diff --git a/.github/rich-codex.yml b/.github/rich-codex.yml index df5ddbbcb1..703fc518ed 100644 --- a/.github/rich-codex.yml +++ b/.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 @@ -50,48 +50,44 @@ 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 @@ -99,13 +95,13 @@ outputs: 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: | @@ -113,16 +109,16 @@ outputs: git config --global user.email "nf-core_bot@example.com" && \ 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 diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx b/sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx index f18716d811..1929ef07d7 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx +++ b/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. diff --git a/sites/main-site/src/components/pipeline/PipelineSidebar.astro b/sites/main-site/src/components/pipeline/PipelineSidebar.astro index 9730b9ecb8..86e7eae191 100644 --- a/sites/main-site/src/components/pipeline/PipelineSidebar.astro +++ b/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}`} />