Merge pull request #2786 from mashehu/update-pipeline-commands

update pipeline commands to new format & clarify sync steps in blog post

.github/rich-codex.yml

@@ -3,12 +3,12 @@ outputs:
   - command: nf-core --help
     img_paths:
       - public/images/contributing/creating_with_nf_core/nfcore_help.svg
-  - command: nf-core list
+  - command: nf-core pipelines list
     head: 19
     img_paths:
       - public/images/contributing/creating_with_nf_core/nfcore_list.svg
-  - command: nf-core create --name demo --description "Pipeline for training" --author "Phil" --plain
-    fake_command: nf-core create
+  - command: nf-core pipelines create --name demo --description "Pipeline for training" --author "Phil" --plain
+    fake_command: nf-core pipelines create
     img_paths:
       - public/images/contributing/creating_with_nf_core/nfcore_create.svg
   - command: cd nf-core-demo && git status
@@ -27,16 +27,16 @@ outputs:
     title: nextflow run
     img_paths:
       - public/images/contributing/creating_with_nf_core/nextflow_run_1.svg
-  - command: cd nf-core-demo && nf-core lint && grep -rl TODO .
-    fake_command: nf-core lint
+  - command: cd nf-core-demo && nf-core pipelines lint && grep -rl TODO .
+    fake_command: nf-core pipelines lint
     img_paths:
       - public/images/contributing/creating_with_nf_core/nfcore_lint_warnings.svg
   - command: |
       cd nf-core-demo && \
       grep -rl TODO . | xargs sed -i 's/TODO//g' && \
       echo "ADDED" >> CODE_OF_CONDUCT.md && \
-      nf-core lint
-    fake_command: nf-core lint
+      nf-core pipelines lint
+    fake_command: nf-core pipelines lint
     img_paths:
       - public/images/contributing/creating_with_nf_core/nfcore_lint_failure.svg
   - command: nextflow run nf-core-demo/ --help
@@ -50,79 +50,75 @@ outputs:
     fake_command: nf-core modules create fastqc --author @janedoe --label process_low --meta
     img_paths:
       - public/images/contributing/modules/nf-core-modules-create.svg
-  - command: nf-core list
+  - command: nf-core pipelines list
     head: 19
     img_paths:
       - public/images/tools/nf-core-list.svg
-  - command: nf-core list rna rna-seq
+  - command: nf-core pipelines list rna rna-seq
     img_paths:
       - public/images/tools/nf-core-list-rna.svg
-  - command: nf-core list -s stars
+  - command: nf-core pipelines list -s stars
     head: 18
     img_paths:
       - public/images/tools/nf-core-list-stars.svg
-  - command: nf-core launch rnaseq -r 3.8.1
+  - command: nf-core pipelines launch rnaseq -r 3.8.1
     trim_after: 'Command line'
     img_paths:
       - public/images/tools/nf-core-launch-rnaseq.svg
-  - command: mkdir tmp && cd tmp && nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d
+  - command: mkdir tmp && cd tmp && nf-core pipelines download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d
     img_paths:
       - public/images/tools/nf-core-download.svg
   - command: cd tmp && tree -L 2 nf-core-rnaseq/
     img_paths:
       - public/images/tools/nf-core-download-tree.svg
-  - command: nf-core licences deepvariant
-    timeout: 10
-    img_paths:
-      - public/images/tools/nf-core-licences.svg
-  - command: cd tmp && nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" -a "Big Steve" --plain
-    fake_command: nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" -a "Big Steve" --plain
+  - command: cd tmp && nf-core pipelines create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" -a "Big Steve" --plain
+    fake_command: nf-core pipelines create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" -a "Big Steve" --plain
     img_paths:
       - public/images/tools/nf-core-create.svg
   - command: |
       cd tmp/nf-core-nextbigthing && \
       echo "lint: { pipeline_todos: false }" >> .nf-core.yml && \
-      nf-core lint
-    fake_command: nf-core lint
+      nf-core pipelines lint
+    fake_command: nf-core pipelines lint
     img_paths:
       - public/images/tools/nf-core-lint.svg
   - command: |
       cd tmp && \
       echo "{input: myfiles.csv, outdir: results}" > nf-params.json
-      nf-core schema validate nf-core-rnaseq/3_8 nf-params.json
+      nf-core pipelines schema validate nf-core-rnaseq/3_8 nf-params.json
     timeout: 10
-    fake_command: nf-core schema validate nf-core-rnaseq/3_8 nf-params.json
+    fake_command: nf-core pipelines schema validate nf-core-rnaseq/3_8 nf-params.json
     after_command: rm nf-params.json
     img_paths:
       - public/images/tools/nf-core-schema-validate.svg
   - command: |
       cd tmp/nf-core-nextbigthing && \
       sed '25,30d' nextflow_schema.json > nextflow_schema.json.tmp && \
       mv nextflow_schema.json.tmp nextflow_schema.json && \
-      nf-core schema build --no-prompts
+      nf-core pipelines schema build --no-prompts
     timeout: 10
-    fake_command: nf-core schema build --no-prompts
+    fake_command: nf-core pipelines schema build --no-prompts
     img_paths:
       - public/images/tools/nf-core-schema-build.svg
-  - command: cd tmp/nf-core-nextbigthing && nf-core schema lint
-    fake_command: nf-core schema lint
+  - command: cd tmp/nf-core-nextbigthing && nf-core pipelines schema lint
+    fake_command: nf-core pipelines schema lint
     img_paths:
       - public/images/tools/nf-core-schema-lint.svg
   - command: |
       cd tmp/nf-core-nextbigthing && \
       git config --global user.email "[email protected]" && \
       git config --global user.name "nf-core_bot" && \
       git commit -am "Bump version" && \
-      nf-core sync
-    fake_command: nf-core sync
+      nf-core pipelines sync
+    fake_command: nf-core pipelines sync
     img_paths:
       - public/images/tools/nf-core-sync.svg
-  - command: cd tmp/nf-core-nextbigthing && nf-core bump-version 1.1
-    fake_command: nf-core bump-version 1.1
+  - command: cd tmp/nf-core-nextbigthing && nf-core pipelines bump-version 1.1
+    fake_command: nf-core pipelines bump-version 1.1
     img_paths:
       - public/images/tools/nf-core-bump-version.svg
-  - command: cd tmp && nf-core create-logo nextbigthing
-    fake_command: nf-core create-logo nextbigthing
+  - command: cd tmp && nf-core pipelines create-logo nextbigthing
+    fake_command: nf-core pipelines create-logo nextbigthing
     img_paths:
       - public/images/tools/nf-core-create-logo.svg
   - command: cd tmp/nf-core-nextbigthing && nf-core modules list remote

sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx

@@ -13,7 +13,7 @@ With a given pipeline name, description and author, it makes a starter pipeline
 After creating the files, the command initialises the folder as a git repository and makes an initial commit.
 This first "vanilla" commit which is identical to the output from the templating tool is important, as it allows us to keep your pipeline in sync with the base template in the future. A full description of the file structure and all files created in the initial pipeline setup can be found [here](https://nf-co.re/docs/contributing/pipelines/pipeline_file_structure). See the [nf-core syncing docs](https://nf-co.re/docs/tutorials/sync/overview) for more information on how the syncing works.
 
-![` nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" -a "Big Steve" --plain`](/images/tools/nf-core-create.svg)
+![` nf-core pipelines create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" -a "Big Steve" --plain`](/images/tools/nf-core-create.svg)
 
 Once you have run the command, create a new empty repository on GitHub under your username (not the `nf-core` organisation, yet) and push the commits from your computer using the example commands in the above log.
 You can then continue to edit, commit and push normally as you build your pipeline.

sites/main-site/src/components/pipeline/PipelineSidebar.astro

@@ -49,7 +49,7 @@ const id = video?.replace('https://www.youtube.com/watch?v=', '').replace('https
                         flatBottom={true}
                         client:idle
                         icon={false}
-                        cmd={`nf-core launch nf-core/${pipeline} -r ${version}`}
+                        cmd={`nf-core pipelines launch nf-core/${pipeline} -r ${version}`}
                     />
                 </div>
                 <div

sites/main-site/src/content/blog/2024/tools-3_0_0.mdx

@@ -126,8 +126,15 @@ git add .nf-core.yml
 git commit -m "Skip fastqc, igenomes and nf_schema"
 ```
 
-6. Retrigger the pipeline sync via the [GitHub Actions workflow](https://github.com/nf-core/tools/actions/workflows/sync.yml) using the name of your pipeline as the input.
-7. Your template update merge should now have fewer conflicts! 🎉
+6. Add the changes to the `dev` branch:
+
+```bash
+git push origin dev
+```
+
+7. Merge the changes into the `dev` branch of the nf-core repository:
+8. Retrigger the pipeline sync via the [GitHub Actions workflow](https://github.com/nf-core/tools/actions/workflows/sync.yml) using the name of your pipeline as the input.
+9. Your template update merge should now have fewer conflicts! 🎉
 
 # Important Template Updates
 

sites/main-site/src/pages/index.astro

@@ -233,7 +233,7 @@ nextflow run nf-core/rnaseq \\
 pip install nf-core
 
 # List all nf-core pipelines and show available updates
-nf-core list`}
+nf-core pipelines list`}
                                 />
                             </div>
                         </div>