           fi
       - name: Report coverage
-        run: coverage report
+        run: |
+          ls -la
+          coverage report --data-file=.coverage
 
       - name: Upload coverage
         uses: actions/upload-artifact@v3
@@ -171,8 +173,8 @@ jobs:
       - name: Download all artifacts
         uses: actions/download-artifact@v3
 
-      - name: Setup ssh session
-        uses: Warpbuilds/action-debugger@v1.3
+      # - name: Setup ssh session
+      #   uses: Warpbuilds/action-debugger@v1.3
 
       - name: Run coverage
         run: |

From fbb50f346cf6606073e4d6c93d35a0377b497217 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Mon, 18 Dec 2023 12:51:12 +0000
Subject: [PATCH 077/117] use files codecov-action argument

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index c48bc74a3f..1e177f10d5 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -187,6 +187,6 @@ jobs:
 
       - uses: codecov/codecov-action@v3
         with:
-          file: coverage.xml
+          files: coverage.xml
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

From b831fb6d81136d2f1dc2f3feb039e778d3f2ec33 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 20 Dec 2023 13:27:49 +0100
Subject: [PATCH 078/117] debug coverage

---
 .github/workflows/pytest.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index d1a6b6db4a..f2c4263158 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -173,13 +173,13 @@ jobs:
       - name: Download all artifacts
         uses: actions/download-artifact@v3
 
-      # - name: Setup ssh session
-      #   uses: Warpbuilds/action-debugger@v1.3
+      - name: Setup ssh session
+        uses: Warpbuilds/action-debugger@v1.3
 
       - name: Run coverage
         run: |
           coverage combine coverage*/.coverage*
-          coverage report --debug=coverage
+          coverage report
           coverage xml
 
       - name: show directory

From 76517c1b3636bfa35af2cd222667bd82217a2bf7 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 10:02:04 +0100
Subject: [PATCH 079/117] update action versions

---
 .github/workflows/create-lint-wf.yml                      | 2 +-
 .github/workflows/create-test-lint-wf-template.yml        | 2 +-
 .github/workflows/create-test-wf.yml                      | 2 +-
 .github/workflows/deploy-pypi.yml                         | 2 +-
 .github/workflows/fix-linting.yml                         | 2 +-
 .github/workflows/lint-code.yml                           | 4 ++--
 .github/workflows/pytest.yml                              | 8 ++++----
 .github/workflows/rich-codex.yml                          | 2 +-
 .github/workflows/sync.yml                                | 2 +-
 .github/workflows/tools-api-docs-dev.yml                  | 2 +-
 .github/workflows/tools-api-docs-release.yml              | 2 +-
 nf_core/pipeline-template/.github/workflows/linting.yml   | 2 +-
 .../.github/workflows/release-announcements.yml           | 2 +-
 13 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 9ddaf4b4c9..973351e2f6 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -38,7 +38,7 @@ jobs:
 
       # Set up nf-core/tools
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 941f6a71d0..cb754a62be 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -43,7 +43,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 1080bba22e..603113d080 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -36,7 +36,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
index 62c53508d8..8d3a154d80 100644
--- a/.github/workflows/deploy-pypi.yml
+++ b/.github/workflows/deploy-pypi.yml
@@ -17,7 +17,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index bf23022c56..d0edee0903 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -41,7 +41,7 @@ jobs:
           options: "--color"
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
       - name: python-isort
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 6bb0a2481f..6462407840 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -83,7 +83,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
       - name: python-isort
@@ -96,7 +96,7 @@ jobs:
     runs-on: ["self-hosted"]
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.11
           cache: "pip"
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index f2c4263158..666a3767cd 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -80,7 +80,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
@@ -144,7 +144,7 @@ jobs:
           coverage report --data-file=.coverage
 
       - name: Upload coverage
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage_${{ matrix.test }}
           path: .coverage
@@ -159,7 +159,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.12
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
@@ -171,7 +171,7 @@ jobs:
           pip install -e .
 
       - name: Download all artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
 
       - name: Setup ssh session
         uses: Warpbuilds/action-debugger@v1.3
diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml
index 8368255390..b3e154c6dd 100644
--- a/.github/workflows/rich-codex.yml
+++ b/.github/workflows/rich-codex.yml
@@ -8,7 +8,7 @@ jobs:
       - name: Check out the repo
         uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.x
           cache: pip
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 789e4410a0..1fcbef89b8 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -49,7 +49,7 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
diff --git a/.github/workflows/tools-api-docs-dev.yml b/.github/workflows/tools-api-docs-dev.yml
index 89720fb137..80d3b9365f 100644
--- a/.github/workflows/tools-api-docs-dev.yml
+++ b/.github/workflows/tools-api-docs-dev.yml
@@ -27,7 +27,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
diff --git a/.github/workflows/tools-api-docs-release.yml b/.github/workflows/tools-api-docs-release.yml
index b0869190d9..3233e00ca9 100644
--- a/.github/workflows/tools-api-docs-release.yml
+++ b/.github/workflows/tools-api-docs-release.yml
@@ -22,7 +22,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 94aa5278be..806e23b332 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -76,7 +76,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
           architecture: "x64"
diff --git a/nf_core/pipeline-template/.github/workflows/release-announcements.yml b/nf_core/pipeline-template/.github/workflows/release-announcements.yml
index ad497db4e1..a0dd5a03cf 100644
--- a/nf_core/pipeline-template/.github/workflows/release-announcements.yml
+++ b/nf_core/pipeline-template/.github/workflows/release-announcements.yml
@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Install dependencies

From 8e52118a5de799b112f12dee41d402de49a20e33 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 10:17:13 +0100
Subject: [PATCH 080/117] fix cleanup step

---
 .github/workflows/create-lint-wf.yml               | 2 +-
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 .github/workflows/create-test-wf.yml               | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 973351e2f6..ccab2af6d4 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -154,5 +154,5 @@ jobs:
           path: create-lint-wf/log.txt
 
       - name: Cleanup work directory
-        run: rm -rf work || true
+        run: rm -rf create-lint-wf || true
         if: always()
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index cb754a62be..8e726a4e25 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -157,5 +157,5 @@ jobs:
           path: create-test-lint-wf/artifact_files.tar
 
       - name: Cleanup work directory
-        run: rm -rf work || true
+        run: rm -rf create-test-lint-wf || true
         if: always()
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 603113d080..86e8711fb2 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -66,5 +66,5 @@ jobs:
 
       - name: Cleanup work directory
         # cleanup and fail gracefully if I get a permission error
-        run: rm -rf work || true
+        run: rm -rf create-test-wf || true
         if: always()

From e389c8c80d2675170abd5cc9559d7de5028be47a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 10:17:29 +0100
Subject: [PATCH 081/117] run small jobs still on github

---
 .github/workflows/pytest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 666a3767cd..a529a0a65c 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -26,7 +26,7 @@ env:
 
 jobs:
   setup:
-    runs-on: ["self-hosted"]
+    runs-on: "ubuntu-latest"
     strategy:
       matrix:
         python-version: ["3.8", "3.11"]
@@ -48,7 +48,7 @@ jobs:
   # create a test matrix based on all python files in /tests
   list_tests:
     name: Get test file matrix
-    runs-on: "self-hosted"
+    runs-on: "ubuntu-latest"
     steps:
       - uses: actions/checkout@v4
         name: Check out source-code repository

From 7eb8d0bc920e921f6da398deb46c02cd142dd631 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 10:25:44 +0100
Subject: [PATCH 082/117] switch to pre-commit for code linting

---
 .github/workflows/lint-code.yml | 111 ++------------------------------
 .pre-commit-config.yaml         |   2 +-
 2 files changed, 7 insertions(+), 106 deletions(-)

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 6462407840..1bd042a6b7 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -14,120 +14,21 @@ concurrency:
 
 jobs:
   EditorConfig:
-    runs-on: ["self-hosted"]
+    runs-on: ubuntu-latest
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      # Run editor config check only on files not covered by a linter
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile')
-
-  Prettier:
-    runs-on: ["self-hosted"]
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  PythonBlack:
-    runs-on: ["self-hosted"]
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Check code lints with Black
-        uses: psf/black@stable
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
-        with:
-          message: |
-            ## Python linting (`black`) is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
-            * Fix formatting errors in your pipeline: `black .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
-
-            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
-
-  isort:
-    runs-on: ["self-hosted"]
-    steps:
-      - name: Check out source-code repository
-        uses: actions/checkout@v4
-
       - name: Set up Python 3.11
         uses: actions/setup-python@v5
-        with:
-          python-version: 3.11
-      - name: python-isort
-        uses: isort/isort-action@v1.1.0
-        with:
-          isortVersion: "latest"
-          requirementsFiles: "requirements.txt requirements-dev.txt"
-
-  static-type-check:
-    runs-on: ["self-hosted"]
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
         with:
           python-version: 3.11
           cache: "pip"
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip -r requirements-dev.txt
-          pip install -e .
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      - name: Cache nf-test installation
-        id: cache-software
-        uses: actions/cache@v3
-        with:
-          path: |
-            /usr/local/bin/nf-test
-            /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
-
-      - name: Install nf-test
-        if: steps.cache-software.outputs.cache-hit != 'true'
-        run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash
-          sudo mv nf-test /usr/local/bin/
-
-      - name: Get Python changed files
-        id: changed-py-files
-        uses: tj-actions/changed-files@v23
-        with:
-          files: |
-            *.py
-            **/*.py
-      - name: Run if any of the listed files above is changed
-        if: steps.changed-py-files.outputs.any_changed == 'true'
-        run: mypy ${{ steps.changed-py-files.outputs.all_changed_files }}
+      - name: Run pre-commit
+        id: prettier_status
+        run: pre-commit run --all-files
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ad23a3c895..31c31800f4 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -17,7 +17,7 @@ repos:
       - id: pyupgrade
         args: [--py38-plus]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.7.1" # Use the sha / tag you want to point at
+    rev: "v1.8.0"
     hooks:
       - id: mypy
         additional_dependencies:

From 5b283d96847dc483054826a18e93effdb977a3dc Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 10:29:37 +0100
Subject: [PATCH 083/117] don't run pyupgrade for now

---
 .pre-commit-config.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 31c31800f4..5833865b62 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,11 +11,11 @@ repos:
     rev: "v2.7.1"
     hooks:
       - id: prettier
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
-    hooks:
-      - id: pyupgrade
-        args: [--py38-plus]
+  # - repo: https://github.com/asottile/pyupgrade
+  #   rev: v3.15.0
+  #   hooks:
+  #     - id: pyupgrade
+  #       args: [--py38-plus]
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: "v1.8.0"
     hooks:

From b6996518199244ea020d9be2b1796df427eb792c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 10:30:43 +0100
Subject: [PATCH 084/117] fix job name

---
 .github/workflows/lint-code.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 1bd042a6b7..b002a705f5 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -13,7 +13,7 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  EditorConfig:
+  Pre-commit:
     runs-on: ubuntu-latest
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

From e5b0f4d53cffb222039efc93ac7dc516d14bce9b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 12:55:58 +0100
Subject: [PATCH 085/117] debugging

---
 .github/workflows/pytest.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index a529a0a65c..a7e5b6a827 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -173,6 +173,7 @@ jobs:
       - name: Download all artifacts
         uses: actions/download-artifact@v4
 
+      #debugging
       - name: Setup ssh session
         uses: Warpbuilds/action-debugger@v1.3
 

From ce1bd2f1143d85306841842aa2baf455b954bf9b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 13:01:05 +0100
Subject: [PATCH 086/117] keep coverage files

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index a7e5b6a827..5d100cfede 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -179,7 +179,7 @@ jobs:
 
       - name: Run coverage
         run: |
-          coverage combine coverage*/.coverage*
+          coverage combine coverage*/.coverage* --keep
           coverage report
           coverage xml
 

From 3b21894923ef9d406521a54f36f194bb5993e532 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 13:47:16 +0100
Subject: [PATCH 087/117] test better cleanup

---
 .github/workflows/create-lint-wf.yml               | 2 +-
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 .github/workflows/create-test-wf.yml               | 2 +-
 .github/workflows/pytest.yml                       | 4 ----
 4 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index ccab2af6d4..1c9c458300 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -154,5 +154,5 @@ jobs:
           path: create-lint-wf/log.txt
 
       - name: Cleanup work directory
-        run: rm -rf create-lint-wf || true
+        run: rm -rf create-lint-wf
         if: always()
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 8e726a4e25..d650b7fa9d 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -157,5 +157,5 @@ jobs:
           path: create-test-lint-wf/artifact_files.tar
 
       - name: Cleanup work directory
-        run: rm -rf create-test-lint-wf || true
+        run: rm -rf create-test-lint-wf
         if: always()
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 86e8711fb2..8cd00e9407 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -66,5 +66,5 @@ jobs:
 
       - name: Cleanup work directory
         # cleanup and fail gracefully if I get a permission error
-        run: rm -rf create-test-wf || true
+        run: rm -rf create-test-wf
         if: always()
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 5d100cfede..3a35c6a215 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -149,10 +149,6 @@ jobs:
           name: coverage_${{ matrix.test }}
           path: .coverage
 
-      - name: Cleanup work directory
-        run: rm -rf work || true
-        if: always()
-
   coverage:
     needs: test
     runs-on: ubuntu-latest

From 0ba7f4927cda289278629665f2f64d2420752472 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 14:18:06 +0100
Subject: [PATCH 088/117] fix parameter position

---
 .github/workflows/pytest.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 3a35c6a215..8891a0cebd 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -154,12 +154,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.12
+      - name: Set up Python 3.11
         uses: actions/setup-python@v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
-          python-version: 3.12
+          python-version: 3.11
+          cache: "pip"
 
       - name: Install deps
         run: |
@@ -175,7 +176,7 @@ jobs:
 
       - name: Run coverage
         run: |
-          coverage combine coverage*/.coverage* --keep
+          coverage combine --keep coverage*/.coverage*
           coverage report
           coverage xml
 

From 10da34dcdeeb0b51ac5b35fdc1be10916e04c2f5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 14:19:35 +0100
Subject: [PATCH 089/117] add cleanup step to nextflow steps

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 .github/workflows/create-test-wf.yml               | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index d650b7fa9d..24a77143c3 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -101,7 +101,7 @@ jobs:
       - name: run the pipeline
         run: |
           cd create-test-lint-wf
-          nextflow run my-prefix-testpipeline -profile test,self_hosted_runner --outdir ./results
+          nextflow run my-prefix-testpipeline -profile test,self_hosted_runner --outdir ./results -cleanup
 
       # Remove results folder before linting
       - name: remove results folder
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 8cd00e9407..f15e9ff5d8 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -55,7 +55,7 @@ jobs:
           mkdir create-test-wf && cd create-test-wf
           export NXF_WORK=$(pwd)
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
-          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
+          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results -cleanup
 
       - name: Upload log file artifact
         if: ${{ always() }}
@@ -65,6 +65,6 @@ jobs:
           path: create-test-wf/log.txt
 
       - name: Cleanup work directory
-        # cleanup and fail gracefully if I get a permission error
+        # cleanup work directory
         run: rm -rf create-test-wf
         if: always()

From 3b2e86a59adff9e4621b8bd3494c3ee6f124b87e Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 14:28:11 +0100
Subject: [PATCH 090/117] use nextflow clean

---
 .github/workflows/create-test-lint-wf-template.yml | 3 ++-
 .github/workflows/create-test-wf.yml               | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 24a77143c3..5b36a2abee 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -101,7 +101,8 @@ jobs:
       - name: run the pipeline
         run: |
           cd create-test-lint-wf
-          nextflow run my-prefix-testpipeline -profile test,self_hosted_runner --outdir ./results -cleanup
+          nextflow run my-prefix-testpipeline -profile test,self_hosted_runner --outdir ./results
+          nextflow clean -f
 
       # Remove results folder before linting
       - name: remove results folder
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index f15e9ff5d8..65df0014b3 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -55,7 +55,8 @@ jobs:
           mkdir create-test-wf && cd create-test-wf
           export NXF_WORK=$(pwd)
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
-          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results -cleanup
+          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
+          nextflow clean -f
 
       - name: Upload log file artifact
         if: ${{ always() }}

From 0f446f658f1ab5b9a0107f4717be8a074c8e2da0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 14:39:52 +0100
Subject: [PATCH 091/117] remove ssh step

---
 .github/workflows/pytest.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 8891a0cebd..4105f6ae44 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -170,9 +170,9 @@ jobs:
       - name: Download all artifacts
         uses: actions/download-artifact@v4
 
-      #debugging
-      - name: Setup ssh session
-        uses: Warpbuilds/action-debugger@v1.3
+      # #debugging
+      # - name: Setup ssh session
+      #   uses: Warpbuilds/action-debugger@v1.3
 
       - name: Run coverage
         run: |

From e2137b633e2d03d68d12219e3f83e4af2dd32921 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 16:09:51 +0100
Subject: [PATCH 092/117] test cirun.io

---
 .cirun.yml                   | 15 +++++++++++++++
 .github/workflows/pytest.yml |  2 +-
 2 files changed, 16 insertions(+), 1 deletion(-)
 create mode 100644 .cirun.yml

diff --git a/.cirun.yml b/.cirun.yml
new file mode 100644
index 0000000000..4b408b1d99
--- /dev/null
+++ b/.cirun.yml
@@ -0,0 +1,15 @@
+# Self-Hosted Github Action Runners on AWS via Cirun.io
+# Reference: https://docs.cirun.io/reference/yaml
+runners:
+  - name: "aws-runner"
+    # Cloud Provider: AWS
+    cloud: "aws"
+    instance_type: "t3a.large"
+    # Ubuntu-20.4, ami image
+    machine_image: "ami-0905a3c97561e0b69"
+    preemptible: false
+    region: "eu-west-1"
+    # Add this label in the "runs-on" param in .github/workflows/<workflow-name>.yml
+    # So that this runner is created for running the workflow
+    labels:
+      - "cirun-aws-runner"
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 4105f6ae44..f10b6fadca 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -64,7 +64,7 @@ jobs:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: [setup, list_tests]
     if: ${{ needs.setup.outputs.run-tests }}
-    runs-on: self-hosted
+    runs-on: cirun-aws-runner
     strategy:
       matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
       fail-fast: false # run all tests even if one fails

From b72914187bf29e2e9ceccf0c9d48894d22a7f8b2 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 16:22:57 +0100
Subject: [PATCH 093/117] don't set AGENT_TOOLSDIRECTORY

---
 .github/workflows/pytest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index f10b6fadca..0481dfd962 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -81,8 +81,8 @@ jobs:
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
         uses: actions/setup-python@v5
-        env:
-          AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
+        # env:
+        #   AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"

From a37f0e46d52113d7fc368d663cd1ab6afe549622 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 16:29:28 +0100
Subject: [PATCH 094/117] add java setup step

---
 .github/workflows/pytest.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 0481dfd962..1a2b7cacc9 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -104,6 +104,12 @@ jobs:
         id: date
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
 
+      - name: Install Java
+        uses: actions/setup-java@v4
+        with:
+          distribution: "temurin" # See 'Supported distributions' for available options
+          java-version: "21"
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 

From af55c3483dafc4b490e3b44a2978be66d8f2bb1a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 19:14:26 +0100
Subject: [PATCH 095/117] use general gitlab branch

---
 .cirun.yml     | 2 +-
 tests/utils.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.cirun.yml b/.cirun.yml
index 4b408b1d99..7a4f9726d0 100644
--- a/.cirun.yml
+++ b/.cirun.yml
@@ -6,7 +6,7 @@ runners:
     cloud: "aws"
     instance_type: "t3a.large"
     # Ubuntu-20.4, ami image
-    machine_image: "ami-0905a3c97561e0b69"
+    machine_image: "ami-for-eu-west-1"
     preemptible: false
     region: "eu-west-1"
     # Add this label in the "runs-on" param in .github/workflows/<workflow-name>.yml
diff --git a/tests/utils.py b/tests/utils.py
index 148912fe64..198ac3d583 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -27,7 +27,7 @@
 GITLAB_BRANCH_ORG_PATH_BRANCH = "org-path"
 GITLAB_BRANCH_TEST_OLD_SHA = "e772abc22c1ff26afdf377845c323172fb3c19ca"
 GITLAB_BRANCH_TEST_NEW_SHA = "7d73e21f30041297ea44367f2b4fd4e045c0b991"
-GITLAB_NFTEST_BRANCH = "nf-test-tests-self-hosted-runners"
+GITLAB_NFTEST_BRANCH = "nf-test-tests"
 
 
 def with_temporary_folder(func: Callable[..., Any]) -> Callable[..., Any]:

From 2c9e44386ef573c1f0c1666a62ac8a9e884e73aa Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 2 Jan 2024 19:20:05 +0100
Subject: [PATCH 096/117] change image id back

---
 .cirun.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.cirun.yml b/.cirun.yml
index 7a4f9726d0..4b408b1d99 100644
--- a/.cirun.yml
+++ b/.cirun.yml
@@ -6,7 +6,7 @@ runners:
     cloud: "aws"
     instance_type: "t3a.large"
     # Ubuntu-20.4, ami image
-    machine_image: "ami-for-eu-west-1"
+    machine_image: "ami-0905a3c97561e0b69"
     preemptible: false
     region: "eu-west-1"
     # Add this label in the "runs-on" param in .github/workflows/<workflow-name>.yml

From 18090fffd295d46845b26641e2bf2d52d42b68f2 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 4 Jan 2024 11:29:36 +0100
Subject: [PATCH 097/117] debug cleanup step

---
 .github/workflows/create-test-lint-wf-template.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 5b36a2abee..2b39d055b3 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -157,6 +157,10 @@ jobs:
           name: nf-core-log-file
           path: create-test-lint-wf/artifact_files.tar
 
+      #debugging
+      - name: Setup ssh session
+        uses: Warpbuilds/action-debugger@v1.3
+
       - name: Cleanup work directory
         run: rm -rf create-test-lint-wf
         if: always()

From 32dcbf3c3a938e927f74bc506e809a6c1ae9fbf1 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 4 Jan 2024 12:04:04 +0100
Subject: [PATCH 098/117] use sudo rm

---
 .github/workflows/create-lint-wf.yml               | 2 +-
 .github/workflows/create-test-lint-wf-template.yml | 6 +-----
 .github/workflows/create-test-wf.yml               | 2 +-
 3 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 1d00eaedbf..cfd36385ea 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -163,5 +163,5 @@ jobs:
           path: create-lint-wf/log.txt
 
       - name: Cleanup work directory
-        run: rm -rf create-lint-wf
+        run: sudo rm -rf create-lint-wf
         if: always()
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 2b39d055b3..94cd4d8663 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -157,10 +157,6 @@ jobs:
           name: nf-core-log-file
           path: create-test-lint-wf/artifact_files.tar
 
-      #debugging
-      - name: Setup ssh session
-        uses: Warpbuilds/action-debugger@v1.3
-
       - name: Cleanup work directory
-        run: rm -rf create-test-lint-wf
+        run: sudo rm -rf create-test-lint-wf
         if: always()
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 65df0014b3..de06df5817 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -67,5 +67,5 @@ jobs:
 
       - name: Cleanup work directory
         # cleanup work directory
-        run: rm -rf create-test-wf
+        run: sudo rm -rf create-test-wf
         if: always()

From e81b6584a3c63094adf316a4ff192034b7e75a9c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 4 Jan 2024 12:50:59 +0100
Subject: [PATCH 099/117] run everything on our own runners again

---
 .github/workflows/pytest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 1a2b7cacc9..922ce4d74d 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -64,7 +64,7 @@ jobs:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: [setup, list_tests]
     if: ${{ needs.setup.outputs.run-tests }}
-    runs-on: cirun-aws-runner
+    runs-on: self-hosted
     strategy:
       matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
       fail-fast: false # run all tests even if one fails
@@ -157,7 +157,7 @@ jobs:
 
   coverage:
     needs: test
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.11

From 1cffa1eeb7c1be8eb66001ee55046f3cc68517e6 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 4 Jan 2024 12:59:27 +0100
Subject: [PATCH 100/117] use correct gitlab branch

---
 tests/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/utils.py b/tests/utils.py
index 44386759ed..89c1328818 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -25,7 +25,7 @@
 GITLAB_BRANCH_ORG_PATH_BRANCH = "org-path"
 GITLAB_BRANCH_TEST_OLD_SHA = "e772abc22c1ff26afdf377845c323172fb3c19ca"
 GITLAB_BRANCH_TEST_NEW_SHA = "7d73e21f30041297ea44367f2b4fd4e045c0b991"
-GITLAB_NFTEST_BRANCH = "nf-test-tests"
+GITLAB_NFTEST_BRANCH = "nf-test-tests-self-hosted-runners"
 
 
 def with_temporary_folder(func: Callable[..., Any]) -> Callable[..., Any]:

From f7fe4f0e710e2f1d1bebde6705bb177c7e95b152 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 4 Jan 2024 14:28:24 +0100
Subject: [PATCH 101/117] use java from runners

---
 .github/workflows/pytest.yml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 922ce4d74d..24888264cb 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -104,12 +104,6 @@ jobs:
         id: date
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
 
-      - name: Install Java
-        uses: actions/setup-java@v4
-        with:
-          distribution: "temurin" # See 'Supported distributions' for available options
-          java-version: "21"
-
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 

From 29534655ebc3bc3981bf161ac3977979cc9b83c0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 4 Jan 2024 14:55:40 +0100
Subject: [PATCH 102/117] test coverage for one file

---
 .github/workflows/pytest.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 24888264cb..95b61c84a6 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -165,7 +165,6 @@ jobs:
       - name: Install deps
         run: |
           python -m pip install --upgrade pip -r requirements-dev.txt
-          pip install -e .
 
       - name: Download all artifacts
         uses: actions/download-artifact@v4
@@ -173,7 +172,9 @@ jobs:
       # #debugging
       # - name: Setup ssh session
       #   uses: Warpbuilds/action-debugger@v1.3
-
+      - name: Run coverage on one file
+        run: |
+          coverage report --data-file=coverage_test_components.py/.coverage
       - name: Run coverage
         run: |
           coverage combine --keep coverage*/.coverage*

From 418e9788bd6053bf64b1d66c23d526e72cd419d8 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 4 Jan 2024 15:49:25 +0100
Subject: [PATCH 103/117] run individual test also parallel

---
 .github/workflows/pytest.yml | 2 +-
 requirements-dev.txt         | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 95b61c84a6..64ab685cd9 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -129,7 +129,7 @@ jobs:
 
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0 || exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 -n auto  && exit_code=0|| exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 6d890f0e1f..dc3bf4f47d 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,6 +1,7 @@
 myst_parser
 pytest-cov
 pytest-datafiles
+pytest-xdist
 responses
 Sphinx
 sphinx-rtd-theme

From e822600b66109c640b5da377b2e93536c5c6786f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 4 Jan 2024 15:51:37 +0100
Subject: [PATCH 104/117] add github token to setup-python

---
 .github/workflows/pytest.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 64ab685cd9..9b71127d0a 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -81,11 +81,10 @@ jobs:
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
         uses: actions/setup-python@v5
-        # env:
-        #   AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
+          token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Install dependencies
         run: |

From 3f5310d8a1b0896ef2c2991fffc1efe525cc6f1b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 4 Jan 2024 16:49:49 +0100
Subject: [PATCH 105/117] use same directory structure for coverage

---
 .github/workflows/pytest.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 9b71127d0a..0b68e3aee2 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -128,7 +128,7 @@ jobs:
 
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 -n auto  && exit_code=0|| exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 -n 2  && exit_code=0|| exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"
@@ -152,6 +152,11 @@ jobs:
     needs: test
     runs-on: self-hosted
     steps:
+      - name: go to subdirectory
+        run: |
+          mkdir -p pytest
+          cd pytest
+
       - uses: actions/checkout@v4
       - name: Set up Python 3.11
         uses: actions/setup-python@v5

From 71c4901b95b95fe51e0fc3fb2b0ee8f657eb2d62 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 4 Jan 2024 17:04:36 +0100
Subject: [PATCH 106/117] don't ran everything parallel

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 0b68e3aee2..db8f2e4da1 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -128,7 +128,7 @@ jobs:
 
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 -n 2  && exit_code=0|| exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"

From ecb21e48b02abaa67a463d5c92213a489055df93 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 08:44:23 +0100
Subject: [PATCH 107/117] move coveragerc

---
 .github/workflows/pytest.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index db8f2e4da1..de4dcf5677 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -166,9 +166,14 @@ jobs:
           python-version: 3.11
           cache: "pip"
 
-      - name: Install deps
+      - name: Install dependencies
         run: |
           python -m pip install --upgrade pip -r requirements-dev.txt
+          pip install -e .
+
+      - name: move coveragerc file up
+        run: |
+          mv .github/.coveragerc .
 
       - name: Download all artifacts
         uses: actions/download-artifact@v4

From 161412996b9afa0231ffb03a93d7ff7db4455c86 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 09:15:40 +0100
Subject: [PATCH 108/117] remove debugging code

---
 .github/workflows/pytest.yml | 18 +-----------------
 1 file changed, 1 insertion(+), 17 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index de4dcf5677..e37c8c00ff 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -74,7 +74,6 @@ jobs:
           mkdir -p pytest
           cd pytest
           export NXF_WORK=$(pwd)
-          echo $"which python: $(which python)"
 
       - uses: actions/checkout@v4
         name: Check out source-code repository
@@ -121,9 +120,8 @@ jobs:
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
 
-      - name: export workdir & move coveragerc file up
+      - name: move coveragerc file up
         run: |
-          export NXF_WORK=$(pwd)
           mv .github/.coveragerc .
 
       - name: Test with pytest
@@ -137,10 +135,6 @@ jobs:
             echo "Tests failed with exit code ${exit_code}"
             exit 1
           fi
-      - name: Report coverage
-        run: |
-          ls -la
-          coverage report --data-file=.coverage
 
       - name: Upload coverage
         uses: actions/upload-artifact@v4
@@ -177,22 +171,12 @@ jobs:
 
       - name: Download all artifacts
         uses: actions/download-artifact@v4
-
-      # #debugging
-      # - name: Setup ssh session
-      #   uses: Warpbuilds/action-debugger@v1.3
-      - name: Run coverage on one file
-        run: |
-          coverage report --data-file=coverage_test_components.py/.coverage
       - name: Run coverage
         run: |
           coverage combine --keep coverage*/.coverage*
           coverage report
           coverage xml
 
-      - name: show directory
-        run: ls -la
-
       - uses: codecov/codecov-action@v3
         with:
           files: coverage.xml

From bcaef36b44b21107226854b65bea1c3dbc304893 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 09:19:26 +0100
Subject: [PATCH 109/117] run some template variations on github

---
 .github/workflows/create-test-lint-wf-template.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 94cd4d8663..4e1997d22d 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -31,6 +31,12 @@ jobs:
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
           # - "template_skip_nf_core_configs.yml"
+        runner: ["self-hosted"]
+        include:
+          - TEMPLATE: "template_skip_all.yml"
+            runner: ubuntu-latest
+          - TEMPLATE: "template_skip_nf_core_configs.yml"
+            runner: ubuntu-latest
 
     steps:
       - name: go to working directory

From 2f0698cb442aa17f027296fc75bad8bedf0ff590 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 09:21:55 +0100
Subject: [PATCH 110/117] remove more left over code

---
 .cirun.yml                                        | 15 ---------------
 .../workflows/create-test-lint-wf-template.yml    |  3 ---
 .github/workflows/create-test-wf.yml              |  1 -
 requirements-dev.txt                              |  1 -
 4 files changed, 20 deletions(-)
 delete mode 100644 .cirun.yml

diff --git a/.cirun.yml b/.cirun.yml
deleted file mode 100644
index 4b408b1d99..0000000000
--- a/.cirun.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-# Self-Hosted Github Action Runners on AWS via Cirun.io
-# Reference: https://docs.cirun.io/reference/yaml
-runners:
-  - name: "aws-runner"
-    # Cloud Provider: AWS
-    cloud: "aws"
-    instance_type: "t3a.large"
-    # Ubuntu-20.4, ami image
-    machine_image: "ami-0905a3c97561e0b69"
-    preemptible: false
-    region: "eu-west-1"
-    # Add this label in the "runs-on" param in .github/workflows/<workflow-name>.yml
-    # So that this runner is created for running the workflow
-    labels:
-      - "cirun-aws-runner"
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 4e1997d22d..af8d306271 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -26,11 +26,9 @@ jobs:
     strategy:
       matrix:
         TEMPLATE:
-          # - "template_skip_all.yml"
           - "template_skip_github_badges.yml"
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
-          # - "template_skip_nf_core_configs.yml"
         runner: ["self-hosted"]
         include:
           - TEMPLATE: "template_skip_all.yml"
@@ -108,7 +106,6 @@ jobs:
         run: |
           cd create-test-lint-wf
           nextflow run my-prefix-testpipeline -profile test,self_hosted_runner --outdir ./results
-          nextflow clean -f
 
       # Remove results folder before linting
       - name: remove results folder
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index de06df5817..c5f35b4d7b 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -56,7 +56,6 @@ jobs:
           export NXF_WORK=$(pwd)
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
           nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
-          nextflow clean -f
 
       - name: Upload log file artifact
         if: ${{ always() }}
diff --git a/requirements-dev.txt b/requirements-dev.txt
index dc3bf4f47d..6d890f0e1f 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,7 +1,6 @@
 myst_parser
 pytest-cov
 pytest-datafiles
-pytest-xdist
 responses
 Sphinx
 sphinx-rtd-theme

From b4d3367d270f47d60be35e79cc7ece39c7a904b3 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 09:24:11 +0100
Subject: [PATCH 111/117] set correct runner

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index af8d306271..3fa81671ff 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -20,7 +20,7 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: self-hosted
+    runs-on: ${{ matrix.runner }}
     env:
       NXF_ANSI_LOG: false
     strategy:

From b00ec697999f19b1b8ee2d81b4d352e90caff9e6 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 09:27:29 +0100
Subject: [PATCH 112/117] set profile depending on runner

---
 .github/workflows/create-test-lint-wf-template.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 3fa81671ff..f8eb3e1e20 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -30,11 +30,14 @@ jobs:
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
         runner: ["self-hosted"]
+        profile: [",self_hosted_runner"]
         include:
           - TEMPLATE: "template_skip_all.yml"
             runner: ubuntu-latest
+            profile: ""
           - TEMPLATE: "template_skip_nf_core_configs.yml"
             runner: ubuntu-latest
+            profile: ""
 
     steps:
       - name: go to working directory
@@ -105,7 +108,7 @@ jobs:
       - name: run the pipeline
         run: |
           cd create-test-lint-wf
-          nextflow run my-prefix-testpipeline -profile test,self_hosted_runner --outdir ./results
+          nextflow run my-prefix-testpipeline -profile test${{matrix.profile}} --outdir ./results
 
       # Remove results folder before linting
       - name: remove results folder

From 2735ee883f72becc74ac848f751070670f9c4ce1 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 09:30:03 +0100
Subject: [PATCH 113/117] set profile docker for github runners

---
 .github/workflows/create-test-lint-wf-template.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index f8eb3e1e20..3c42464ce6 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -30,14 +30,14 @@ jobs:
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
         runner: ["self-hosted"]
-        profile: [",self_hosted_runner"]
+        profile: ["self_hosted_runner"]
         include:
           - TEMPLATE: "template_skip_all.yml"
             runner: ubuntu-latest
-            profile: ""
+            profile: "docker"
           - TEMPLATE: "template_skip_nf_core_configs.yml"
             runner: ubuntu-latest
-            profile: ""
+            profile: "docker"
 
     steps:
       - name: go to working directory
@@ -108,7 +108,7 @@ jobs:
       - name: run the pipeline
         run: |
           cd create-test-lint-wf
-          nextflow run my-prefix-testpipeline -profile test${{matrix.profile}} --outdir ./results
+          nextflow run my-prefix-testpipeline -profile test,${{matrix.profile}} --outdir ./results
 
       # Remove results folder before linting
       - name: remove results folder

From 8227bc3ee884af7b78cf7f4a03e26a729b0c290f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 10:07:00 +0100
Subject: [PATCH 114/117] use pre-commit for all linting jobs

---
 .github/workflows/create-lint-wf.yml          | 25 +------
 .../create-test-lint-wf-template.yml          | 19 +-----
 .github/workflows/fix-linting.yml             | 24 ++-----
 .github/workflows/lint-code.yml               |  1 -
 .pre-commit-config.yaml                       | 10 ++-
 .../.github/workflows/fix-linting.yml         | 29 ++++-----
 .../.github/workflows/linting.yml             | 65 ++-----------------
 .../pipeline-template/.pre-commit-config.yaml |  7 +-
 8 files changed, 43 insertions(+), 137 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index cfd36385ea..989358694c 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -41,6 +41,7 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3.11
+          cache: pip
 
       - name: Install python dependencies
         run: |
@@ -53,19 +54,6 @@ jobs:
         with:
           version: ${{ matrix.NXF_VER }}
 
-      # Install the Prettier linting tools
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier and editorconfig-checker
-        run: npm install -g prettier editorconfig-checker
-
-      - name: Install ruff
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-
       # Build a pipeline from the template
       - name: nf-core create
         run: |
@@ -84,15 +72,8 @@ jobs:
         working-directory: create-lint-wf
 
       # Run code style linting
-      - name: Run Prettier --check
-        run: prettier --check create-lint-wf/nf-core-testpipeline
-
-      - name: Run Ruff check
-        run: ruff check create-lint-wf/nf-core-testpipeline
-      - name: Run Ruff format
-        run: ruff format create-lint-wf/nf-core-testpipeline
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find nf-core-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+      - name: run pre-commit
+        run: pre-commit run --all-files
         working-directory: create-lint-wf
 
       # Update modules to the latest version
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 3c42464ce6..843546fb35 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -64,18 +64,6 @@ jobs:
         with:
           version: latest-everything
 
-      # Install the Prettier linting tools
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      # Install the editorconfig linting tools
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
       # Create template files
       - name: Create template skip all (except github)
         run: |
@@ -120,11 +108,8 @@ jobs:
         run: nf-core --log-file log.txt sync --dir create-test-lint-wf/my-prefix-testpipeline/
 
       # Run code style linting
-      - name: Run Prettier --check
-        run: prettier --check create-test-lint-wf/my-prefix-testpipeline
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find my-prefix-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+      - name: Run pre-commit
+        run: pre-commit run --all-files
         working-directory: create-test-lint-wf
 
       # Remove TODO statements
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index b29ed26641..5e857e8dbb 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -24,29 +24,17 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
-
-      - name: Run 'prettier --write'
-        run: prettier --write ${GITHUB_WORKSPACE}
-
       - name: Set up Python 3.11
         uses: actions/setup-python@v5
         with:
           python-version: 3.11
+          cache: "pip"
 
-      - name: Install Ruff
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-      - name: Run Ruff
-        run: |
-          ruff check --fix .
-          ruff format .
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
       - name: Commit & push changes
         run: |
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index b002a705f5..d9847dd365 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -30,5 +30,4 @@ jobs:
         run: pip install pre-commit
 
       - name: Run pre-commit
-        id: prettier_status
         run: pre-commit run --all-files
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index fd51226d54..fb2a67bace 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,12 +6,18 @@ repos:
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
       - id: ruff-format # formatter
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.7.1"
+    rev: "v3.1.0"
     hooks:
       - id: prettier
 
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.8.0" # Use the sha / tag you want to point at
+    rev: "v1.8.0"
     hooks:
       - id: mypy
         additional_dependencies:
diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
index 31e8cd2b36..d9986bd30f 100644
--- a/nf_core/pipeline-template/.github/workflows/fix-linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
@@ -24,32 +24,25 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v4
-
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+          cache: "pip"
 
-      # Check that we actually need to fix something
-      - name: Run 'prettier --check'
-        id: prettier_status
-        run: |
-          if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "result=pass" >> $GITHUB_OUTPUT
-          else
-            echo "result=fail" >> $GITHUB_OUTPUT
-          fi
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      - name: Run 'prettier --write'
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: prettier --write ${GITHUB_WORKSPACE}
+      - name: Run pre-commit
+        run: pre-commit run --all-files || echo "status=fail" >> $GITHUB_ENV
 
       - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        if: env.status == 'fail'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
           git config push.default upstream
           git add .
           git status
-          git commit -m "[automated] Fix linting with Prettier"
+          git commit -m "[automated] Fix linting with pre-commit"
           git push {%- endraw %}
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index acacb8aef3..fa332827b0 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -11,73 +11,22 @@ on:
     types: [published]
 
 jobs:
-  EditorConfig:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v4
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
-
-  Prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  Ruff:
-    runs-on: ["self-hosted"]
-    steps:
-      - name: Check out source-code repository
-        uses: actions/checkout@v4
-
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
-      - name: Install Ruff
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-      - name: Run Ruff check
-        run: ruff check .
-
-      - name: Run Ruff format
-        run: ruff format .
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v2
-        with:
-          message: |
-            ## Python linting (`ruff`) is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install [`ruff`](https://github.com/astral-sh/ruff): `pip install ruff`
-            * Fix formatting errors in your pipeline: `ruff check --fix .` and `ruff format .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
+          cache: "pip"
 
-            We highly recommend setting up Ruff in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
   nf-core:
     runs-on: ubuntu-latest
diff --git a/nf_core/pipeline-template/.pre-commit-config.yaml b/nf_core/pipeline-template/.pre-commit-config.yaml
index 0c31cdb99f..984321ff26 100644
--- a/nf_core/pipeline-template/.pre-commit-config.yaml
+++ b/nf_core/pipeline-template/.pre-commit-config.yaml
@@ -1,5 +1,10 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.7.1"
+    rev: "v3.1.1"
     hooks:
       - id: prettier
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec

From cd75ff921d2e76ebcaa39cf632cd737dec39eca7 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 10:07:16 +0100
Subject: [PATCH 115/117] fix editorconfig

---
 .editorconfig                           | 4 ++++
 docs/api/Makefile                       | 4 ++--
 nf_core/pipeline-template/.editorconfig | 8 ++++++++
 3 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/.editorconfig b/.editorconfig
index 014c2383bd..eaf7834976 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -10,3 +10,7 @@ indent_style = space
 
 [*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
+
+# ignore python and markdown files
+[*.{py,md}]
+indent_style = unset
diff --git a/docs/api/Makefile b/docs/api/Makefile
index f961e4ded1..69f3987065 100644
--- a/docs/api/Makefile
+++ b/docs/api/Makefile
@@ -9,11 +9,11 @@ BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+    @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 .PHONY: help Makefile
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
+    @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig
index b6b3190776..9b990088ab 100644
--- a/nf_core/pipeline-template/.editorconfig
+++ b/nf_core/pipeline-template/.editorconfig
@@ -22,3 +22,11 @@ indent_size = unset
 
 [/assets/email*]
 indent_size = unset
+
+# ignore Readme
+[README.md]
+indent_style = unset
+
+# ignore python
+[*.{py}]
+indent_style = unset

From c9377c450109466e8bd949a4be4e5be897adb33d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 10:12:20 +0100
Subject: [PATCH 116/117] fix .editorconfig and makefile

---
 .editorconfig     | 8 +++++++-
 docs/api/Makefile | 4 ++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/.editorconfig b/.editorconfig
index eaf7834976..449f446a3b 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -12,5 +12,11 @@ indent_style = space
 indent_size = 2
 
 # ignore python and markdown files
-[*.{py,md}]
+[*.py]
+indent_style = unset
+
+[**/{CONTRIBUTING,README}.md]
+indent_style = unset
+
+[**/Makefile]
 indent_style = unset
diff --git a/docs/api/Makefile b/docs/api/Makefile
index 69f3987065..ab30a5051e 100644
--- a/docs/api/Makefile
+++ b/docs/api/Makefile
@@ -9,11 +9,11 @@ BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:
-    @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 .PHONY: help Makefile
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-    @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

From 43d56d56159844c54706200d250d822766a99b6d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 11:02:48 +0100
Subject: [PATCH 117/117] update changelog

---
 CHANGELOG.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2c8f522fe4..2f18b559b4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,8 @@
 
 ### Template
 
+- Use `pre-commit` to lint files in GitHub CI ([#2635](https://github.com/nf-core/tools/pull/2635))
+
 ### Download
 
 ### Linting
@@ -14,6 +16,8 @@
 
 ### General
 
+- Run CI-pytests for nf-core tools on self-hosted runners ([#2550](https://github.com/nf-core/tools/pull/2550))
+
 - Add Ruff linter and formatter replacing Black, isort and pyupgrade ([#2620](https://github.com/nf-core/tools/pull/2620))
 - Update pre-commit hook pre-commit/mirrors-mypy to v1.8.0 ([#2630](https://github.com/nf-core/tools/pull/2630))
 - Update mshick/add-pr-comment action to v2 ([#2632](https://github.com/nf-core/tools/pull/2632))
@@ -24,7 +28,6 @@
 
 - Rename `release-announcments.yml` to `release-announcements.yml` ([#2610](https://github.com/nf-core/tools/pull/2610))
 - Fix `nextflow.config` `docker.runOptions` ([#2607](https://github.com/nf-core/tools/pull/2607))
-- Use `pre-commit` to lint files in GitHub CI ([#2635](https://github.com/nf-core/tools/pull/2635))
 
 ### General