From 203712f4a0030deec426e69e636e6573022b6cb2 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 23 Feb 2023 12:02:58 +0000 Subject: [PATCH] Generate new screengrabs with rich-codex --- docs/images/nf-core-lint.svg | 498 ++++++++++++++----- docs/images/nf-core-modules-bump-version.svg | 118 ++--- docs/images/nf-core-modules-create-test.svg | 128 ++--- docs/images/nf-core-modules-create.svg | 136 ++--- 4 files changed, 508 insertions(+), 372 deletions(-) diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg index 6e0bf2af48..47acc16cce 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: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 2.5.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-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index 48049fcfbb..94ba436bb6 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 -    There is a new version of nf-core/tools available! (2.7.2) - - - - -╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ -│[!] 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 5711bd8431..3f72db085a 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_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 + + + + $ 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 b485e9bc8c..662e5e596f 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 -    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 -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 + + $ 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