diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml index 829282e7f9..d2894e9dad 100644 --- a/.github/workflows/rich-codex.yml +++ b/.github/workflows/rich-codex.yml @@ -1,5 +1,10 @@ name: Generate images for docs -on: [push] +on: + push: + branches-ignore: + - "master" + - "dev" + workflow_dispatch: jobs: rich_codex: runs-on: ubuntu-latest @@ -22,6 +27,10 @@ jobs: - name: Generate terminal images with rich-codex uses: ewels/rich-codex@v1 + env: + COLUMNS: 100 + NFCORE_LINT_HIDE_PROGRESS: true + NFCORE_MODULES_LINT_HIDE_PROGRESS: true with: commit_changes: "true" clean_img_paths: docs/images/*.svg @@ -31,4 +40,3 @@ jobs: which nf-core && nextflow -version && nf-core --version - PY_COLORS=true diff --git a/CHANGELOG.md b/CHANGELOG.md index af9a486b38..4a673609e6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ - Make `nf-core create` fail if Git default branch name is dev or TEMPLATE ([#1705](https://github.com/nf-core/tools/pull/1705)) - Convert `console` snippets to `bash` snippets in the template where applicable ([#1729](https://github.com/nf-core/tools/pull/1729)) - Add `branch` field to module entries in `modules.json` to record what branch a module was installed from ([#1728](https://github.com/nf-core/tools/issues/1728)) +- Add customisation option to remove all GitHub support with `nf-core create` ([#1766](https://github.com/nf-core/tools/pull/1766)) ### Linting @@ -49,6 +50,7 @@ - Replace use of the deprecated `distutils` Version object with that from `packaging` ([#1735](https://github.com/nf-core/tools/pull/1735)) - Add code to cancel CI run if a new run starts ([#1760](https://github.com/nf-core/tools/pull/1760)) - CI for the API docs generation now uses the ubuntu-latest base image ([#1762](https://github.com/nf-core/tools/pull/1762)) +- Add option to hide progress bars in `nf-core lint` and `nf-core modules lint` with `--hide-progress`. ### Modules diff --git a/README.md b/README.md index 189ebca461..7703a91c83 100644 --- a/README.md +++ b/README.md @@ -287,6 +287,10 @@ working_dir: tmp Once downloaded, you will see something like the following file structure for the downloaded pipeline: + + ![`tree -L 2 nf-core-rnaseq/`](docs/images/nf-core-download-tree.svg) You can run the pipeline by simply providing the directory path for the `workflow` folder to your `nextflow run` command: diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg index f42cb69e5f..6e8b89d1c2 100644 --- a/docs/images/nf-core-bump-version.svg +++ b/docs/images/nf-core-bump-version.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core bump-version 1.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Changing version number from '1.0dev' to '1.1'bump_version.py:35 -INFO     Updated version in 'nextflow.config'bump_version.py:164 - - version         = '1.0dev' - + version = '1.1' - - + + $ nf-core bump-version 1.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO     Changing version number from '1.0dev' to '1.1'bump_version.py:35 +INFO     Updated version in 'nextflow.config'bump_version.py:164 + - version         = '1.0dev' + + version = '1.1' + + diff --git a/docs/images/nf-core-create.svg b/docs/images/nf-core-create.svg index d90cdfdaa7..343fd47281 100644 --- a/docs/images/nf-core-create.svg +++ b/docs/images/nf-core-create.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - - - - - - - - - - - - - - - - - - - - + + - + - - - - $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next  -big omics technique" -a "Big Steve" --plain - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Creating new nf-core pipeline: 'nf-core/nextbigthing'create.py:226 -INFO     Initialising pipeline git repository                      create.py:518 -INFO     Done. Remember to add a remote and push to GitHub:        create.py:525 - cd  -/home/runner/work/nf-core-tools/nf-core-tools/tmp/nf-core --nextbigthing - git remote add origin  -git@github.com:USERNAME/REPO_NAME.git  - git push --all origin                                    -INFO     This will also push your newly created dev branch and the create.py:531 -         TEMPLATE branch for syncing.                               -INFO    !!!!!! IMPORTANT !!!!!!create.py:217 - -If you are interested in adding your pipeline to the  -nf-core community, -PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE  -WRITING ANY CODE! - -Please read:  -https://nf-co.re/developers/adding_pipelines#join-the-com -munity + + + + $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique"  +-a "Big Steve" --plain + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO     Creating new nf-core pipeline: 'nf-core/nextbigthing'create.py:233 +INFO     Initialising pipeline git repository                                          create.py:535 +INFO     Done. Remember to add a remote and push to GitHub:                            create.py:542 + cd /home/runner/work/tools/tools/tmp/nf-core-nextbigthing + git remote add origin git@github.com:USERNAME/REPO_NAME.git  + git push --all origin                                        +INFO     This will also push your newly created dev branch and the TEMPLATE branch for create.py:548 +         syncing.                                                                       +INFO    !!!!!! IMPORTANT !!!!!!create.py:224 + +If you are interested in adding your pipeline to the nf-core community, +PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE! + +Please read: https://nf-co.re/developers/adding_pipelines#join-the-community diff --git a/docs/images/nf-core-download-tree.svg b/docs/images/nf-core-download-tree.svg index eeaad252b1..24a0f671fe 100644 --- a/docs/images/nf-core-download-tree.svg +++ b/docs/images/nf-core-download-tree.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ tree -L 2 nf-core-rnaseq/ -nf-core-rnaseq/ [error opening dir] - -0 directories, 0 files + + $ tree -L 2 nf-core-rnaseq/ +nf-core-rnaseq/ +├── configs +│   ├── CITATION.cff +│   ├── LICENSE +│   ├── README.md +│   ├── bin +│   ├── conf +│   ├── configtest.nf +│   ├── docs +│   ├── nextflow.config +│   ├── nfcore_custom.config +│   └── pipeline +└── workflow +    ├── CHANGELOG.md +    ├── CITATIONS.md +    ├── CODE_OF_CONDUCT.md +    ├── LICENSE +    ├── README.md +    ├── assets +    ├── bin +    ├── conf +    ├── docs +    ├── lib +    ├── main.nf +    ├── modules +    ├── modules.json +    ├── nextflow.config +    ├── nextflow_schema.json +    ├── subworkflows +    ├── tower.yml +    └── workflows + +14 directories, 16 files diff --git a/docs/images/nf-core-download.svg b/docs/images/nf-core-download.svg index 5b479971ae..5502d4fc46 100644 --- a/docs/images/nf-core-download.svg +++ b/docs/images/nf-core-download.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -c none - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Saving 'nf-core/rnaseq'download.py:158 -          Pipeline revision: '3.8' -          Pull containers: 'none' -          Output directory: 'nf-core-rnaseq' -INFO     Downloading workflow files from GitHub                  download.py:161 -INFO     Downloading centralised configs from GitHub             download.py:165 + + $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -c none + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO     Saving 'nf-core/rnaseq'download.py:158 +          Pipeline revision: '3.8' +          Pull containers: 'none' +          Output directory: 'nf-core-rnaseq' +INFO     Downloading workflow files from GitHub                                      download.py:161 +INFO     Downloading centralised configs from GitHub                                 download.py:165 diff --git a/docs/images/nf-core-launch-rnaseq.svg b/docs/images/nf-core-launch-rnaseq.svg index f60ff94212..96ecbd3426 100644 --- a/docs/images/nf-core-launch-rnaseq.svg +++ b/docs/images/nf-core-launch-rnaseq.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core launch rnaseq -r 3.8.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     NOTE: This tool ignores any pipeline parameter defaults   launch.py:131 -         overwritten by Nextflow config files or profiles           - -INFO     Downloading workflow: nf-core/rnaseq (3.8.1)list.py:67 + + $ nf-core launch rnaseq -r 3.8.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO     NOTE: This tool ignores any pipeline parameter defaults overwritten by        launch.py:131 +         Nextflow config files or profiles                                              + +INFO     Downloading workflow: nf-core/rnaseq (3.8.1)list.py:67 diff --git a/docs/images/nf-core-licences.svg b/docs/images/nf-core-licences.svg index ced30525e1..5f84e722e9 100644 --- a/docs/images/nf-core-licences.svg +++ b/docs/images/nf-core-licences.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - - + + - + - + - - $ nf-core licences deepvariant - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Fetching licence information for 8 tools                 licences.py:77 -INFO     Warning: This tool only prints licence information for   licences.py:98 -         the software tools packaged using conda.                  -INFO     The pipeline may use other software and dependencies not licences.py:99 -         described here.                                           -┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓ -┃Package Name┃Version┃Licence┃ -┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩ -│ lbzip2       │ 2.5     │ GPL v3  │ -│ deepvariant  │ 0.7.0   │ MIT     │ -│ htslib       │ 1.9     │ MIT     │ -│ picard       │ 2.18.7  │ MIT     │ -│ pip          │ 10.0.1  │ MIT     │ -│ samtools     │ 1.9     │ MIT     │ -│ python       │ 2.7.15  │ PSF     │ -│ bzip2        │ 1.0.6   │ bzip2   │ -└──────────────┴─────────┴─────────┘ + + $ nf-core licences deepvariant + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO     Fetching licence information for 8 tools                                     licences.py:77 +INFO     Warning: This tool only prints licence information for the software tools    licences.py:98 +         packaged using conda.                                                         +INFO     The pipeline may use other software and dependencies not described here.     licences.py:99 +┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓ +┃Package Name┃Version┃Licence┃ +┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩ +│ lbzip2       │ 2.5     │ GPL v3  │ +│ deepvariant  │ 0.7.0   │ MIT     │ +│ htslib       │ 1.9     │ MIT     │ +│ picard       │ 2.18.7  │ MIT     │ +│ pip          │ 10.0.1  │ MIT     │ +│ samtools     │ 1.9     │ MIT     │ +│ python       │ 2.7.15  │ PSF     │ +│ bzip2        │ 1.0.6   │ bzip2   │ +└──────────────┴─────────┴─────────┘ diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg index c1993494e2..03d39778ef 100644 --- a/docs/images/nf-core-lint.svg +++ b/docs/images/nf-core-lint.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + - + - - $ nf-core lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Testing pipeline: .__init__.py:258 - - -Linting local modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━0 of 1 » samplesheet_check -Linting local modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » samplesheet_check - - -Linting nf-core modules━━━━━━━━━━━━━━━━━━━0 of 3 » custom/dumpsoftwareversions -Linting nf-core modules━━━━━━╺━━━━━━━━━━━━1 of 3 » custom/dumpsoftwareversions -Linting nf-core modules━━━━━━╺━━━━━━━━━━━━1 of 3 » custom/dumpsoftwareversions -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━2 of 3 » fastqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━2 of 3 » fastqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━2 of 3 » fastqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━3 of 3 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━3 of 3 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━3 of 3 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━3 of 3 » multiqc - - -╭─[?] 1 Pipeline Test Ignored ────────────────────────────────────────────────╮ -││ -│pipeline_todos: pipeline_todos│ -││ -╰──────────────────────────────────────────────────────────────────────────────╯ - -╭─[!] 5 Module Test Warnings ─────────────────────────────────────────────────╮ -│                                           ╷                ╷                 │ -│Module name                              │File path     │Test message   │ -│╶──────────────────────────────────────────┼────────────────┼────────────────╴│ -│custom/dumpsoftwareversions│modules/nf-co…│New version │ -│││available│ -│fastqc│modules/nf-co…│New version │ -│││available│ -│multiqc│modules/nf-co…│New version │ -│││available│ -│samplesheet_check│modules/local…│Process label │ -│││unspecified│ -│samplesheet_check│modules/local…│when: condition│ -│││has been │ -│││removed│ -│                                           ╵                ╵                 │ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────╮ -│LINT RESULTS SUMMARY │ -├───────────────────────┤ -│[✔] 169 Tests Passed│ -│[?]   1 Test Ignored│ -│[!]   5 Test Warnings│ -│[✗]   0 Tests Failed│ -╰───────────────────────╯ + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +INFO     Testing pipeline: .__init__.py:263 + + +╭─[?] 1 Pipeline Test Ignored ────────────────────────────────────────────────────────────────────╮ +││ +│pipeline_todos: pipeline_todos│ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + +╭─[!] 5 Module Test Warnings ─────────────────────────────────────────────────────────────────────╮ +│                                           ╷                          ╷                           │ +│Module name                              │File path               │Test message             │ +│╶──────────────────────────────────────────┼──────────────────────────┼──────────────────────────╴│ +│custom/dumpsoftwareversions│modules/nf-core/modules…│New version available│ +│fastqc│modules/nf-core/modules…│New version available│ +│multiqc│modules/nf-core/modules…│New version available│ +│samplesheet_check│modules/local/sampleshe…│Process label unspecified│ +│samplesheet_check│modules/local/sampleshe…│when: condition has been │ +│││removed│ +│                                           ╵                          ╵                           │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭───────────────────────╮ +│LINT RESULTS SUMMARY │ +├───────────────────────┤ +│[✔] 169 Tests Passed│ +│[?]   1 Test Ignored│ +│[!]   5 Test Warnings│ +│[✗]   0 Tests Failed│ +╰───────────────────────╯ diff --git a/docs/images/nf-core-list-rna.svg b/docs/images/nf-core-list-rna.svg index 235b4a479a..cbd098b947 100644 --- a/docs/images/nf-core-list-rna.svg +++ b/docs/images/nf-core-list-rna.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core list rna rna-seq - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -┏━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┓ -┃Pipeline   ┃┃     Latest┃┃┃Have latest┃ -┃Name       ┃Stars┃    Release┃    Released┃Last Pulled┃release?   ┃ -┡━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━┩ -│ rnafusion   │    76 │       2.1.0 │ 1 months ago │           - │ -           │ -│ smrnaseq    │    42 │       2.0.0 │ 3 months ago │           - │ -           │ -│ rnaseq      │   499 │       3.8.1 │ 3 months ago │           - │ -           │ -│ dualrnaseq  │     7 │       1.0.0 │  2 years ago │           - │ -           │ -│ circrna     │    19 │         dev │            - │           - │ -           │ -│ lncpipe     │    23 │         dev │            - │           - │ -           │ -│ scflow      │    12 │         dev │            - │           - │ -           │ -│ spatialtra… │    10 │         dev │            - │           - │ -           │ -└─────────────┴───────┴─────────────┴──────────────┴─────────────┴─────────────┘ + + $ nf-core list rna rna-seq + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnafusion            │    76 │          2.1.0 │ 2 months ago │           - │ -                   │ +│ smrnaseq             │    42 │          2.0.0 │ 3 months ago │           - │ -                   │ +│ rnaseq               │   501 │          3.8.1 │ 3 months ago │           - │ -                   │ +│ dualrnaseq           │     7 │          1.0.0 │  2 years ago │           - │ -                   │ +│ circrna              │    19 │            dev │            - │           - │ -                   │ +│ lncpipe              │    23 │            dev │            - │           - │ -                   │ +│ scflow               │    12 │            dev │            - │           - │ -                   │ +│ spatialtranscriptom… │    10 │            dev │            - │           - │ -                   │ +└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg index cf4b23118e..da3f02c7db 100644 --- a/docs/images/nf-core-list-stars.svg +++ b/docs/images/nf-core-list-stars.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core list -s stars - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -┏━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓ -┃Pipeline   ┃┃     Latest┃┃┃Have latest ┃ -┃Name       ┃Stars┃    Release┃   Released┃Last Pulled┃release?    ┃ -┡━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━┩ -│ rnaseq      │   499 │       3.8.1 │    3 months │           - │ -            │ -│             │       │             │         ago │             │              │ -│ sarek       │   186 │       3.0.1 │  6 days ago │           - │ -            │ -│ chipseq     │   121 │       1.2.2 │ 1 years ago │           - │ -            │ -[..truncated..] + + $ nf-core list -s stars + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq               │   501 │          3.8.1 │ 3 months ago │           - │ -                   │ +│ sarek                │   186 │          3.0.1 │  2 weeks ago │           - │ -                   │ +│ chipseq              │   121 │          1.2.2 │  1 years ago │           - │ -                   │ +│ atacseq              │   116 │          1.2.2 │ 4 months ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg index 5b0721e32e..c5e7e17dd8 100644 --- a/docs/images/nf-core-list.svg +++ b/docs/images/nf-core-list.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -┏━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓ -┃Pipeline   ┃┃     Latest┃┃┃Have latest ┃ -┃Name       ┃Stars┃    Release┃   Released┃Last Pulled┃release?    ┃ -┡━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━┩ -│ sarek       │   186 │       3.0.1 │  6 days ago │           - │ -            │ -│ epitopepre… │    22 │       2.1.0 │ 3 weeks ago │           - │ -            │ -│ eager       │    70 │       2.4.5 │ 3 weeks ago │           - │ -            │ -│ viralrecon  │    74 │         2.5 │    1 months │           - │ -            │ -│             │       │             │         ago │             │              │ -[..truncated..] + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ mag                  │    99 │          2.2.1 │   4 days ago │           - │ -                   │ +│ sarek                │   186 │          3.0.1 │  2 weeks ago │           - │ -                   │ +│ epitopeprediction    │    22 │          2.1.0 │  4 weeks ago │           - │ -                   │ +│ eager                │    71 │          2.4.5 │  4 weeks ago │           - │ -                   │ +│ viralrecon           │    74 │            2.5 │ 2 months ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index 8ac0040588..e76e7a0a12 100644 --- a/docs/images/nf-core-modules-bump-version.svg +++ b/docs/images/nf-core-modules-bump-version.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core modules bump-versions fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - - -╭──────────────────────────────────────────────────────────────────────────────╮ -│[!] 1 Module version up to date.│ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭──────────────────────────────────────────┬───────────────────────────────────╮ -│Module name                             │Update Message                   │ -├──────────────────────────────────────────┼───────────────────────────────────┤ -│ fastqc                                   │ Module version up to date: fastqc │ -╰──────────────────────────────────────────┴───────────────────────────────────╯ + + $ nf-core modules bump-versions fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + + +╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ +│[!] 1 Module version up to date.│ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ +│Module name                             │Update Message                                       │ +├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ +│ fastqc                                   │ Module version up to date: fastqc                     │ +╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ diff --git a/docs/images/nf-core-modules-create-test.svg b/docs/images/nf-core-modules-create-test.svg index a008170278..5711bd8431 100644 --- a/docs/images/nf-core-modules-create-test.svg +++ b/docs/images/nf-core-modules-create-test.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - - - - - - - - + + - + - + - - $ nf-core modules create-test-yml fastqc --no-prompts --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Looking for test workflow entry points:         test_yml_builder.py:123 -'tests/modules/fastqc/main.nf' -──────────────────────────────────────────────────────────────────────────────── -INFO     Building test meta for entry point              test_yml_builder.py:157 -'test_fastqc_single_end' -INFO     Setting env var '$PROFILE' to an empty string   test_yml_builder.py:301 -         as not set.                                      -         Tests will run with Docker by default. To use    -         Singularity set 'export PROFILE=singularity' in  -         your shell before running this command.          -INFO     Running 'fastqc' test with command:             test_yml_builder.py:325 -nextflow run ./tests/modules/fastqc -entry  -test_fastqc_single_end -c  -./tests/config/nextflow.config  -c  -./tests/modules/fastqc/nextflow.config --outdir -/tmp/tmp9j5cgz49 -work-dir /tmp/tmpbhouxlpr + + $ nf-core modules create-test-yml fastqc --no-prompts --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO     Looking for test workflow entry points:                             test_yml_builder.py:123 +'tests/modules/fastqc/main.nf' +──────────────────────────────────────────────────────────────────────────────────────────────────── +INFO     Building test meta for entry point 'test_fastqc'test_yml_builder.py:157 +INFO     Setting env var '$PROFILE' to an empty string as not set.           test_yml_builder.py:301 +         Tests will run with Docker by default. To use Singularity set        +'export PROFILE=singularity' in your shell before running this       +         command.                                                             +INFO     Running 'fastqc' test with command:                                 test_yml_builder.py:325 +nextflow run ./tests/modules/fastqc -entry test_fastqc -c  +./tests/config/nextflow.config  -c  +./tests/modules/fastqc/nextflow.config --outdir /tmp/tmpzotojksy +-work-dir /tmp/tmps14qhvf6 diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index 69b382a0ad..13e19b5e7a 100644 --- a/docs/images/nf-core-modules-create.svg +++ b/docs/images/nf-core-modules-create.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - - - - - - - - - - - + + - + - + - - $ nf-core modules create fastqc --author @nf-core-bot  --label process_low  ---meta --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Repository type: modulescreate.py:93 -INFO    Press enter to use default values (shown in brackets)or create.py:97 -type your own responses. ctrl+click underlined text to  -open links. -INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9'create.py:165 -INFO     Using Docker container:                                   create.py:191 -'quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1' -INFO     Using Singularity container:                              create.py:192 -'https://depot.galaxyproject.org/singularity/fastqc:0.11. -9--hdfd78af_1' -INFO     Created / edited following files:                         create.py:270 -           ./modules/fastqc/main.nf -           ./modules/fastqc/meta.yml -           ./tests/modules/fastqc/main.nf -           ./tests/modules/fastqc/test.yml -           ./tests/modules/fastqc/nextflow.config -           ./tests/config/pytest_modules.yml + + $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO     Repository type: modulescreate.py:93 +INFO    Press enter to use default values (shown in brackets)or type your own create.py:97 +responses. ctrl+click underlined text to open links. +INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9'create.py:165 +INFO     Using Docker container: 'quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1'create.py:191 +INFO     Using Singularity container:                                                  create.py:192 +'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--hdfd78af_1' +INFO     Created / edited following files:                                             create.py:270 +           ./modules/fastqc/main.nf +           ./modules/fastqc/meta.yml +           ./tests/modules/fastqc/main.nf +           ./tests/modules/fastqc/test.yml +           ./tests/modules/fastqc/nextflow.config +           ./tests/config/pytest_modules.yml diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg index 69b4109b23..5c3a82569d 100644 --- a/docs/images/nf-core-modules-info.svg +++ b/docs/images/nf-core-modules-info.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - - - - - - - - + + - + - - - - $ nf-core modules info abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -╭─ Module: abacas  ────────────────────────────────────────────────────────────╮ -│ 🌐 Repository: https://github.com/nf-core/modules.git                        │ -│ 🔧 Tools: abacas                                                             │ -│ 📖 Description: contiguate draft genome assembly                             │ -╰──────────────────────────────────────────────────────────────────────────────╯ -                  ╷                                               ╷              -📥 Inputs        │Description                                    │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [│ -                  │id:'test', single_end:false ]                  │ -╶─────────────────┼───────────────────────────────────────────────┼────────────╴ - scaffold  (file)│Fasta file containing scaffold                 │*.{fasta,fa} -╶─────────────────┼───────────────────────────────────────────────┼────────────╴ - fasta  (file)   │FASTA reference file                           │*.{fasta,fa} -                  ╵                                               ╵              -                  ╷                                               ╷              -📤 Outputs       │Description                                    │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [│ -                  │id:'test', single_end:false ]                  │ -╶─────────────────┼───────────────────────────────────────────────┼────────────╴ - results  (files)│List containing abacas output files [          │ *.{abacas}* -                  │'test.abacas.bin', 'test.abacas.fasta',        │ -                  │'test.abacas.gaps', 'test.abacas.gaps.tab',    │ -                  │'test.abacas.nucmer.delta',                    │ -                  │'test.abacas.nucmer.filtered.delta',           │ -                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',│ -                  │'test.abacas.unused.contigs.out',              │ -                  │'test.abacas.MULTIFASTA.fa' ]                  │ -╶─────────────────┼───────────────────────────────────────────────┼────────────╴ - versions  (file)│File containing software versions              │versions.yml -                  ╵                                               ╵              - - 💻  Installation command: nf-core modules install abacas - + + + + $ nf-core modules info abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ +│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ +│ 🔧 Tools: abacas                                                                                 │ +│ 📖 Description: contiguate draft genome assembly                                                 │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +                  ╷                                                                   ╷              +📥 Inputs        │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} +                  ╵                                                                   ╵              +                  ╷                                                                   ╷              +📤 Outputs       │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + results  (files)│List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* +                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ +                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ +                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ +                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + versions  (file)│File containing software versions                                  │versions.yml +                  ╵                                                                   ╵              + + 💻  Installation command: nf-core modules install abacas + diff --git a/docs/images/nf-core-modules-install.svg b/docs/images/nf-core-modules-install.svg index 9a57d28b44..ce016fe92b 100644 --- a/docs/images/nf-core-modules-install.svg +++ b/docs/images/nf-core-modules-install.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core modules install abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Installing 'abacas'install.py:116 -INFO     Include statement: include { ABACAS } from               install.py:125 -'../modules/nf-core/modules/abacas/main' + + $ nf-core modules install abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +INFO     Installing 'abacas'install.py:116 +INFO     Include statement: include { ABACAS } from                                   install.py:125 +'../modules/nf-core/modules/abacas/main' diff --git a/docs/images/nf-core-modules-lint.svg b/docs/images/nf-core-modules-lint.svg index d0503aac4d..e74151121d 100644 --- a/docs/images/nf-core-modules-lint.svg +++ b/docs/images/nf-core-modules-lint.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + - - - - $ nf-core modules lint multiqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Linting modules repo: '.'__init__.py:195 -INFO     Linting module: 'multiqc'__init__.py:199 - -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━0 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc - - -╭─[!] 1 Module Test Warning ──────────────────────────────────────────────────╮ -│                                           ╷                ╷                 │ -│Module name                              │File path     │Test message   │ -│╶──────────────────────────────────────────┼────────────────┼────────────────╴│ -│multiqc│modules/multi…│Conda update: │ -│││bioconda::mult…│ -│││1.10 -> 1.13a│ -│                                           ╵                ╵                 │ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭──────────────────────╮ -│LINT RESULTS SUMMARY│ -├──────────────────────┤ -│[✔]  22 Tests Passed│ -│[!]   1 Test Warning│ -│[✗]   0 Tests Failed│ -╰──────────────────────╯ + + + + $ nf-core modules lint multiqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +INFO     Linting modules repo: '.'__init__.py:206 +INFO     Linting module: 'multiqc'__init__.py:210 + +╭─[!] 1 Module Test Warning ──────────────────────────────────────────────────────────────────────╮ +│                                           ╷                         ╷                            │ +│Module name                              │File path              │Test message              │ +│╶──────────────────────────────────────────┼─────────────────────────┼───────────────────────────╴│ +│multiqc│modules/multiqc/main.nf│Conda update: │ +│││bioconda::multiqc 1.10 -> │ +│││1.13a│ +│                                           ╵                         ╵                            │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────╮ +│LINT RESULTS SUMMARY│ +├──────────────────────┤ +│[✔]  22 Tests Passed│ +│[!]   1 Test Warning│ +│[✗]   0 Tests Failed│ +╰──────────────────────╯ diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index e53839201b..61c394913e 100644 --- a/docs/images/nf-core-modules-list-local.svg +++ b/docs/images/nf-core-modules-list-local.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Modules installed in '.':                                   list.py:128 - -┏━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -┃Module Name  ┃Repository    ┃Version SHA  ┃Message       ┃Date      ┃ -┡━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ custom/dumps… │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ -│               │                │               │ in yaml files, │            │ -│               │                │               │ add yamllint   │            │ -│               │                │               │ config (#1279) │            │ -│ fastqc        │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ -│               │                │               │ in yaml files, │            │ -│               │                │               │ add yamllint   │            │ -│               │                │               │ config (#1279) │            │ -│ multiqc       │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ -[..truncated..] + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +INFO     Modules installed in '.':                                                       list.py:124 + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +┃Module Name         ┃Repository     ┃Version SHA        ┃Message             ┃Date      ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ custom/dumpsoftware… │ nf-core/modules │ e745e167c1020928ef… │ Fix formatting in    │ 2022-02-15 │ +│                      │                 │                     │ yaml files, add      │            │ +│                      │                 │                     │ yamllint config      │            │ +│                      │                 │                     │ (#1279)              │            │ +│ fastqc               │ nf-core/modules │ e745e167c1020928ef… │ Fix formatting in    │ 2022-02-15 │ +│                      │                 │                     │ yaml files, add      │            │ +│                      │                 │                     │ yamllint config      │            │ +│                      │                 │                     │ (#1279)              │            │ +│ multiqc              │ nf-core/modules │ e745e167c1020928ef… │ Fix formatting in    │ 2022-02-15 │ +[..truncated..] diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index 328d5f100f..96b91a83f9 100644 --- a/docs/images/nf-core-modules-list-remote.svg +++ b/docs/images/nf-core-modules-list-remote.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core modules list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Modules available from nf-core/modules (master):            list.py:123 - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Module Name                             ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ abacas                                   │ -│ abricate/run                             │ -│ abricate/summary                         │ -│ adapterremoval                           │ -│ adapterremovalfixprefix                  │ -│ agrvate                                  │ -│ allelecounter                            │ -│ ampir                                    │ -│ amplify/predict                          │ -[..truncated..] + + $ nf-core modules list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +INFO     Modules available from nf-core/modules (master):                                list.py:119 + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Module Name                             ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ abacas                                   │ +│ abricate/run                             │ +│ abricate/summary                         │ +│ adapterremoval                           │ +│ adapterremovalfixprefix                  │ +│ agrvate                                  │ +│ allelecounter                            │ +│ ampir                                    │ +│ amplify/predict                          │ +[..truncated..] diff --git a/docs/images/nf-core-modules-mulled.svg b/docs/images/nf-core-modules-mulled.svg index 0fcd819ed8..b7ac11336c 100644 --- a/docs/images/nf-core-modules-mulled.svg +++ b/docs/images/nf-core-modules-mulled.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - - + + - + - + - - $ nf-core modules mulled pysam==0.16.0.1 biopython==1.78 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Found docker image on quay.io! ✨                          mulled.py:68 -INFO     Mulled container hash:                                  __main__.py:810 -mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f -5ac4481e91f-0 + + $ nf-core modules mulled pysam==0.16.0.1 biopython==1.78 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO     Found docker image on quay.io! ✨                                              mulled.py:68 +INFO     Mulled container hash:                                                      __main__.py:826 +mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 diff --git a/docs/images/nf-core-modules-patch.svg b/docs/images/nf-core-modules-patch.svg index ef6bf2f2ff..8dea1566a8 100644 --- a/docs/images/nf-core-modules-patch.svg +++ b/docs/images/nf-core-modules-patch.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - - + + - + - + - - $ nf-core modules patch fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Changes in module 'nf-core/modules/fastqc'modules_differ.py:252 -INFO    'modules/nf-core/modules/fastqc/meta.yml' is      modules_differ.py:257 -         unchanged                                          -INFO     Changes in 'fastqc/main.nf':                      modules_differ.py:266 - ---- modules/nf-core/modules/fastqc/main.nf -+++ modules/nf-core/modules/fastqc/main.nf -@@ -1,6 +1,6 @@ -process FASTQC {                                                               -    tag "$meta.id"                                                             --    label 'process_medium' -+    label 'process_low' - -    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)             -    container "${ workflow.containerEngine == 'singularity' && !task.ext.sing  - - -INFO     Patch file of 'nf-core/modules/fastqc' written to          patch.py:115 -'modules/nf-core/modules/fastqc/fastqc.diff' + + $ nf-core modules patch fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +INFO     Changes in module 'nf-core/modules/fastqc'modules_differ.py:252 +INFO    'modules/nf-core/modules/fastqc/meta.yml' is unchanged                modules_differ.py:257 +INFO     Changes in 'fastqc/main.nf':                                          modules_differ.py:266 + +--- modules/nf-core/modules/fastqc/main.nf ++++ modules/nf-core/modules/fastqc/main.nf +@@ -1,6 +1,6 @@ +process FASTQC {                                                                                   +    tag "$meta.id"                                                                                 +-    label 'process_medium' ++    label 'process_low' + +    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)                                 +    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_  + + +INFO     Patch file of 'nf-core/modules/fastqc' written to                              patch.py:115 +'modules/nf-core/modules/fastqc/fastqc.diff' diff --git a/docs/images/nf-core-modules-remove.svg b/docs/images/nf-core-modules-remove.svg index 2c9d755ab1..1deb2efd38 100644 --- a/docs/images/nf-core-modules-remove.svg +++ b/docs/images/nf-core-modules-remove.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core modules remove abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Removing abacas                                            remove.py:51 + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +INFO     Removing abacas                                                                remove.py:52 diff --git a/docs/images/nf-core-modules-test.svg b/docs/images/nf-core-modules-test.svg index b08d0f3039..20b7f7bb7f 100644 --- a/docs/images/nf-core-modules-test.svg +++ b/docs/images/nf-core-modules-test.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core modules test samtools/view --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -──────────────────────────────── samtools/view ───────────────────────────────── -INFO     Running pytest for module 'samtools/view'module_test.py:184 + + $ nf-core modules test samtools/view --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +────────────────────────────────────────── samtools/view ─────────────────────────────────────────── +INFO     Running pytest for module 'samtools/view'module_test.py:184 diff --git a/docs/images/nf-core-modules-update.svg b/docs/images/nf-core-modules-update.svg index 559506e75e..20db553630 100644 --- a/docs/images/nf-core-modules-update.svg +++ b/docs/images/nf-core-modules-update.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core modules update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO    'nf-core/modules/abacas' is already up to date            update.py:160 -INFO     Updating 'nf-core/modules/custom/dumpsoftwareversions'update.py:516 -INFO     Updating 'nf-core/modules/fastqc'update.py:516 -INFO     Updating 'nf-core/modules/multiqc'update.py:516 -INFO     Updates complete ✨                                       update.py:242 + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +INFO    'nf-core/modules/abacas' is already up to date                                update.py:160 +INFO     Updating 'nf-core/modules/custom/dumpsoftwareversions'update.py:516 +INFO     Updating 'nf-core/modules/fastqc'update.py:516 +INFO     Updating 'nf-core/modules/multiqc'update.py:516 +INFO     Updates complete ✨                                                           update.py:242 diff --git a/docs/images/nf-core-schema-build.svg b/docs/images/nf-core-schema-build.svg index 3d1e555dc6..3c5f4b3370 100644 --- a/docs/images/nf-core-schema-build.svg +++ b/docs/images/nf-core-schema-build.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validationschema.py:237 -INFO    [✓] Pipeline schema looks valid(found 27 params)schema.py:95 -INFO     Writing schema with 28 params: './nextflow_schema.json'schema.py:173 + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validationschema.py:237 +INFO    [✓] Pipeline schema looks valid(found 27 params)schema.py:95 +INFO     Writing schema with 28 params: './nextflow_schema.json'schema.py:173 diff --git a/docs/images/nf-core-schema-lint.svg b/docs/images/nf-core-schema-lint.svg index 0e70f4518b..aa28d99e0e 100644 --- a/docs/images/nf-core-schema-lint.svg +++ b/docs/images/nf-core-schema-lint.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core schema lint nextflow_schema.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validationschema.py:237 -INFO    [✓] Pipeline schema looks valid(found 28 params)schema.py:95 + + $ nf-core schema lint nextflow_schema.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validationschema.py:237 +INFO    [✓] Pipeline schema looks valid(found 28 params)schema.py:95 diff --git a/docs/images/nf-core-schema-validate.svg b/docs/images/nf-core-schema-validate.svg index 8ba9a2d519..41376f5bdb 100644 --- a/docs/images/nf-core-schema-validate.svg +++ b/docs/images/nf-core-schema-validate.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - $ nf-core schema validate nf-core-rnaseq/workflow nf-params.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validationschema.py:237 -INFO    [✓] Pipeline schema looks valid(found 93 params)schema.py:95 -INFO    [✓] Input parameters look validschema.py:213 + + $ nf-core schema validate nf-core-rnaseq/workflow nf-params.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validationschema.py:237 +INFO    [✓] Pipeline schema looks valid(found 93 params)schema.py:95 +INFO    [✓] Input parameters look validschema.py:213 diff --git a/docs/images/nf-core-sync.svg b/docs/images/nf-core-sync.svg index 81f992bf71..1b6f3a9e83 100644 --- a/docs/images/nf-core-sync.svg +++ b/docs/images/nf-core-sync.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - - - - - + + - + - + - - $ nf-core sync - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Pipeline directory:                                          sync.py:95 -/home/runner/work/nf-core-tools/nf-core-tools/tmp/nf-core-ne -xtbigthing -INFO     Original pipeline repository branch is 'master'sync.py:149 -INFO     Deleting all files in 'TEMPLATE' branch                     sync.py:205 -INFO     Making a new template pipeline using pipeline variables     sync.py:223 + + $ nf-core sync + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthingsync.py:95 +INFO     Original pipeline repository branch is 'master'sync.py:149 +INFO     Deleting all files in 'TEMPLATE' branch                                         sync.py:205 +INFO     Making a new template pipeline using pipeline variables                         sync.py:223 diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 3ef6888ef7..0746e80c0e 100755 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -90,7 +90,19 @@ def run_nf_core(): stderr.print("\n") # Lanch the click cli - nf_core_cli() + nf_core_cli(auto_envvar_prefix="NFCORE") + + +# taken from https://github.com/pallets/click/issues/108#issuecomment-194465429 +_common_options = [ + click.option("--hide-progress", is_flag=True, default=False, help="Don't show progress bars."), +] + + +def common_options(func): + for option in reversed(_common_options): + func = option(func) + return func @click.group(context_settings=dict(help_option_names=["-h", "--help"])) @@ -304,7 +316,8 @@ def create(name, description, author, version, no_git, force, outdir, template_y @click.option("-w", "--fail-warned", is_flag=True, help="Convert warn tests to failures") @click.option("--markdown", type=str, metavar="", help="File to write linting results to (Markdown)") @click.option("--json", type=str, metavar="", help="File to write linting results to (JSON)") -def lint(dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json): +@common_options +def lint(dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, hide_progress): """ Check pipeline code against nf-core guidelines. @@ -326,7 +339,7 @@ def lint(dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdow # Run the lint tests! try: lint_obj, module_lint_obj = nf_core.lint.run_linting( - dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json + dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, hide_progress ) if len(lint_obj.failed) + len(module_lint_obj.failed) > 0: sys.exit(1) @@ -666,7 +679,8 @@ def create_test_yml(ctx, tool, run_tests, output, force, no_prompts): @click.option("--local", is_flag=True, help="Run additional lint tests for local modules") @click.option("--passed", is_flag=True, help="Show passed tests") @click.option("--fix-version", is_flag=True, help="Fix the module version if a newer version is available") -def lint(ctx, tool, dir, key, all, fail_warned, local, passed, fix_version): +@common_options +def lint(ctx, tool, dir, key, all, fail_warned, local, passed, fix_version, hide_progress): """ Lint one or more modules in a directory. @@ -683,11 +697,13 @@ def lint(ctx, tool, dir, key, all, fail_warned, local, passed, fix_version): ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], ctx.obj["modules_repo_no_pull"], + hide_progress, ) module_lint.lint( module=tool, key=key, all_modules=all, + hide_progress=hide_progress, print_results=True, local=local, show_passed=passed, diff --git a/nf_core/create.py b/nf_core/create.py index 8e58306cd8..619a7b6cc8 100644 --- a/nf_core/create.py +++ b/nf_core/create.py @@ -58,6 +58,10 @@ def __init__( ) skippable_paths = { + "github": [ + ".github/", + ".gitignore", + ], "ci": [".github/workflows/"], "igenomes": ["conf/igenomes.config"], "branded": [ @@ -74,7 +78,9 @@ def __init__( self.name = self.template_params["name"] # Set fields used by the class methods - self.no_git = no_git + self.no_git = ( + no_git if self.template_params["github"] else True + ) # Set to True if template was configured without github hosting self.force = force if outdir is None: outdir = os.path.join(os.getcwd(), self.template_params["name_noslash"]) @@ -110,6 +116,7 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa # Define the different template areas, and what actions to take for each # if they are skipped template_areas = { + "github": {"name": "GitHub hosting", "file": True, "content": False}, "ci": {"name": "GitHub CI", "file": True, "content": False}, "github_badges": {"name": "GitHub badges", "file": False, "content": True}, "igenomes": {"name": "iGenomes config", "file": True, "content": True}, @@ -313,9 +320,10 @@ def render_template(self): # Make a logo and save it, if it is a nf-core pipeline self.make_pipeline_logo() else: - # Remove field mentioning nf-core docs - # in the github bug report template - self.remove_nf_core_in_bug_report_template() + if self.template_params["github"]: + # Remove field mentioning nf-core docs + # in the github bug report template + self.remove_nf_core_in_bug_report_template() # Update the .nf-core.yml with linting configurations self.fix_linting() @@ -395,6 +403,15 @@ def fix_linting(self): "multiqc_config": ["report_comment"], } + # Add GitHub hosting specific configurations + if not self.template_params["github"]: + lint_config["files_exist"].extend( + [ + ".github/ISSUE_TEMPLATE/bug_report.yml", + ] + ) + lint_config["files_unchanged"] = [".github/ISSUE_TEMPLATE/bug_report.yml"] + # Add CI specific configurations if not self.template_params["ci"]: lint_config["files_exist"].extend( diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py index 73d858608b..7e61de3ac1 100644 --- a/nf_core/lint/__init__.py +++ b/nf_core/lint/__init__.py @@ -40,6 +40,7 @@ def run_linting( fail_warned=False, md_fn=None, json_fn=None, + hide_progress=False, ): """Runs all nf-core linting checks on a given Nextflow pipeline project in either `release` mode or `normal` mode (default). Returns an object @@ -77,7 +78,7 @@ def run_linting( pipeline_keys = None # Create the lint object - lint_obj = PipelineLint(pipeline_dir, release_mode, fix, pipeline_keys, fail_ignored, fail_warned) + lint_obj = PipelineLint(pipeline_dir, release_mode, fix, pipeline_keys, fail_ignored, fail_warned, hide_progress) # Load the various pipeline configs lint_obj._load_lint_config() @@ -85,7 +86,7 @@ def run_linting( lint_obj._list_files() # Create the modules lint object - module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir) + module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress) # Verify that the pipeline is correctly configured and has a modules.json file module_lint_obj.has_valid_directory() @@ -182,7 +183,9 @@ class PipelineLint(nf_core.utils.Pipeline): from .template_strings import template_strings from .version_consistency import version_consistency - def __init__(self, wf_path, release_mode=False, fix=(), key=None, fail_ignored=False, fail_warned=False): + def __init__( + self, wf_path, release_mode=False, fix=(), key=None, fail_ignored=False, fail_warned=False, hide_progress=False + ): """Initialise linting object""" # Initialise the parent object @@ -192,6 +195,7 @@ def __init__(self, wf_path, release_mode=False, fix=(), key=None, fail_ignored=F self.release_mode = release_mode self.fail_ignored = fail_ignored self.fail_warned = fail_warned + self.hide_progress = hide_progress self.failed = [] self.ignored = [] self.fixed = [] @@ -307,6 +311,7 @@ def _lint_pipeline(self): rich.progress.BarColumn(bar_width=None), "[magenta]{task.completed} of {task.total}[reset] » [bold yellow]{task.fields[test_name]}", transient=True, + disable=self.hide_progress, ) with self.progress_bar: lint_progress = self.progress_bar.add_task( diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index 3910ef829e..32bfa8ce95 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -64,7 +64,15 @@ class ModuleLint(ModuleCommand): from .module_todos import module_todos from .module_version import module_version - def __init__(self, dir, fail_warned=False, remote_url=None, branch=None, no_pull=False): + def __init__( + self, + dir, + fail_warned=False, + remote_url=None, + branch=None, + no_pull=False, + hide_progress=False, + ): self.dir = dir try: self.dir, self.repo_type = nf_core.modules.module_utils.get_repo_type(self.dir) @@ -75,7 +83,8 @@ def __init__(self, dir, fail_warned=False, remote_url=None, branch=None, no_pull self.passed = [] self.warned = [] self.failed = [] - self.modules_repo = ModulesRepo(remote_url, branch, no_pull) + self.hide_progress = hide_progress + self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress) self.lint_tests = self.get_all_lint_tests(self.repo_type == "pipeline") if self.repo_type == "pipeline": @@ -131,6 +140,7 @@ def lint( module=None, key=(), all_modules=False, + hide_progress=False, print_results=True, show_passed=False, local=False, @@ -153,6 +163,7 @@ def lint( :param print_results: Whether to print the linting results :param show_passed: Whether passed tests should be shown as well :param fix_version: Update the module version if a newer version is available + :param hide_progress: Don't show progress bars :returns: A ModuleLint object containing information of the passed, warned and failed tests @@ -261,6 +272,7 @@ def lint_modules(self, modules, local=False, fix_version=False): "[magenta]{task.completed} of {task.total}[reset] » [bold yellow]{task.fields[test_name]}", transient=True, console=console, + disable=self.hide_progress, ) with progress_bar: lint_progress = progress_bar.add_task( diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index fbc9f4a8f2..005baa84a5 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -253,7 +253,7 @@ def determine_module_branches_and_shas(self, repo_name, remote_url, modules): break # Create a new modules repo with the selected branch, and retry find the sha modules_repo = nf_core.modules.modules_repo.ModulesRepo( - remote_url=remote_url, branch=branch, no_pull=True, no_progress=True + remote_url=remote_url, branch=branch, no_pull=True, hide_progress=True ) else: found_sha = True diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py index 2a559b1112..1bb2770f33 100644 --- a/nf_core/modules/modules_repo.py +++ b/nf_core/modules/modules_repo.py @@ -111,7 +111,7 @@ def get_remote_branches(remote_url): branches[sha] = branch_name return set(branches.values()) - def __init__(self, remote_url=None, branch=None, no_pull=False, no_progress=False): + def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=False): """ Initializes the object and clones the git repository if it is not already present """ @@ -127,7 +127,7 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, no_progress=Fals self.fullname = nf_core.modules.module_utils.path_from_remote(self.remote_url) - self.setup_local_repo(remote_url, branch, no_progress) + self.setup_local_repo(remote_url, branch, hide_progress) # Verify that the repo seems to be correctly configured if self.fullname != NF_CORE_MODULES_NAME or self.branch: @@ -138,7 +138,7 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, no_progress=Fals self.avail_module_names = None - def setup_local_repo(self, remote, branch, no_progress=True): + def setup_local_repo(self, remote, branch, hide_progress=True): """ Sets up the local git repository. If the repository has been cloned previously, it returns a git.Repo object of that clone. Otherwise it tries to clone the repository from @@ -152,21 +152,19 @@ def setup_local_repo(self, remote, branch, no_progress=True): self.local_repo_dir = os.path.join(NFCORE_DIR, self.fullname) if not os.path.exists(self.local_repo_dir): try: - if no_progress: - self.repo = git.Repo.clone_from(remote, self.local_repo_dir) - else: - pbar = rich.progress.Progress( - "[bold blue]{task.description}", - rich.progress.BarColumn(bar_width=None), - "[bold yellow]{task.fields[state]}", - transient=True, + pbar = rich.progress.Progress( + "[bold blue]{task.description}", + rich.progress.BarColumn(bar_width=None), + "[bold yellow]{task.fields[state]}", + transient=True, + disable=hide_progress, + ) + with pbar: + self.repo = git.Repo.clone_from( + remote, + self.local_repo_dir, + progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Cloning"), ) - with pbar: - self.repo = git.Repo.clone_from( - remote, - self.local_repo_dir, - progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Cloning"), - ) ModulesRepo.update_local_repo_status(self.fullname, True) except GitCommandError: raise LookupError(f"Failed to clone from the remote: `{remote}`") @@ -179,19 +177,17 @@ def setup_local_repo(self, remote, branch, no_progress=True): ModulesRepo.update_local_repo_status(self.fullname, True) # If the repo is already cloned, fetch the latest changes from the remote if not ModulesRepo.local_repo_synced(self.fullname): - if no_progress: - self.repo.remotes.origin.fetch() - else: - pbar = rich.progress.Progress( - "[bold blue]{task.description}", - rich.progress.BarColumn(bar_width=None), - "[bold yellow]{task.fields[state]}", - transient=True, + pbar = rich.progress.Progress( + "[bold blue]{task.description}", + rich.progress.BarColumn(bar_width=None), + "[bold yellow]{task.fields[state]}", + transient=True, + disable=hide_progress, + ) + with pbar: + self.repo.remotes.origin.fetch( + progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Pulling") ) - with pbar: - self.repo.remotes.origin.fetch( - progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Pulling") - ) ModulesRepo.update_local_repo_status(self.fullname, True) # Before verifying the branch, fetch the changes