diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg index 89843856b..41d7b74f8 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 2.7.2 - https://nf-co.re - - -INFO     Changing version number from '1.0dev' to '1.1' -INFO     Updated version in 'nextflow.config' - - version         = '1.0dev' - + version = '1.1' - - + + $ nf-core bump-version 1.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +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 17b28b0b6..ca414a5c5 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 2.7.2 - https://nf-co.re - - -INFO     Creating new nf-core pipeline: 'nf-core/nextbigthing' -INFO     Initialising pipeline git repository                                                        -INFO     Done. Remember to add a remote and push to GitHub:                                          - 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 syncing.      -INFO    !!!!!! IMPORTANT !!!!!! - -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 + + + + $ 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 +    There is a new version of nf-core/tools available! (2.7.2) + + +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/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:531 +         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-community diff --git a/docs/images/nf-core-download.svg b/docs/images/nf-core-download.svg index d26c6011d..cf54cf6ef 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 2.7.2 - https://nf-co.re - - -INFO     Saving 'nf-core/rnaseq' -          Pipeline revision: '3.8' -          Pull containers: 'none' -          Output directory: 'nf-core-rnaseq' -INFO     Downloading workflow files from GitHub                                                      -INFO     Downloading centralised configs from GitHub                                                 + + $ 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 +    There is a new version of nf-core/tools available! (2.7.2) + + +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 c36c892e5..1250c9d5f 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 2.7.2 - https://nf-co.re - - -INFO     NOTE: This tool ignores any pipeline parameter defaults overwritten by Nextflow config      -         files or profiles                                                                           - -INFO     Downloading workflow: nf-core/rnaseq (3.8.1) + + $ nf-core launch rnaseq -r 3.8.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +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 f96e13548..3a4d3015b 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 2.7.2 - https://nf-co.re - - -INFO     Fetching licence information for 8 tools                                                    -INFO     Warning: This tool only prints licence information for the software tools packaged using    -         conda.                                                                                      -INFO     The pipeline may use other software and dependencies not 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 +    There is a new version of nf-core/tools available! (2.7.2) + + +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 f31644df1..47acc16cc 100644 --- a/docs/images/nf-core-lint.svg +++ b/docs/images/nf-core-lint.svg @@ -1,8 +1,4 @@ -<<<<<<< HEAD - -======= - ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - -======= - .terminal-1536629657-r1 { fill: #c5c8c6 } -.terminal-1536629657-r2 { fill: #98a84b } -.terminal-1536629657-r3 { fill: #9a9b99 } -.terminal-1536629657-r4 { fill: #608ab1 } -.terminal-1536629657-r5 { fill: #d0b344 } -.terminal-1536629657-r6 { fill: #98729f } -.terminal-1536629657-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-1536629657-r8 { fill: #1984e9 } -.terminal-1536629657-r9 { fill: #cc555a } - - - - - - - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + -<<<<<<< HEAD - - - - $ nf-core lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Testing pipeline: .__init__.py:263 - - -╭─[?] 2 Pipeline Tests Ignored ───────────────────────────────────────────────────────────────────╮ -││ -│files_unchanged: File does not exist: lib/NfcoreSchema.groovy│ -│pipeline_todos: pipeline_todos│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─[✗] 3 Pipeline Tests Failed ────────────────────────────────────────────────────────────────────╮ -││ -│files_exist: File not found: lib/NfcoreSchema.groovy│ -│schema_params: Param fail_unrecognised_params from nextflow config not found in │ -│nextflow_schema.json│ -│schema_params: Param lenient_mode from nextflow config not found in nextflow_schema.json│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - -╭─[!] 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 │ -├───────────────────────┤ -│[✔] 166 Tests Passed│ -│[?]   2 Tests Ignored│ -│[!]   5 Test Warnings│ -│[✗]   3 Tests Failed│ -╰───────────────────────╯ -======= - + - - $ nf-core lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.2 - https://nf-co.re - - - -INFO     Testing pipeline: . - - -╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ -││ -│pipeline_todos: pipeline_todos│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - -╭───────────────────────╮ -│LINT RESULTS SUMMARY │ -├───────────────────────┤ -│[✔] 181 Tests Passed│ -│[?]   1 Test Ignored│ -│[!]   0 Test Warnings│ -│[✗]   0 Tests Failed│ -╰───────────────────────╯ ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ +│/opt/hostedtoolcache/Python/3.11.2/x64/bin/nf-core:8 in <module>│ +││ +│7 │   sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])                         │ +│❱ 8 │   sys.exit(run_nf_core())                                                                  │ +│9 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/nf_core/__main__.py:93 in    │ +│run_nf_core│ +││ +│  92 │   # Lanch the click cli│ +│❱   93 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │ +│  94 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/click/core.py:1130 in        │ +│__call__│ +││ +│1129 │   │   """Alias for :meth:`main`."""│ +│❱ 1130 │   │   returnself.main(*args, **kwargs)                                                 │ +│1131 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/rich_click/rich_group.py:21│ +│ in main│ +││ +│20 │   │   try:                                                                                │ +│❱ 21 │   │   │   rv = super().main(*args, standalone_mode=False, **kwargs)                       │ +│22 │   │   │   ifnot standalone_mode:                                                         │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/click/core.py:1055 in main│ +││ +│1054 │   │   │   │   withself.make_context(prog_name, args, **extra) as ctx:                  │ +│❱ 1055 │   │   │   │   │   rv = self.invoke(ctx)                                                 │ +│1056 │   │   │   │   │   ifnot standalone_mode:                                               │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/click/core.py:1657 in invoke│ +││ +│1656 │   │   │   │   with sub_ctx:                                                             │ +│❱ 1657 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │ +│1658 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/click/core.py:1404 in invoke│ +││ +│1403 │   │   ifself.callback isnotNone:                                                     │ +│❱ 1404 │   │   │   return ctx.invoke(self.callback, **ctx.params)                                │ +│1405 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/click/core.py:760 in invoke│ +││ +│ 759 │   │   │   with ctx:                                                                     │ +│❱  760 │   │   │   │   return __callback(*args, **kwargs)                                        │ +│ 761 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/nf_core/__main__.py:341 in   │ +│lint│ +││ +│ 340 │   try:                                                                                  │ +│❱  341 │   │   lint_obj, module_lint_obj = nf_core.lint.run_linting(                             │ +│ 342 │   │   │   dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown,     │ +│        json, hide_progress                                                                       │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/nf_core/lint/__init__.py:89│ +│ in run_linting│ +││ +│ 88 │   # Create the modules lint object│ +│❱  89 │   module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir,                        │ +│       hide_progress=hide_progress)                                                               │ +│ 90 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/nf_core/modules/lint/__init_│ +│_.py:105 in __init__│ +││ +│104 │   │   │   │   │   NFCoreModule(m, None, local_module_dir / m, self.repo_type,            │ +│       Path(self.dir), nf_core_module=False)                                                      │ +│❱ 105 │   │   │   │   │   for m inself.get_local_modules()                                      │ +│106 │   │   │   │   ]                                                                          │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/nf_core/modules/modules_comm│ +│and.py:52 in get_local_modules│ +││ +│ 51 │   │   local_module_dir = Path(self.dir, "modules", "local")                              │ +│❱  52 │   │   return [str(path.relative_to(local_module_dir)) for path in│ +│       local_module_dir.iterdir() if path.suffix == ".nf"]                                        │ +│ 53 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/nf_core/modules/modules_comm│ +│and.py:52 in <listcomp>│ +││ +│ 51 │   │   local_module_dir = Path(self.dir, "modules", "local")                              │ +│❱  52 │   │   return [str(path.relative_to(local_module_dir)) for path in│ +│       local_module_dir.iterdir() if path.suffix == ".nf"]                                        │ +│ 53 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/pathlib.py:931 in iterdir│ +││ +│ 930 │   │   """│ +│❱  931 │   │   for name in os.listdir(self):                                                     │ +│ 932 │   │   │   yieldself._make_child_relpath(name)                                          │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +FileNotFoundError: [Errno 2] No such file or directory: 'modules/local' diff --git a/docs/images/nf-core-list-rna.svg b/docs/images/nf-core-list-rna.svg index 30c4496b2..057546d4e 100644 --- a/docs/images/nf-core-list-rna.svg +++ b/docs/images/nf-core-list-rna.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - -======= - .terminal-3844799147-r1 { fill: #c5c8c6 } -.terminal-3844799147-r2 { fill: #98a84b } -.terminal-3844799147-r3 { fill: #9a9b99 } -.terminal-3844799147-r4 { fill: #608ab1 } -.terminal-3844799147-r5 { fill: #d0b344 } -.terminal-3844799147-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3844799147-r7 { fill: #868887 } - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + + + + - + -<<<<<<< HEAD - - - - $ 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 │            - │           - │ -                   │ -└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ -======= - + - - $ nf-core list rna rna-seq - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.2 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ smrnaseq             │    44 │          2.1.0 │ 2 months ago │           - │ -                   │ -│ rnaseq               │   542 │            3.9 │ 3 months ago │           - │ -                   │ -│ rnafusion            │    85 │          2.1.0 │ 5 months ago │           - │ -                   │ -│ dualrnaseq           │     8 │          1.0.0 │  2 years ago │           - │ -                   │ -│ circrna              │    23 │            dev │            - │           - │ -                   │ -│ lncpipe              │    23 │            dev │            - │           - │ -                   │ -│ scflow               │    15 │            dev │            - │           - │ -                   │ -│ spatialtranscriptom… │    12 │            dev │            - │           - │ -                   │ -└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + + $ nf-core list rna rna-seq + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq               │   570 │         3.10.1 │ 2 months ago │           - │ -                   │ +│ smrnaseq             │    48 │          2.1.0 │ 4 months ago │           - │ -                   │ +│ rnafusion            │    89 │          2.1.0 │ 8 months ago │           - │ -                   │ +│ dualrnaseq           │     9 │          1.0.0 │  2 years ago │           - │ -                   │ +│ circrna              │    26 │            dev │            - │           - │ -                   │ +│ lncpipe              │    24 │            dev │            - │           - │ -                   │ +│ scflow               │    18 │            dev │            - │           - │ -                   │ +│ spatialtranscriptom… │    16 │            dev │            - │           - │ -                   │ +└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg index 4696bbf1f..0524ecb02 100644 --- a/docs/images/nf-core-list-stars.svg +++ b/docs/images/nf-core-list-stars.svg @@ -19,168 +19,89 @@ font-weight: 700; } -<<<<<<< HEAD - .terminal-1473353797-matrix { -======= - .terminal-1326709712-matrix { ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + .terminal-3466505919-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } -<<<<<<< HEAD - .terminal-1473353797-title { -======= - .terminal-1326709712-title { ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + .terminal-3466505919-title { font-size: 18px; font-weight: bold; font-family: arial; } -<<<<<<< HEAD - .terminal-1473353797-r1 { fill: #c5c8c6 } -.terminal-1473353797-r2 { fill: #98a84b } -.terminal-1473353797-r3 { fill: #9a9b99 } -.terminal-1473353797-r4 { fill: #608ab1 } -.terminal-1473353797-r5 { fill: #d0b344 } -.terminal-1473353797-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1473353797-r7 { fill: #868887 } -.terminal-1473353797-r8 { fill: #868887;font-style: italic; } + .terminal-3466505919-r1 { fill: #c5c8c6 } +.terminal-3466505919-r2 { fill: #98a84b } +.terminal-3466505919-r3 { fill: #9a9b99 } +.terminal-3466505919-r4 { fill: #608ab1 } +.terminal-3466505919-r5 { fill: #d0b344 } +.terminal-3466505919-r6 { fill: #d08442;font-weight: bold } +.terminal-3466505919-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-3466505919-r8 { fill: #868887 } +.terminal-3466505919-r9 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - -======= - .terminal-1326709712-r1 { fill: #c5c8c6 } -.terminal-1326709712-r2 { fill: #98a84b } -.terminal-1326709712-r3 { fill: #9a9b99 } -.terminal-1326709712-r4 { fill: #608ab1 } -.terminal-1326709712-r5 { fill: #d0b344 } -.terminal-1326709712-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1326709712-r7 { fill: #868887 } -.terminal-1326709712-r8 { fill: #868887;font-style: italic; } - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + @@ -192,55 +113,29 @@ -<<<<<<< HEAD - - - - $ 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..] -======= - + - - $ nf-core list -s stars - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.2 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq               │   542 │            3.9 │ 3 months ago │           - │ -                   │ -│ sarek                │   211 │          3.1.1 │  4 weeks ago │           - │ -                   │ -│ chipseq              │   133 │          2.0.0 │ 3 months ago │           - │ -                   │ -│ atacseq              │   124 │            2.0 │  3 weeks ago │           - │ -                   │ -[..truncated..] ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + + $ nf-core list -s stars + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq              │   570 │         3.10.1 │  2 months ago │           - │ -                   │ +│ sarek               │   227 │          3.1.2 │  2 months ago │           - │ -                   │ +│ chipseq             │   140 │          2.0.0 │  5 months ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg index 65be0d131..acc607561 100644 --- a/docs/images/nf-core-list.svg +++ b/docs/images/nf-core-list.svg @@ -19,174 +19,92 @@ font-weight: 700; } -<<<<<<< HEAD - .terminal-2711598360-matrix { -======= - .terminal-4187913691-matrix { ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + .terminal-4220727666-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } -<<<<<<< HEAD - .terminal-2711598360-title { -======= - .terminal-4187913691-title { ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + .terminal-4220727666-title { font-size: 18px; font-weight: bold; font-family: arial; } -<<<<<<< HEAD - .terminal-2711598360-r1 { fill: #c5c8c6 } -.terminal-2711598360-r2 { fill: #98a84b } -.terminal-2711598360-r3 { fill: #9a9b99 } -.terminal-2711598360-r4 { fill: #608ab1 } -.terminal-2711598360-r5 { fill: #d0b344 } -.terminal-2711598360-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2711598360-r7 { fill: #868887 } -.terminal-2711598360-r8 { fill: #868887;font-style: italic; } + .terminal-4220727666-r1 { fill: #c5c8c6 } +.terminal-4220727666-r2 { fill: #98a84b } +.terminal-4220727666-r3 { fill: #9a9b99 } +.terminal-4220727666-r4 { fill: #608ab1 } +.terminal-4220727666-r5 { fill: #d0b344 } +.terminal-4220727666-r6 { fill: #d08442;font-weight: bold } +.terminal-4220727666-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-4220727666-r8 { fill: #868887 } +.terminal-4220727666-r9 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - -======= - .terminal-4187913691-r1 { fill: #c5c8c6 } -.terminal-4187913691-r2 { fill: #98a84b } -.terminal-4187913691-r3 { fill: #9a9b99 } -.terminal-4187913691-r4 { fill: #608ab1 } -.terminal-4187913691-r5 { fill: #d0b344 } -.terminal-4187913691-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-4187913691-r7 { fill: #868887 } -.terminal-4187913691-r8 { fill: #868887;font-style: italic; } - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + @@ -198,57 +116,30 @@ -<<<<<<< HEAD - - - - $ 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..] -======= - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.2 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ methylseq            │    95 │          2.3.0 │   2 days ago │           - │ -                   │ -│ ampliseq             │   102 │          2.4.1 │  2 weeks ago │           - │ -                   │ -│ airrflow             │    23 │          2.4.0 │  2 weeks ago │           - │ -                   │ -│ mhcquant             │    21 │          2.4.0 │  2 weeks ago │           - │ -                   │ -│ atacseq              │   124 │            2.0 │  3 weeks ago │           - │ -                   │ -[..truncated..] ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ nascent             │     6 │          2.1.1 │    5 days ago │           - │ -                   │ +│ phyloplace          │     2 │          1.0.0 │    1 week ago │           - │ -                   │ +│ funcscan            │    21 │          1.0.0 │   1 weeks ago │           - │ -                   │ +│ proteinfold         │    15 │          1.0.0 │   2 weeks ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index 227de6bb2..94ba436bb 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 2.7.2 - 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 +    There is a new version of nf-core/tools available! (2.7.2) + + + +ERROR    Could not find the specified module: 'fastqc'__main__.py:780 diff --git a/docs/images/nf-core-modules-create-test.svg b/docs/images/nf-core-modules-create-test.svg index 57e29b961..3f72db085 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 2.7.2 - https://nf-co.re - - - -INFO     Looking for test workflow entry points: 'tests/modules/nf-core/fastqc/main.nf' -──────────────────────────────────────────────────────────────────────────────────────────────────── -INFO     Building test meta for entry point 'test_fastqc_single_end' -INFO     Running 'fastqc' test with command:                                                         -nextflow run ./tests/modules/nf-core/fastqc -entry test_fastqc_single_end -c  -./tests/config/nextflow.config -c ./tests/modules/nf-core/fastqc/nextflow.config --outdir  -/tmp/tmp17isquh4 -work-dir /tmp/tmpseaglcoa + + + + $ nf-core modules create-test-yml fastqc --no-prompts --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +CRITICAL Cannot find directory 'modules/fastqc'. Should be TOOL/SUBTOOL or TOOL      __main__.py:667 diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index 6b3ce27a4..662e5e596 100644 --- a/docs/images/nf-core-modules-create.svg +++ b/docs/images/nf-core-modules-create.svg @@ -19,74 +19,76 @@ font-weight: 700; } - .terminal-3073846549-matrix { + .terminal-323527755-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3073846549-title { + .terminal-323527755-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3073846549-r1 { fill: #c5c8c6 } -.terminal-3073846549-r2 { fill: #98a84b } -.terminal-3073846549-r3 { fill: #9a9b99 } -.terminal-3073846549-r4 { fill: #608ab1 } -.terminal-3073846549-r5 { fill: #d0b344 } -.terminal-3073846549-r6 { fill: #68a0b3;font-weight: bold } + .terminal-323527755-r1 { fill: #c5c8c6 } +.terminal-323527755-r2 { fill: #98a84b } +.terminal-323527755-r3 { fill: #9a9b99 } +.terminal-323527755-r4 { fill: #608ab1 } +.terminal-323527755-r5 { fill: #d0b344 } +.terminal-323527755-r6 { fill: #d08442;font-weight: bold } +.terminal-323527755-r7 { fill: #868887 } +.terminal-323527755-r8 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -98,25 +100,25 @@ - + - - $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.2 - https://nf-co.re - - - -INFO     Repository type: modules -INFO    Press enter to use default values (shown in brackets)or type your own responses.  -ctrl+click underlined text to open links. -INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9' + + $ 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 +    There is a new version of nf-core/tools available! (2.7.2) + + +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 diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg index 320672f91..46fc01463 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 2.7.2 - 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 - + + + + $ nf-core modules info abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +ERROR    Could not find module 'abacas'__main__.py:755 diff --git a/docs/images/nf-core-modules-install.svg b/docs/images/nf-core-modules-install.svg index 6fb029df0..aa2e329d6 100644 --- a/docs/images/nf-core-modules-install.svg +++ b/docs/images/nf-core-modules-install.svg @@ -19,70 +19,73 @@ font-weight: 700; } - .terminal-3957689443-matrix { + .terminal-2052881942-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3957689443-title { + .terminal-2052881942-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3957689443-r1 { fill: #c5c8c6 } -.terminal-3957689443-r2 { fill: #98a84b } -.terminal-3957689443-r3 { fill: #9a9b99 } -.terminal-3957689443-r4 { fill: #608ab1 } -.terminal-3957689443-r5 { fill: #d0b344 } + .terminal-2052881942-r1 { fill: #c5c8c6 } +.terminal-2052881942-r2 { fill: #98a84b } +.terminal-2052881942-r3 { fill: #9a9b99 } +.terminal-2052881942-r4 { fill: #608ab1 } +.terminal-2052881942-r5 { fill: #d0b344 } +.terminal-2052881942-r6 { fill: #d08442;font-weight: bold } +.terminal-2052881942-r7 { fill: #cc555a;font-weight: bold } +.terminal-2052881942-r8 { fill: #868887 } - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +103,24 @@ - + - - $ nf-core modules install abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.2 - https://nf-co.re - - - -INFO     Installing 'abacas' -INFO     Use the following statement to include this module:                                         - - include { ABACAS } from '../modules/nf-core/abacas/main'                                            - + + $ nf-core modules install abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +ERROR    Module 'abacas' not found in list of available modules.                       install.py:63 +INFO     Use the command 'nf-core modules list' to view available software             install.py:64 diff --git a/docs/images/nf-core-modules-lint.svg b/docs/images/nf-core-modules-lint.svg index b39f7aa4f..bc95f77e2 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 2.7.2 - https://nf-co.re - - - -INFO     Linting modules repo: '.' -INFO     Linting module: 'multiqc' - -╭───────────────────────╮ -│LINT RESULTS SUMMARY│ -├───────────────────────┤ -│[✔]  23 Tests Passed │ -│[!]   0 Test Warnings│ -│[✗]   0 Tests Failed │ -╰───────────────────────╯ + + $ nf-core modules lint multiqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +ERROR    Could not find the specified module: 'multiqc'__main__.py:715 diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index fab2cecf7..532289347 100644 --- a/docs/images/nf-core-modules-list-local.svg +++ b/docs/images/nf-core-modules-list-local.svg @@ -19,108 +19,110 @@ font-weight: 700; } - .terminal-2617511112-matrix { + .terminal-1197768805-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2617511112-title { + .terminal-1197768805-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2617511112-r1 { fill: #c5c8c6 } -.terminal-2617511112-r2 { fill: #98a84b } -.terminal-2617511112-r3 { fill: #9a9b99 } -.terminal-2617511112-r4 { fill: #608ab1 } -.terminal-2617511112-r5 { fill: #d0b344 } -.terminal-2617511112-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2617511112-r7 { fill: #868887;font-style: italic; } + .terminal-1197768805-r1 { fill: #c5c8c6 } +.terminal-1197768805-r2 { fill: #98a84b } +.terminal-1197768805-r3 { fill: #9a9b99 } +.terminal-1197768805-r4 { fill: #608ab1 } +.terminal-1197768805-r5 { fill: #d0b344 } +.terminal-1197768805-r6 { fill: #d08442;font-weight: bold } +.terminal-1197768805-r7 { fill: #868887 } +.terminal-1197768805-r8 { fill: #c5c8c6;font-weight: bold } +.terminal-1197768805-r9 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,36 +134,36 @@ - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.2 - https://nf-co.re - - - -INFO     Modules installed in '.':                                                                   - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -┃Module Name        ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ custom/dumpsoftwar… │ https://github.co… │ c8e35eb2055c099720… │ Bulk change conda  │ 2022-12-13 │ -│                     │                    │                     │ syntax for all     │            │ -│                     │                    │                     │ modules (#2654)    │            │ -│ fastqc              │ https://github.co… │ c8e35eb2055c099720… │ Bulk change conda  │ 2022-12-13 │ -│                     │                    │                     │ syntax for all     │            │ -│                     │                    │                     │ modules (#2654)    │            │ -│ multiqc             │ https://github.co… │ c8e35eb2055c099720… │ Bulk change conda  │ 2022-12-13 │ -│                     │                    │                     │ syntax for all     │            │ -│                     │                    │                     │ modules (#2654)    │            │ -[..truncated..] + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +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)              │            │ +[..truncated..] diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index cd2d1df6e..b26e5fc24 100644 --- a/docs/images/nf-core-modules-list-remote.svg +++ b/docs/images/nf-core-modules-list-remote.svg @@ -19,109 +19,110 @@ font-weight: 700; } - .terminal-3444989756-matrix { + .terminal-1507654550-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3444989756-title { + .terminal-1507654550-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3444989756-r1 { fill: #c5c8c6 } -.terminal-3444989756-r2 { fill: #98a84b } -.terminal-3444989756-r3 { fill: #9a9b99 } -.terminal-3444989756-r4 { fill: #608ab1 } -.terminal-3444989756-r5 { fill: #d0b344 } -.terminal-3444989756-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-3444989756-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-3444989756-r8 { fill: #868887;font-style: italic; } + .terminal-1507654550-r1 { fill: #c5c8c6 } +.terminal-1507654550-r2 { fill: #98a84b } +.terminal-1507654550-r3 { fill: #9a9b99 } +.terminal-1507654550-r4 { fill: #608ab1 } +.terminal-1507654550-r5 { fill: #d0b344 } +.terminal-1507654550-r6 { fill: #d08442;font-weight: bold } +.terminal-1507654550-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-1507654550-r8 { fill: #868887 } +.terminal-1507654550-r9 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +134,36 @@ - + - - $ nf-core modules list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.2 - https://nf-co.re - - - -INFO     Modules available from https://github.com/nf-core/modules.git(master):                     - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Module Name                                          ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ abacas                                                │ -│ abricate/run                                          │ -│ abricate/summary                                      │ -│ adapterremoval                                        │ -│ adapterremovalfixprefix                               │ -│ agat/convertspgff2gtf                                 │ -│ agat/convertspgxf2gxf                                 │ -│ agat/spstatistics                                     │ -│ agat/sqstatbasic                                      │ -[..truncated..] + + $ nf-core modules list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +INFO     Modules available from nf-core/modules (master):                                list.py:119 + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Module Name                                                  ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ nf-core/abacas                                                │ +│ nf-core/abricate/run                                          │ +│ nf-core/abricate/summary                                      │ +│ nf-core/adapterremoval                                        │ +│ nf-core/adapterremovalfixprefix                               │ +│ nf-core/admixture                                             │ +│ nf-core/affy/justrma                                          │ +│ nf-core/agat/convertspgff2gtf                                 │ +[..truncated..] diff --git a/docs/images/nf-core-modules-mulled.svg b/docs/images/nf-core-modules-mulled.svg index 2ac4b28f2..d03e7a665 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 2.7.2 - https://nf-co.re - - -INFO     Found docker image on quay.io! ✨                                                           -INFO     Mulled container hash:                                                                      -mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 + + $ nf-core modules mulled pysam==0.16.0.1 biopython==1.78 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +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 729bb1d51..bad2028c3 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 2.7.2 - https://nf-co.re - - - -ERROR    Module 'modules/nf-core/fastqc' is unchanged. No patch to compute                           + + $ nf-core modules patch fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +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 ce72c00e1..17157949a 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 2.7.2 - https://nf-co.re - - - -INFO     Removed files for 'abacas' and it's dependencies 'abacas'.                                  + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +ERROR    Module directory does not exist: 'modules/nf-core/modules/abacas'remove.py:45 diff --git a/docs/images/nf-core-modules-test.svg b/docs/images/nf-core-modules-test.svg index c11314a7d..89e562691 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 2.7.2 - https://nf-co.re - - - -────────────────────────────────────────── samtools/view ─────────────────────────────────────────── -INFO     Running pytest for module 'samtools/view' + + + + $ nf-core modules test samtools/view --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +CRITICAL Cannot find directory 'modules/samtools/view'. Should be TOOL/SUBTOOL or    __main__.py:846 +         TOOL. Are you running the tests inside the nf-core/modules main directory?   diff --git a/docs/images/nf-core-modules-update.svg b/docs/images/nf-core-modules-update.svg index 161c6b2a5..5d1a0ed52 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 2.7.2 - https://nf-co.re - - - -INFO    'modules/nf-core/abacas' is already up to date                                              -INFO    'modules/nf-core/custom/dumpsoftwareversions' is already up to date                         -INFO    'modules/nf-core/fastqc' is already up to date                                              -INFO    'modules/nf-core/multiqc' is already up to date                                             -INFO     Updates complete ✨                                                                         + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +WARNING  Module 'custom/dumpsoftwareversions' does not exist in 'nf-core/modules'.     update.py:448 +         Skipping... +WARNING  Module 'fastqc' does not exist in 'nf-core/modules'. Skipping...update.py:448 +WARNING  Module 'multiqc' does not exist in 'nf-core/modules'. Skipping...update.py:448 +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 6ebf92dc2..396cb52f1 100644 --- a/docs/images/nf-core-schema-build.svg +++ b/docs/images/nf-core-schema-build.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - -======= - .terminal-1833749233-r1 { fill: #c5c8c6 } -.terminal-1833749233-r2 { fill: #98a84b } -.terminal-1833749233-r3 { fill: #9a9b99 } -.terminal-1833749233-r4 { fill: #608ab1 } -.terminal-1833749233-r5 { fill: #d0b344 } -.terminal-1833749233-r6 { fill: #98a84b;font-weight: bold } -.terminal-1833749233-r7 { fill: #868887;font-weight: bold } -.terminal-1833749233-r8 { fill: #868887 } -.terminal-1833749233-r9 { fill: #4e707b;font-weight: bold } -.terminal-1833749233-r10 { fill: #68a0b3;font-weight: bold } - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + + + + - + -<<<<<<< HEAD - - - - $ 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 30 params: './nextflow_schema.json'schema.py:173 -======= - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.2 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 30 params) -INFO     Writing schema with 31 params: './nextflow_schema.json' ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO    [✓] Default parameters match schema validationschema.py:237 +INFO    [✓] Pipeline schema looks valid(found 27 params)schema.py:95 +INFO     Writing schema with 30 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 17d7fb521..1551da73e 100644 --- a/docs/images/nf-core-schema-lint.svg +++ b/docs/images/nf-core-schema-lint.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - -======= - .terminal-1041388458-r1 { fill: #c5c8c6 } -.terminal-1041388458-r2 { fill: #98a84b } -.terminal-1041388458-r3 { fill: #9a9b99 } -.terminal-1041388458-r4 { fill: #608ab1 } -.terminal-1041388458-r5 { fill: #d0b344 } -.terminal-1041388458-r6 { fill: #98a84b;font-weight: bold } -.terminal-1041388458-r7 { fill: #868887;font-weight: bold } -.terminal-1041388458-r8 { fill: #868887 } -.terminal-1041388458-r9 { fill: #4e707b;font-weight: bold } - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + - + - + - + - + + + + - + -<<<<<<< HEAD - - - - $ 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    [✗] Invalid default parameters found:schema.py:84 -  --fail_unrecognised_params: String should not be set to `false` -  --lenient_mode: String should not be set to `false` - -NOTE: Use null in config for no default. -======= - + - - $ nf-core schema lint nextflow_schema.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.2 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 31 params) ->>>>>>> 7f305024edcfe6e58109daa5a644c905e314bab8 + + $ nf-core schema lint nextflow_schema.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO    [✓] Default parameters match schema validationschema.py:237 +INFO    [✗] Invalid default parameters found:schema.py:84 +  --fail_unrecognised_params: String should not be set to `false` +  --lenient_mode: String should not be set to `false` + +NOTE: Use null in config for no default. diff --git a/docs/images/nf-core-schema-validate.svg b/docs/images/nf-core-schema-validate.svg index 3133ec66b..55ad64204 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 2.7.2 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 93 params) -INFO    [✓] Input parameters look valid + + $ nf-core schema validate nf-core-rnaseq/workflow nf-params.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +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 99c164c14..71e9a6bf2 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 2.7.2 - https://nf-co.re - - -INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthing -INFO     Original pipeline repository branch is 'master' -INFO     Deleting all files in 'TEMPLATE' branch                                                     -INFO     Making a new template pipeline using pipeline variables                                     + + $ nf-core sync + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +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