From da7636a3e44ead54ffacce02f20dd175cc06121a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 13:25:03 +0100
Subject: [PATCH 1/9] fix subworkflow tag in template

---
 nf_core/subworkflow-template/subworkflows/tests/main.nf.test | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nf_core/subworkflow-template/subworkflows/tests/main.nf.test b/nf_core/subworkflow-template/subworkflows/tests/main.nf.test
index b0a212f2a..59c4fdb67 100644
--- a/nf_core/subworkflow-template/subworkflows/tests/main.nf.test
+++ b/nf_core/subworkflow-template/subworkflows/tests/main.nf.test
@@ -8,7 +8,6 @@ nextflow_workflow {
 
     tag "subworkflows"
     tag "subworkflows_nfcore"
-    tag "{{ component_name }}"
     tag "subworkflows/{{ component_name }}"
     // TODO nf-core: Add tags for all modules used within this subworkflow. Example:
     tag "samtools"

From cc3b6e1b9b15fb2b2bbbcb1bcd8eb521669e0182 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 15:59:14 +0100
Subject: [PATCH 2/9] fix linting tests

---
 .github/workflows/pytest.yml                  |  1 +
 .../subworkflows/lint/subworkflow_tests.py    |  1 -
 tests/subworkflows/lint.py                    | 11 +++++++----
 tests/test_subworkflows.py                    | 19 ++++++++-----------
 4 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 03d5bc65e..2557c4fa4 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -55,6 +55,7 @@ jobs:
       run-tests: ${{ env.run-tests }}
 
   test:
+    name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: setup
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
     runs-on: ${{ needs.setup.outputs.runner }}
diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py
index 30439a8d0..a125be152 100644
--- a/nf_core/subworkflows/lint/subworkflow_tests.py
+++ b/nf_core/subworkflows/lint/subworkflow_tests.py
@@ -102,7 +102,6 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
                 "subworkflows",
                 f"subworkflows/{subworkflow.component_name}",
                 "subworkflows_nfcore",
-                subworkflow.component_name,
             ]
             included_components = []
             if subworkflow.main_nf.is_file():
diff --git a/tests/subworkflows/lint.py b/tests/subworkflows/lint.py
index 5bbe746f2..1380db226 100644
--- a/tests/subworkflows/lint.py
+++ b/tests/subworkflows/lint.py
@@ -28,9 +28,8 @@ def test_subworkflows_lint_new_subworkflow(self):
     """lint a new subworkflow"""
     subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
     subworkflow_lint.lint(print_results=True, all_subworkflows=True)
-    assert (
-        len(subworkflow_lint.failed) == 1  # test snap missing after creating a subworkflow
-    ), f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+    assert len(subworkflow_lint.failed) == 0
+
     assert len(subworkflow_lint.passed) > 0
     assert len(subworkflow_lint.warned) >= 0
 
@@ -68,7 +67,6 @@ def test_subworkflows_lint_multiple_remotes(self):
 
 def test_subworkflows_lint_snapshot_file(self):
     """Test linting a subworkflow with a snapshot file"""
-    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch()
     subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
     subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
     assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
@@ -78,8 +76,10 @@ def test_subworkflows_lint_snapshot_file(self):
 
 def test_subworkflows_lint_snapshot_file_missing_fail(self):
     """Test linting a subworkflow with a snapshot file missing, which should fail"""
+    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").unlink()
     subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
     subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch()
     assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
     assert len(subworkflow_lint.passed) > 0
     assert len(subworkflow_lint.warned) >= 0
@@ -96,8 +96,11 @@ def test_subworkflows_lint_snapshot_file_not_needed(self):
         Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test"), "w"
     ) as fh:
         fh.write(new_content)
+
+    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").unlink()
     subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
     subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch()
     assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
     assert len(subworkflow_lint.passed) > 0
     assert len(subworkflow_lint.warned) >= 0
diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py
index 33cad81e3..a4ab959fb 100644
--- a/tests/test_subworkflows.py
+++ b/tests/test_subworkflows.py
@@ -4,6 +4,7 @@
 import os
 import shutil
 import unittest
+from pathlib import Path
 
 import nf_core.create
 import nf_core.modules
@@ -21,22 +22,18 @@
 def create_modules_repo_dummy(tmp_dir):
     """Create a dummy copy of the nf-core/modules repo"""
 
-    root_dir = os.path.join(tmp_dir, "modules")
-    os.makedirs(os.path.join(root_dir, "modules"))
-    os.makedirs(os.path.join(root_dir, "subworkflows"))
-    os.makedirs(os.path.join(root_dir, "subworkflows", "nf-core"))
-    os.makedirs(os.path.join(root_dir, "tests", "modules"))
-    os.makedirs(os.path.join(root_dir, "tests", "subworkflows"))
-    os.makedirs(os.path.join(root_dir, "tests", "config"))
-    with open(os.path.join(root_dir, "tests", "config", "pytest_modules.yml"), "w") as fh:
-        fh.writelines(["test:", "\n  - modules/test/**", "\n  - tests/modules/test/**"])
-    with open(os.path.join(root_dir, ".nf-core.yml"), "w") as fh:
+    root_dir = Path(tmp_dir, "modules")
+    Path(root_dir, "modules").mkdir(parents=True, exist_ok=True)
+    Path(root_dir, "subworkflows").mkdir(parents=True, exist_ok=True)
+    Path(root_dir, "subworkflows", "nf-core").mkdir(parents=True, exist_ok=True)
+    Path(root_dir, "tests", "config").mkdir(parents=True, exist_ok=True)
+    with open(Path(root_dir, ".nf-core.yml"), "w") as fh:
         fh.writelines(["repository_type: modules", "\n", "org_path: nf-core", "\n"])
-
     # TODO Add a mock here
     subworkflow_create = nf_core.subworkflows.SubworkflowCreate(root_dir, "test_subworkflow", "@author", True)
     subworkflow_create.create()
 
+    Path(root_dir, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch()
     return root_dir
 
 

From c6ff441dca15da1162d2018ea063dc76d4073dc5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 16:13:04 +0100
Subject: [PATCH 3/9] try once more on self hosted

---
 .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 2557c4fa4..573c1364b 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -58,7 +58,7 @@ jobs:
     name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: setup
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
-    runs-on: ${{ needs.setup.outputs.runner }}
+    runs-on: ["self-hosted"]
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
@@ -80,7 +80,7 @@ jobs:
           sudo apt update
           sudo apt remove git git-man
           sudo add-apt-repository --remove ppa:git-core/ppa
-          sudo apt install git
+          sudo apt install -y git
       - name: Get current date
         id: date
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV

From ffba25fa46cda05931e72f0a6cfcabe9a131f099 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 16:22:32 +0100
Subject: [PATCH 4/9] run even more things on aws

---
 .github/workflows/lint-code.yml | 10 +++++-----
 .github/workflows/pytest.yml    |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index baaaedcb4..b348496c3 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
 
@@ -28,7 +28,7 @@ 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
 
@@ -41,7 +41,7 @@ jobs:
         run: prettier --check ${GITHUB_WORKSPACE}
 
   PythonBlack:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
       - uses: actions/checkout@v4
 
@@ -71,7 +71,7 @@ jobs:
           allow-repeats: false
 
   isort:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
       - name: Check out source-code repository
         uses: actions/checkout@v4
@@ -87,7 +87,7 @@ 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/pytest.yml b/.github/workflows/pytest.yml
index 573c1364b..4f370bc28 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -25,7 +25,7 @@ env:
 
 jobs:
   setup:
-    runs-on: ${{ matrix.runner }}
+    runs-on: ["self-hosted"]
     strategy:
       matrix:
         python-version: ["3.8", "3.12"]

From d64c3b9aa5e1a6523f5e2c5ea137723a6355d36d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 16:26:11 +0100
Subject: [PATCH 5/9] fix node setup

---
 .github/workflows/lint-code.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index b348496c3..168fac653 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -19,6 +19,8 @@ jobs:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -33,6 +35,8 @@ jobs:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier

From 7f6bc73b7577547c28bc6041a8a0d11b4bcb651d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 16:37:17 +0100
Subject: [PATCH 6/9] fix apt command

---
 .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 4f370bc28..c6de90d93 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -78,7 +78,7 @@ jobs:
         if: ${{ needs.setup.outputs.runner == 'ubuntu-20.04' && needs.setup.outputs.python-version == '3.8' }}
         run: |
           sudo apt update
-          sudo apt remove git git-man
+          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

From a84d064d2ade1412d8704d72879692d02d3a7dde Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 17:16:49 +0100
Subject: [PATCH 7/9] reset aws runner for nf-test related things, try it with
 other workflows

---
 .github/workflows/create-lint-wf.yml               | 4 +++-
 .github/workflows/create-test-lint-wf-template.yml | 4 +++-
 .github/workflows/create-test-wf.yml               | 2 +-
 .github/workflows/fix-linting.yml                  | 2 ++
 .github/workflows/push_dockerhub_dev.yml           | 2 +-
 .github/workflows/pytest.yml                       | 2 +-
 .github/workflows/tools-api-docs-dev.yml           | 2 +-
 7 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 51daec21b..a3941f3ce 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:
@@ -49,6 +49,8 @@ jobs:
 
       # Install the Prettier linting tools
       - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index f1c6c4d14..b14a0fac5 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:
@@ -53,6 +53,8 @@ jobs:
 
       # Install the Prettier linting tools
       - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 4f66adae6..7b6a868f9 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 a6cf14956..d84615120 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -25,6 +25,8 @@ jobs:
           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
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index 169a917d8..1230bfc9d 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: ubuntu-latest
+    runs-on: self-hosted
     # 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 c6de90d93..0561be25e 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -58,7 +58,7 @@ jobs:
     name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: setup
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
-    runs-on: ["self-hosted"]
+    runs-on: ${{ needs.setup.outputs.runner }}
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
diff --git a/.github/workflows/tools-api-docs-dev.yml b/.github/workflows/tools-api-docs-dev.yml
index 7de8913e0..f6106bd8b 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: ubuntu-latest
+    runs-on: self-hosted
 
     steps:
       - name: Check out source-code repository

From 9599287f7fe67fab93e57dee4a4dc67c8a91eec0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 17:24:01 +0100
Subject: [PATCH 8/9] try fixing aws runs

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

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 6a6bee6a8..31917a3e3 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -121,6 +121,7 @@ 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 88e8bce12ac8c967e0fc36e153388f6f772e0c47 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 23:18:08 +0100
Subject: [PATCH 9/9] run on github runners

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 .github/workflows/create-test-wf.yml               | 2 +-
 .github/workflows/pytest.yml                       | 2 +-
 3 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 b14a0fac5..4be309862 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: ubuntu-latest
     env:
       NXF_ANSI_LOG: false
     strategy:
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 7b6a868f9..4f66adae6 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -17,7 +17,7 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     env:
       NXF_ANSI_LOG: false
     strategy:
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 0561be25e..9f8172a3b 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -25,7 +25,7 @@ env:
 
 jobs:
   setup:
-    runs-on: ["self-hosted"]
+    runs-on: ["ubuntu-latest"]
     strategy:
       matrix:
         python-version: ["3.8", "3.12"]