Remove release announcement from non nf-core pipelines

.editorconfig

@@ -20,3 +20,11 @@ indent_style = unset
 
 [**/Makefile]
 indent_style = unset
+
+[tests/__snapshots__/*]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset

.github/actions/create-lint-wf/action.yml

@@ -27,7 +27,7 @@ runs:
       run: |
         mkdir -p create-lint-wf && cd create-lint-wf
         export NXF_WORK=$(pwd)
-        nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
+        nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
 
     # Try syncing it before we change anything
     - name: nf-core sync

.github/workflows/create-test-lint-wf-template.yml

@@ -84,29 +84,29 @@ jobs:
         run: |
           mkdir create-test-lint-wf
           export NXF_WORK=$(pwd)
-          printf "prefix: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > create-test-lint-wf/template_skip_all.yml
+          printf "org: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > create-test-lint-wf/template_skip_all.yml
 
       - name: Create template skip github_badges
         run: |
-          printf "prefix: my-prefix\nskip: github_badges" > create-test-lint-wf/template_skip_github_badges.yml
+          printf "org: my-prefix\nskip: github_badges" > create-test-lint-wf/template_skip_github_badges.yml
 
       - name: Create template skip igenomes
         run: |
-          printf "prefix: my-prefix\nskip: igenomes" > create-test-lint-wf/template_skip_igenomes.yml
+          printf "org: my-prefix\nskip: igenomes" > create-test-lint-wf/template_skip_igenomes.yml
 
       - name: Create template skip ci
         run: |
-          printf "prefix: my-prefix\nskip: ci" > create-test-lint-wf/template_skip_ci.yml
+          printf "org: my-prefix\nskip: ci" > create-test-lint-wf/template_skip_ci.yml
 
       - name: Create template skip nf_core_configs
         run: |
-          printf "prefix: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml
+          printf "org: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml
 
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |
           cd create-test-lint-wf
-          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
+          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
 
       - name: run the pipeline
         run: |

.github/workflows/create-test-wf.yml

@@ -70,7 +70,11 @@ jobs:
         run: |
           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
+          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
+          # echo current directory
+          pwd
+          # echo content of current directory
+          ls -la
           nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
 
       - name: Upload log file artifact

.github/workflows/pytest.yml

@@ -142,6 +142,13 @@ jobs:
             exit 1
           fi
 
+      - name: Store snapshot report
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        if: always()
+        with:
+          name: Snapshot Report ${{ matrix.test }}
+          path: ./snapshot_report.html
+
       - name: Upload coverage
         uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:

.gitignore

@@ -115,3 +115,6 @@ ENV/
 pip-wheel-metadata
 .vscode
 .*.sw?
+
+# Textual
+snapshot_report.html

.gitpod.yml

@@ -1,4 +1,4 @@
-image: nfcore/gitpod:latest
+image: nfcore/gitpod:dev
 tasks:
   - name: install current state of nf-core/tools and setup pre-commit
     command: |

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    rev: v0.4.9
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

CHANGELOG.md

@@ -1,10 +1,44 @@
 # nf-core/tools: Changelog
 
+## v2.14.2dev
+
+### Template
+
+- Change paths to test data ([#2985](https://github.com/nf-core/tools/pull/2985))
+
+### Linting
+
+- Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976))
+- Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014))
+
+### Download
+
+### Components
+
+- The `modules_nfcore` tag in the `main.nf.test` file of modules/subworkflows now displays the organization name in custom modules repositories ([#3005](https://github.com/nf-core/tools/pull/3005))
+
+### General
+
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.4 ([#2974](https://github.com/nf-core/tools/pull/2974))
+- Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982))
+- Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988))
+- Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991))
+- update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998))
+- return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006))
+- Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008))
+- README - absolute image paths ([#3013](https://github.com/nf-core/tools/pull/3013))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.7 ([#3015](https://github.com/nf-core/tools/pull/3015))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.8 ([#3017](https://github.com/nf-core/tools/pull/3017))
+- Update python:3.12-slim Docker digest to e3ae8cf ([#3020](https://github.com/nf-core/tools/pull/3020))
+- Update python:3.12-slim Docker digest to 2fba8e7 ([#3023](https://github.com/nf-core/tools/pull/3023))
+
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 
 ### Template
 
 - Don't cache pip in `linting.yml` ([#2961](https://github.com/nf-core/tools/pull/2961))
+- Lint pipelines with the nf-core template version and post comment if it is outdated ([#2978](https://github.com/nf-core/tools/pull/2978))
 
 ### General
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:2be8daddbb82756f7d1f2c7ece706aadcb284bf6ab6d769ea695cc3ed6016743
+FROM python:3.12-slim@sha256:2fba8e70a87bcc9f6edd20dda0a1d4adb32046d2acbca7361bc61da5a106a914
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

MANIFEST.in

@@ -9,3 +9,4 @@ include nf_core/assets/logo/nf-core-repo-logo-base-lightbg.png
 include nf_core/assets/logo/nf-core-repo-logo-base-darkbg.png
 include nf_core/assets/logo/placeholder_logo.svg
 include nf_core/assets/logo/MavenPro-Bold.ttf
+include nf_core/pipelines/create/create.tcss