From 5c4477b28581f8aa06dc0a49eec2c63dc88adfdd Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 8 Dec 2022 11:52:11 +0000 Subject: [PATCH 1/4] Generate new screengrabs with rich-codex --- docs/images/nf-core-bump-version.svg | 89 ++-- docs/images/nf-core-create.svg | 137 +++--- docs/images/nf-core-download.svg | 87 ++-- docs/images/nf-core-launch-rnaseq.svg | 83 ++-- docs/images/nf-core-licences.svg | 131 +++-- docs/images/nf-core-lint.svg | 189 ++++--- docs/images/nf-core-list-rna.svg | 118 ++--- docs/images/nf-core-list-stars.svg | 104 ++-- docs/images/nf-core-list.svg | 108 ++-- docs/images/nf-core-modules-bump-version.svg | 106 ++-- docs/images/nf-core-modules-create-test.svg | 113 ++--- docs/images/nf-core-modules-create.svg | 135 ++--- docs/images/nf-core-modules-info.svg | 206 ++++---- docs/images/nf-core-modules-install.svg | 94 ++-- docs/images/nf-core-modules-lint.svg | 113 +++-- docs/images/nf-core-modules-list-local.svg | 131 +++-- docs/images/nf-core-modules-list-remote.svg | 133 +++-- docs/images/nf-core-modules-mulled.svg | 79 ++- docs/images/nf-core-modules-patch.svg | 73 ++- docs/images/nf-core-modules-remove.svg | 71 ++- docs/images/nf-core-modules-test.svg | 75 ++- docs/images/nf-core-modules-update.svg | 87 ++-- docs/images/nf-core-schema-build.svg | 84 ++-- docs/images/nf-core-schema-lint.svg | 78 +-- docs/images/nf-core-schema-validate.svg | 82 +-- .../nf-core-subworkflows-create-test.svg | 167 +++++++ docs/images/nf-core-subworkflows-create.svg | 143 ++++++ docs/images/nf-core-subworkflows-info.svg | 465 ++++++++++++++++++ docs/images/nf-core-subworkflows-install.svg | 167 +++++++ .../nf-core-subworkflows-list-local.svg | 168 +++++++ .../nf-core-subworkflows-list-remote.svg | 169 +++++++ docs/images/nf-core-subworkflows-remove.svg | 167 +++++++ docs/images/nf-core-subworkflows-test.svg | 167 +++++++ docs/images/nf-core-subworkflows-update.svg | 167 +++++++ docs/images/nf-core-sync.svg | 83 ++-- 35 files changed, 3175 insertions(+), 1394 deletions(-) create mode 100644 docs/images/nf-core-subworkflows-create-test.svg create mode 100644 docs/images/nf-core-subworkflows-create.svg create mode 100644 docs/images/nf-core-subworkflows-info.svg create mode 100644 docs/images/nf-core-subworkflows-install.svg create mode 100644 docs/images/nf-core-subworkflows-list-local.svg create mode 100644 docs/images/nf-core-subworkflows-list-remote.svg create mode 100644 docs/images/nf-core-subworkflows-remove.svg create mode 100644 docs/images/nf-core-subworkflows-test.svg create mode 100644 docs/images/nf-core-subworkflows-update.svg diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg index aed99cd069..0dc1616cb8 100644 --- a/docs/images/nf-core-bump-version.svg +++ b/docs/images/nf-core-bump-version.svg @@ -19,78 +19,77 @@ font-weight: 700; } - .terminal-1201319354-matrix { + .terminal-456906266-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1201319354-title { + .terminal-456906266-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1201319354-r1 { fill: #c5c8c6 } -.terminal-1201319354-r2 { fill: #98a84b } -.terminal-1201319354-r3 { fill: #9a9b99 } -.terminal-1201319354-r4 { fill: #608ab1 } -.terminal-1201319354-r5 { fill: #d0b344 } -.terminal-1201319354-r6 { fill: #868887 } -.terminal-1201319354-r7 { fill: #cc555a } + .terminal-456906266-r1 { fill: #c5c8c6 } +.terminal-456906266-r2 { fill: #98a84b } +.terminal-456906266-r3 { fill: #9a9b99 } +.terminal-456906266-r4 { fill: #608ab1 } +.terminal-456906266-r5 { fill: #d0b344 } +.terminal-456906266-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -102,26 +101,26 @@ - + - - $ nf-core bump-version 1.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - -INFO     Changing version number from '1.0dev' to '1.1'bump_version.py:35 -INFO     Updated version in 'nextflow.config'bump_version.py:164 - - version         = '1.0dev' - + version = '1.1' - - + + $ nf-core bump-version 1.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - 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' + + diff --git a/docs/images/nf-core-create.svg b/docs/images/nf-core-create.svg index e9731ad1a3..4c7e243fff 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 2.6 - https://nf-co.re - - -INFO     Creating new nf-core pipeline: 'nf-core/nextbigthing'create.py:236 -INFO     Initialising pipeline git repository                                          create.py:538 -INFO     Done. Remember to add a remote and push to GitHub:                            create.py:545 - 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:551 -         syncing.                                                                       -INFO    !!!!!! IMPORTANT !!!!!!create.py:227 - -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 2.7 - 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 diff --git a/docs/images/nf-core-download.svg b/docs/images/nf-core-download.svg index 51be23194a..6b19cc6433 100644 --- a/docs/images/nf-core-download.svg +++ b/docs/images/nf-core-download.svg @@ -19,77 +19,76 @@ font-weight: 700; } - .terminal-1992655221-matrix { + .terminal-3721474111-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1992655221-title { + .terminal-3721474111-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1992655221-r1 { fill: #c5c8c6 } -.terminal-1992655221-r2 { fill: #98a84b } -.terminal-1992655221-r3 { fill: #9a9b99 } -.terminal-1992655221-r4 { fill: #608ab1 } -.terminal-1992655221-r5 { fill: #d0b344 } -.terminal-1992655221-r6 { fill: #868887 } + .terminal-3721474111-r1 { fill: #c5c8c6 } +.terminal-3721474111-r2 { fill: #98a84b } +.terminal-3721474111-r3 { fill: #9a9b99 } +.terminal-3721474111-r4 { fill: #608ab1 } +.terminal-3721474111-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -101,26 +100,26 @@ - + - - $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -c none - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - -INFO     Saving 'nf-core/rnaseq'download.py:159 -          Pipeline revision: '3.8' -          Pull containers: 'none' -          Output directory: 'nf-core-rnaseq' -INFO     Downloading workflow files from GitHub                                      download.py:162 -INFO     Downloading centralised configs from GitHub                                 download.py:166 + + $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -c none + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - 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                                                 diff --git a/docs/images/nf-core-launch-rnaseq.svg b/docs/images/nf-core-launch-rnaseq.svg index a52e1d7891..55a70279d9 100644 --- a/docs/images/nf-core-launch-rnaseq.svg +++ b/docs/images/nf-core-launch-rnaseq.svg @@ -19,73 +19,72 @@ font-weight: 700; } - .terminal-100502750-matrix { + .terminal-1175629223-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-100502750-title { + .terminal-1175629223-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-100502750-r1 { fill: #c5c8c6 } -.terminal-100502750-r2 { fill: #98a84b } -.terminal-100502750-r3 { fill: #9a9b99 } -.terminal-100502750-r4 { fill: #608ab1 } -.terminal-100502750-r5 { fill: #d0b344 } -.terminal-100502750-r6 { fill: #868887 } -.terminal-100502750-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-100502750-r8 { fill: #68a0b3;font-weight: bold } + .terminal-1175629223-r1 { fill: #c5c8c6 } +.terminal-1175629223-r2 { fill: #98a84b } +.terminal-1175629223-r3 { fill: #9a9b99 } +.terminal-1175629223-r4 { fill: #608ab1 } +.terminal-1175629223-r5 { fill: #d0b344 } +.terminal-1175629223-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1175629223-r7 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -97,24 +96,24 @@ - + - - $ nf-core launch rnaseq -r 3.8.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - -INFO     NOTE: This tool ignores any pipeline parameter defaults overwritten by        launch.py:131 -         Nextflow config files or profiles                                              - -INFO     Downloading workflow: nf-core/rnaseq (3.8.1)list.py:67 + + $ nf-core launch rnaseq -r 3.8.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - 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) diff --git a/docs/images/nf-core-licences.svg b/docs/images/nf-core-licences.svg index 4173e2faa0..db45603a7b 100644 --- a/docs/images/nf-core-licences.svg +++ b/docs/images/nf-core-licences.svg @@ -19,109 +19,108 @@ font-weight: 700; } - .terminal-1928727807-matrix { + .terminal-2422327830-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1928727807-title { + .terminal-2422327830-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1928727807-r1 { fill: #c5c8c6 } -.terminal-1928727807-r2 { fill: #98a84b } -.terminal-1928727807-r3 { fill: #9a9b99 } -.terminal-1928727807-r4 { fill: #608ab1 } -.terminal-1928727807-r5 { fill: #d0b344 } -.terminal-1928727807-r6 { fill: #68a0b3;font-weight: bold } -.terminal-1928727807-r7 { fill: #868887 } -.terminal-1928727807-r8 { fill: #c5c8c6;font-weight: bold } + .terminal-2422327830-r1 { fill: #c5c8c6 } +.terminal-2422327830-r2 { fill: #98a84b } +.terminal-2422327830-r3 { fill: #9a9b99 } +.terminal-2422327830-r4 { fill: #608ab1 } +.terminal-2422327830-r5 { fill: #d0b344 } +.terminal-2422327830-r6 { fill: #68a0b3;font-weight: bold } +.terminal-2422327830-r7 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +132,36 @@ - + - - $ nf-core licences deepvariant - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - -INFO     Fetching licence information for 8 tools                                     licences.py:77 -INFO     Warning: This tool only prints licence information for the software tools    licences.py:98 -         packaged using conda.                                                         -INFO     The pipeline may use other software and dependencies not described here.     licences.py:99 -┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓ -┃Package Name┃Version┃Licence┃ -┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩ -│ lbzip2       │ 2.5     │ GPL v3  │ -│ deepvariant  │ 0.7.0   │ MIT     │ -│ htslib       │ 1.9     │ MIT     │ -│ picard       │ 2.18.7  │ MIT     │ -│ pip          │ 10.0.1  │ MIT     │ -│ samtools     │ 1.9     │ MIT     │ -│ python       │ 2.7.15  │ PSF     │ -│ bzip2        │ 1.0.6   │ bzip2   │ -└──────────────┴─────────┴─────────┘ + + $ nf-core licences deepvariant + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - 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   │ +└──────────────┴─────────┴─────────┘ diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg index d5b62b7c01..b255a7c4de 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 2.6 - https://nf-co.re - - - -INFO     Testing pipeline: .__init__.py:265 - - -╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ -││ -│pipeline_todos: pipeline_todos│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - -╭─[!] 2 Module Test Warnings─────────────────────────────────────────────────────────────────────╮ -│                                           ╷                          ╷                           │ -│Module name                              │File path               │Test message             │ -│╶──────────────────────────────────────────┼──────────────────────────┼──────────────────────────╴│ -│samplesheet_check│modules/local/sampleshe…│Process label unspecified│ -│samplesheet_check│modules/local/sampleshe…│when: condition has been │ -│││removed│ -│                                           ╵                          ╵                           │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────╮ -│LINT RESULTS SUMMARY │ -├───────────────────────┤ -│[✔] 178 Tests Passed│ -│[?]   1 Test Ignored│ -│[!]   2 Test Warnings│ -│[✗]   0 Tests Failed│ -╰───────────────────────╯ + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +INFO     Testing pipeline: . + + +╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ +││ +│pipeline_todos: pipeline_todos│ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + +╭─[!] 2 Module Test Warnings─────────────────────────────────────────────────────────────────────╮ +│                                           ╷                          ╷                           │ +│Module name                              │File path               │Test message             │ +│╶──────────────────────────────────────────┼──────────────────────────┼──────────────────────────╴│ +│custom/dumpsoftwareversions│modules/nf-core/custom/…│New version available│ +│fastqc│modules/nf-core/fastqc  │New version available│ +│                                           ╵                          ╵                           │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭───────────────────────╮ +│LINT RESULTS SUMMARY │ +├───────────────────────┤ +│[✔] 178 Tests Passed│ +│[?]   1 Test Ignored│ +│[!]   2 Test Warnings│ +│[✗]   0 Tests Failed│ +╰───────────────────────╯ diff --git a/docs/images/nf-core-list-rna.svg b/docs/images/nf-core-list-rna.svg index 00b4170ed2..0dfaae8459 100644 --- a/docs/images/nf-core-list-rna.svg +++ b/docs/images/nf-core-list-rna.svg @@ -19,99 +19,99 @@ font-weight: 700; } - .terminal-1720318354-matrix { + .terminal-1440873036-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1720318354-title { + .terminal-1440873036-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1720318354-r1 { fill: #c5c8c6 } -.terminal-1720318354-r2 { fill: #98a84b } -.terminal-1720318354-r3 { fill: #9a9b99 } -.terminal-1720318354-r4 { fill: #608ab1 } -.terminal-1720318354-r5 { fill: #d0b344 } -.terminal-1720318354-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1720318354-r7 { fill: #868887 } + .terminal-1440873036-r1 { fill: #c5c8c6 } +.terminal-1440873036-r2 { fill: #98a84b } +.terminal-1440873036-r3 { fill: #9a9b99 } +.terminal-1440873036-r4 { fill: #608ab1 } +.terminal-1440873036-r5 { fill: #d0b344 } +.terminal-1440873036-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1440873036-r7 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -123,33 +123,33 @@ - + - - $ nf-core list rna rna-seq - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq               │   510 │            3.9 │   4 days ago │           - │ -                   │ -│ rnafusion            │    80 │          2.1.0 │ 3 months ago │           - │ -                   │ -│ smrnaseq             │    44 │          2.0.0 │ 4 months ago │           - │ -                   │ -│ dualrnaseq           │     8 │          1.0.0 │  2 years ago │           - │ -                   │ -│ circrna              │    20 │            dev │            - │           - │ -                   │ -│ lncpipe              │    22 │            dev │            - │           - │ -                   │ -│ scflow               │    13 │            dev │            - │           - │ -                   │ -│ spatialtranscriptom… │    12 │            dev │            - │           - │ -                   │ -└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ + + $ nf-core list rna rna-seq + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ smrnaseq             │    44 │          2.1.0 │ 1 months ago │           - │ -                   │ +│ rnaseq               │   538 │            3.9 │ 2 months ago │           - │ -                   │ +│ rnafusion            │    83 │          2.1.0 │ 5 months ago │           - │ -                   │ +│ dualrnaseq           │     8 │          1.0.0 │  2 years ago │           - │ -                   │ +│ circrna              │    24 │            dev │            - │           - │ -                   │ +│ lncpipe              │    23 │            dev │            - │           - │ -                   │ +│ scflow               │    14 │            dev │            - │           - │ -                   │ +│ spatialtranscriptom… │    12 │            dev │            - │           - │ -                   │ +└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg index 5c61a13a3a..80d81c4dcd 100644 --- a/docs/images/nf-core-list-stars.svg +++ b/docs/images/nf-core-list-stars.svg @@ -19,88 +19,88 @@ font-weight: 700; } - .terminal-1833040706-matrix { + .terminal-2329934618-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1833040706-title { + .terminal-2329934618-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1833040706-r1 { fill: #c5c8c6 } -.terminal-1833040706-r2 { fill: #98a84b } -.terminal-1833040706-r3 { fill: #9a9b99 } -.terminal-1833040706-r4 { fill: #608ab1 } -.terminal-1833040706-r5 { fill: #d0b344 } -.terminal-1833040706-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1833040706-r7 { fill: #868887 } -.terminal-1833040706-r8 { fill: #868887;font-style: italic; } + .terminal-2329934618-r1 { fill: #c5c8c6 } +.terminal-2329934618-r2 { fill: #98a84b } +.terminal-2329934618-r3 { fill: #9a9b99 } +.terminal-2329934618-r4 { fill: #608ab1 } +.terminal-2329934618-r5 { fill: #d0b344 } +.terminal-2329934618-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-2329934618-r7 { fill: #868887 } +.terminal-2329934618-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -112,29 +112,29 @@ - + - - $ nf-core list -s stars - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq               │   510 │            3.9 │   4 days ago │           - │ -                   │ -│ sarek                │   193 │          3.0.2 │  1 weeks ago │           - │ -                   │ -│ chipseq              │   127 │          2.0.0 │    yesterday │           - │ -                   │ -│ atacseq              │   117 │          1.2.2 │ 5 months ago │           - │ -                   │ -[..truncated..] + + $ nf-core list -s stars + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq               │   538 │            3.9 │ 2 months ago │           - │ -                   │ +│ sarek                │   210 │          3.1.1 │  2 weeks ago │           - │ -                   │ +│ chipseq              │   133 │          2.0.0 │ 2 months ago │           - │ -                   │ +│ atacseq              │   123 │            2.0 │   1 week ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg index 3c20bf2e71..efd90f47f8 100644 --- a/docs/images/nf-core-list.svg +++ b/docs/images/nf-core-list.svg @@ -19,91 +19,91 @@ font-weight: 700; } - .terminal-602830802-matrix { + .terminal-2923789563-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-602830802-title { + .terminal-2923789563-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-602830802-r1 { fill: #c5c8c6 } -.terminal-602830802-r2 { fill: #98a84b } -.terminal-602830802-r3 { fill: #9a9b99 } -.terminal-602830802-r4 { fill: #608ab1 } -.terminal-602830802-r5 { fill: #d0b344 } -.terminal-602830802-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-602830802-r7 { fill: #868887 } -.terminal-602830802-r8 { fill: #868887;font-style: italic; } + .terminal-2923789563-r1 { fill: #c5c8c6 } +.terminal-2923789563-r2 { fill: #98a84b } +.terminal-2923789563-r3 { fill: #9a9b99 } +.terminal-2923789563-r4 { fill: #608ab1 } +.terminal-2923789563-r5 { fill: #d0b344 } +.terminal-2923789563-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-2923789563-r7 { fill: #868887 } +.terminal-2923789563-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +115,30 @@ - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ chipseq              │   127 │          2.0.0 │    yesterday │           - │ -                   │ -│ rnaseq               │   510 │            3.9 │   4 days ago │           - │ -                   │ -│ isoseq               │     5 │          1.1.1 │   1 week ago │           - │ -                   │ -│ sarek                │   193 │          3.0.2 │  1 weeks ago │           - │ -                   │ -│ airrflow             │    19 │          2.3.0 │  3 weeks ago │           - │ -                   │ -[..truncated..] + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ ampliseq             │   101 │          2.4.1 │ 20 hours ago │           - │ -                   │ +│ airrflow             │    24 │          2.4.0 │   2 days ago │           - │ -                   │ +│ mhcquant             │    21 │          2.4.0 │   6 days ago │           - │ -                   │ +│ atacseq              │   123 │            2.0 │   1 week ago │           - │ -                   │ +│ methylseq            │    95 │          2.2.0 │  1 weeks ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index ee5dd12b1b..9f760347a3 100644 --- a/docs/images/nf-core-modules-bump-version.svg +++ b/docs/images/nf-core-modules-bump-version.svg @@ -19,90 +19,90 @@ font-weight: 700; } - .terminal-578811831-matrix { + .terminal-824833976-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-578811831-title { + .terminal-824833976-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-578811831-r1 { fill: #c5c8c6 } -.terminal-578811831-r2 { fill: #98a84b } -.terminal-578811831-r3 { fill: #9a9b99 } -.terminal-578811831-r4 { fill: #608ab1 } -.terminal-578811831-r5 { fill: #d0b344 } -.terminal-578811831-r6 { fill: #98a84b;font-weight: bold } -.terminal-578811831-r7 { fill: #c5c8c6;font-weight: bold } + .terminal-824833976-r1 { fill: #c5c8c6 } +.terminal-824833976-r2 { fill: #98a84b } +.terminal-824833976-r3 { fill: #9a9b99 } +.terminal-824833976-r4 { fill: #608ab1 } +.terminal-824833976-r5 { fill: #d0b344 } +.terminal-824833976-r6 { fill: #98a84b;font-weight: bold } +.terminal-824833976-r7 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -114,30 +114,30 @@ - + - - $ nf-core modules bump-versions fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - 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 2.7 - https://nf-co.re + + + + +╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ +│[!] 1 Module version up to date.│ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ +│Module name                             │Update Message                                       │ +├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ +│ fastqc                                   │ Module version up to date: fastqc                     │ +╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ diff --git a/docs/images/nf-core-modules-create-test.svg b/docs/images/nf-core-modules-create-test.svg index 8f05428006..a9bf5835bc 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 2.6 - https://nf-co.re - - - -INFO     Looking for test workflow entry points:                             test_yml_builder.py:128 -'tests/modules/nf-core/fastqc/main.nf' -──────────────────────────────────────────────────────────────────────────────────────────────────── -INFO     Building test meta for entry point 'test_fastqc_single_end'test_yml_builder.py:162 -INFO     Running 'fastqc' test with command:                                 test_yml_builder.py:330 -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/tmpha4zaib5 -work-dir /tmp/tmp1swft0ph + + $ nf-core modules create-test-yml fastqc --no-prompts --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - 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' +INFO     Running 'fastqc' test with command:                                                         +nextflow run ./tests/modules/nf-core/fastqc -entry test_fastqc -c  +./tests/config/nextflow.config -c ./tests/modules/nf-core/fastqc/nextflow.config --outdir  +/tmp/tmpk231usbb -work-dir /tmp/tmpvt2u8pj3 diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index b845061eb0..90626c9a55 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 2.6 - https://nf-co.re - - - -INFO     Repository type: modulescreate.py:99 -INFO    Press enter to use default values (shown in brackets)or type your own create.py:103 -responses. ctrl+click underlined text to open links. -INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9'create.py:171 -INFO     Could not find a Docker/Singularity container (Unexpected response code `503` create.py:200 -         for                                                                            -https://api.biocontainers.pro/ga4gh/trs/v2/tools/fastqc/versions/fastqc-0.11. -9) + + $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - 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' +INFO     Using Docker container: 'quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1' +INFO     Using Singularity container:                                                                +'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--hdfd78af_1' +INFO     Created / edited following files:                                                           +           ./modules/nf-core/fastqc/main.nf +           ./modules/nf-core/fastqc/meta.yml +           ./tests/modules/nf-core/fastqc/main.nf +           ./tests/modules/nf-core/fastqc/test.yml +           ./tests/modules/nf-core/fastqc/nextflow.config +           ./tests/config/pytest_modules.yml diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg index 546a92b854..b22069ca8c 100644 --- a/docs/images/nf-core-modules-info.svg +++ b/docs/images/nf-core-modules-info.svg @@ -19,163 +19,163 @@ font-weight: 700; } - .terminal-4091539959-matrix { + .terminal-377483768-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4091539959-title { + .terminal-377483768-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4091539959-r1 { fill: #c5c8c6 } -.terminal-4091539959-r2 { fill: #98a84b } -.terminal-4091539959-r3 { fill: #9a9b99 } -.terminal-4091539959-r4 { fill: #608ab1 } -.terminal-4091539959-r5 { fill: #d0b344 } -.terminal-4091539959-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-4091539959-r7 { fill: #98a84b;font-weight: bold } -.terminal-4091539959-r8 { fill: #868887 } -.terminal-4091539959-r9 { fill: #d08442 } -.terminal-4091539959-r10 { fill: #868887;font-style: italic; } -.terminal-4091539959-r11 { fill: #98729f } + .terminal-377483768-r1 { fill: #c5c8c6 } +.terminal-377483768-r2 { fill: #98a84b } +.terminal-377483768-r3 { fill: #9a9b99 } +.terminal-377483768-r4 { fill: #608ab1 } +.terminal-377483768-r5 { fill: #d0b344 } +.terminal-377483768-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-377483768-r7 { fill: #98a84b;font-weight: bold } +.terminal-377483768-r8 { fill: #868887 } +.terminal-377483768-r9 { fill: #d08442 } +.terminal-377483768-r10 { fill: #868887;font-style: italic; } +.terminal-377483768-r11 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -187,53 +187,53 @@ - + - - $ nf-core modules info abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - 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 2.7 - https://nf-co.re + + + +╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ +│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ +│ 🔧 Tools: abacas                                                                                 │ +│ 📖 Description: contiguate draft genome assembly                                                 │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +                  ╷                                                                   ╷              +📥 Inputs        │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} +                  ╵                                                                   ╵              +                  ╷                                                                   ╷              +📤 Outputs       │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + results  (files)│List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* +                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ +                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ +                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ +                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + versions  (file)│File containing software versions                                  │versions.yml +                  ╵                                                                   ╵              + + 💻  Installation command: nf-core modules install abacas + diff --git a/docs/images/nf-core-modules-install.svg b/docs/images/nf-core-modules-install.svg index def3a19771..4a53bd06c8 100644 --- a/docs/images/nf-core-modules-install.svg +++ b/docs/images/nf-core-modules-install.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + - + - + - - $ nf-core modules install abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - - -INFO     Installing 'abacas'install.py:131 -INFO     Include statement: include { ABACAS } from '../modules/nf-core/abacas/main'install.py:140 + + $ nf-core modules install abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +INFO     Installing 'abacas' +INFO     Use the following statement to include this module:                                         + + include { ABACAS } from '../modules/nf-core/abacas/main'                                            + diff --git a/docs/images/nf-core-modules-lint.svg b/docs/images/nf-core-modules-lint.svg index fdaf8e8bad..0531cdfe79 100644 --- a/docs/images/nf-core-modules-lint.svg +++ b/docs/images/nf-core-modules-lint.svg @@ -19,95 +19,94 @@ font-weight: 700; } - .terminal-663186508-matrix { + .terminal-2882701330-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-663186508-title { + .terminal-2882701330-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-663186508-r1 { fill: #c5c8c6 } -.terminal-663186508-r2 { fill: #98a84b } -.terminal-663186508-r3 { fill: #9a9b99 } -.terminal-663186508-r4 { fill: #608ab1 } -.terminal-663186508-r5 { fill: #d0b344 } -.terminal-663186508-r6 { fill: #868887 } -.terminal-663186508-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-663186508-r8 { fill: #98a84b;font-weight: bold } -.terminal-663186508-r9 { fill: #cc555a } + .terminal-2882701330-r1 { fill: #c5c8c6 } +.terminal-2882701330-r2 { fill: #98a84b } +.terminal-2882701330-r3 { fill: #9a9b99 } +.terminal-2882701330-r4 { fill: #608ab1 } +.terminal-2882701330-r5 { fill: #d0b344 } +.terminal-2882701330-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-2882701330-r7 { fill: #98a84b;font-weight: bold } +.terminal-2882701330-r8 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -119,31 +118,31 @@ - + - - $ nf-core modules lint multiqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - - -INFO     Linting modules repo: '.'__init__.py:200 -INFO     Linting module: 'multiqc'__init__.py:204 - -╭───────────────────────╮ -│LINT RESULTS SUMMARY│ -├───────────────────────┤ -│[✔]  23 Tests Passed │ -│[!]   0 Test Warnings│ -│[✗]   0 Tests Failed │ -╰───────────────────────╯ + + $ nf-core modules lint multiqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +INFO     Linting modules repo: '.' +INFO     Linting module: 'multiqc' + +╭───────────────────────╮ +│LINT RESULTS SUMMARY│ +├───────────────────────┤ +│[✔]  23 Tests Passed │ +│[!]   0 Test Warnings│ +│[✗]   0 Tests Failed │ +╰───────────────────────╯ diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index 02bc53bd4c..0d5cdf6f2f 100644 --- a/docs/images/nf-core-modules-list-local.svg +++ b/docs/images/nf-core-modules-list-local.svg @@ -19,109 +19,108 @@ font-weight: 700; } - .terminal-3572137377-matrix { + .terminal-2639661206-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3572137377-title { + .terminal-2639661206-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3572137377-r1 { fill: #c5c8c6 } -.terminal-3572137377-r2 { fill: #98a84b } -.terminal-3572137377-r3 { fill: #9a9b99 } -.terminal-3572137377-r4 { fill: #608ab1 } -.terminal-3572137377-r5 { fill: #d0b344 } -.terminal-3572137377-r6 { fill: #868887 } -.terminal-3572137377-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-3572137377-r8 { fill: #868887;font-style: italic; } + .terminal-2639661206-r1 { fill: #c5c8c6 } +.terminal-2639661206-r2 { fill: #98a84b } +.terminal-2639661206-r3 { fill: #9a9b99 } +.terminal-2639661206-r4 { fill: #608ab1 } +.terminal-2639661206-r5 { fill: #d0b344 } +.terminal-2639661206-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-2639661206-r7 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +132,36 @@ - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - - -INFO     Modules installed in '.':                                                       list.py:138 - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -┃Module Name        ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ custom/dumpsoftwar… │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ -│                     │                    │                     │ nf-core/modules    │            │ -│                     │                    │                     │ repo (#2141)       │            │ -│ fastqc              │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ -│                     │                    │                     │ nf-core/modules    │            │ -│                     │                    │                     │ repo (#2141)       │            │ -│ multiqc             │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ -│                     │                    │                     │ nf-core/modules    │            │ -│                     │                    │                     │ repo (#2141)       │            │ -[..truncated..] + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +INFO     Modules installed in '.':                                                                   + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +┃Module Name        ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ custom/dumpsoftwar… │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ +│                     │                    │                     │ nf-core/modules    │            │ +│                     │                    │                     │ repo (#2141)       │            │ +│ fastqc              │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ +│                     │                    │                     │ nf-core/modules    │            │ +│                     │                    │                     │ repo (#2141)       │            │ +│ multiqc             │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ +│                     │                    │                     │ nf-core/modules    │            │ +│                     │                    │                     │ repo (#2141)       │            │ +[..truncated..] diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index 2d43fab033..0f37822110 100644 --- a/docs/images/nf-core-modules-list-remote.svg +++ b/docs/images/nf-core-modules-list-remote.svg @@ -19,110 +19,109 @@ font-weight: 700; } - .terminal-1649706811-matrix { + .terminal-3342753500-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1649706811-title { + .terminal-3342753500-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1649706811-r1 { fill: #c5c8c6 } -.terminal-1649706811-r2 { fill: #98a84b } -.terminal-1649706811-r3 { fill: #9a9b99 } -.terminal-1649706811-r4 { fill: #608ab1 } -.terminal-1649706811-r5 { fill: #d0b344 } -.terminal-1649706811-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-1649706811-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-1649706811-r8 { fill: #868887 } -.terminal-1649706811-r9 { fill: #868887;font-style: italic; } + .terminal-3342753500-r1 { fill: #c5c8c6 } +.terminal-3342753500-r2 { fill: #98a84b } +.terminal-3342753500-r3 { fill: #9a9b99 } +.terminal-3342753500-r4 { fill: #608ab1 } +.terminal-3342753500-r5 { fill: #d0b344 } +.terminal-3342753500-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-3342753500-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-3342753500-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -134,36 +133,36 @@ - + - - $ nf-core modules list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - - -INFO     Modules available from https://github.com/nf-core/modules.git(master):         list.py:133 - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Module Name                             ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ abacas                                   │ -│ abricate/run                             │ -│ abricate/summary                         │ -│ adapterremoval                           │ -│ adapterremovalfixprefix                  │ -│ agrvate                                  │ -│ allelecounter                            │ -│ ampir                                    │ -│ amplify/predict                          │ -[..truncated..] + + $ nf-core modules list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - 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..] diff --git a/docs/images/nf-core-modules-mulled.svg b/docs/images/nf-core-modules-mulled.svg index 3581be2c97..5373182936 100644 --- a/docs/images/nf-core-modules-mulled.svg +++ b/docs/images/nf-core-modules-mulled.svg @@ -19,70 +19,69 @@ font-weight: 700; } - .terminal-670140257-matrix { + .terminal-3390485959-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-670140257-title { + .terminal-3390485959-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-670140257-r1 { fill: #c5c8c6 } -.terminal-670140257-r2 { fill: #98a84b } -.terminal-670140257-r3 { fill: #9a9b99 } -.terminal-670140257-r4 { fill: #608ab1 } -.terminal-670140257-r5 { fill: #d0b344 } -.terminal-670140257-r6 { fill: #868887 } -.terminal-670140257-r7 { fill: #00823d;font-weight: bold } -.terminal-670140257-r8 { fill: #68a0b3;font-weight: bold } + .terminal-3390485959-r1 { fill: #c5c8c6 } +.terminal-3390485959-r2 { fill: #98a84b } +.terminal-3390485959-r3 { fill: #9a9b99 } +.terminal-3390485959-r4 { fill: #608ab1 } +.terminal-3390485959-r5 { fill: #d0b344 } +.terminal-3390485959-r6 { fill: #00823d;font-weight: bold } +.terminal-3390485959-r7 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -94,23 +93,23 @@ - + - - $ nf-core modules mulled pysam==0.16.0.1 biopython==1.78 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - -INFO     Found docker image on quay.io! ✨                                              mulled.py:68 -INFO     Mulled container hash:                                                      __main__.py:834 -mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 + + $ nf-core modules mulled pysam==0.16.0.1 biopython==1.78 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + +INFO     Found docker image on quay.io! ✨                                                           +INFO     Mulled container hash:                                                                      +mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 diff --git a/docs/images/nf-core-modules-patch.svg b/docs/images/nf-core-modules-patch.svg index 77432e0e75..3bc3f80ffc 100644 --- a/docs/images/nf-core-modules-patch.svg +++ b/docs/images/nf-core-modules-patch.svg @@ -19,66 +19,65 @@ font-weight: 700; } - .terminal-1687321738-matrix { + .terminal-239277571-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1687321738-title { + .terminal-239277571-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1687321738-r1 { fill: #c5c8c6 } -.terminal-1687321738-r2 { fill: #98a84b } -.terminal-1687321738-r3 { fill: #9a9b99 } -.terminal-1687321738-r4 { fill: #608ab1 } -.terminal-1687321738-r5 { fill: #d0b344 } -.terminal-1687321738-r6 { fill: #cc555a;font-weight: bold } -.terminal-1687321738-r7 { fill: #868887 } + .terminal-239277571-r1 { fill: #c5c8c6 } +.terminal-239277571-r2 { fill: #98a84b } +.terminal-239277571-r3 { fill: #9a9b99 } +.terminal-239277571-r4 { fill: #608ab1 } +.terminal-239277571-r5 { fill: #d0b344 } +.terminal-239277571-r6 { fill: #cc555a;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -90,22 +89,22 @@ - + - - $ nf-core modules patch fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - - -ERROR    Module 'modules/nf-core/fastqc' is unchanged. No patch to compute           __main__.py:571 + + $ nf-core modules patch fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +ERROR    Module 'modules/nf-core/fastqc' is unchanged. No patch to compute                           diff --git a/docs/images/nf-core-modules-remove.svg b/docs/images/nf-core-modules-remove.svg index 68f27318a4..a2dc8099d4 100644 --- a/docs/images/nf-core-modules-remove.svg +++ b/docs/images/nf-core-modules-remove.svg @@ -19,65 +19,64 @@ font-weight: 700; } - .terminal-1533629559-matrix { + .terminal-3629854034-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1533629559-title { + .terminal-3629854034-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1533629559-r1 { fill: #c5c8c6 } -.terminal-1533629559-r2 { fill: #98a84b } -.terminal-1533629559-r3 { fill: #9a9b99 } -.terminal-1533629559-r4 { fill: #608ab1 } -.terminal-1533629559-r5 { fill: #d0b344 } -.terminal-1533629559-r6 { fill: #868887 } + .terminal-3629854034-r1 { fill: #c5c8c6 } +.terminal-3629854034-r2 { fill: #98a84b } +.terminal-3629854034-r3 { fill: #9a9b99 } +.terminal-3629854034-r4 { fill: #608ab1 } +.terminal-3629854034-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -89,22 +88,22 @@ - + - - $ nf-core modules remove abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - - -INFO     Removing abacas                                                                remove.py:56 + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +INFO     Removed files for 'abacas' and it's dependencies 'abacas'.                                  diff --git a/docs/images/nf-core-modules-test.svg b/docs/images/nf-core-modules-test.svg index d815fd6787..92943a04a3 100644 --- a/docs/images/nf-core-modules-test.svg +++ b/docs/images/nf-core-modules-test.svg @@ -19,68 +19,67 @@ font-weight: 700; } - .terminal-566836186-matrix { + .terminal-53791440-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-566836186-title { + .terminal-53791440-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-566836186-r1 { fill: #c5c8c6 } -.terminal-566836186-r2 { fill: #98a84b } -.terminal-566836186-r3 { fill: #9a9b99 } -.terminal-566836186-r4 { fill: #608ab1 } -.terminal-566836186-r5 { fill: #d0b344 } -.terminal-566836186-r6 { fill: #868887 } + .terminal-53791440-r1 { fill: #c5c8c6 } +.terminal-53791440-r2 { fill: #98a84b } +.terminal-53791440-r3 { fill: #9a9b99 } +.terminal-53791440-r4 { fill: #608ab1 } +.terminal-53791440-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -92,23 +91,23 @@ - + - - $ nf-core modules test samtools/view --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - - -────────────────────────────────────────── samtools/view ─────────────────────────────────────────── -INFO     Running pytest for module 'samtools/view'module_test.py:180 + + $ nf-core modules test samtools/view --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +────────────────────────────────────────── samtools/view ─────────────────────────────────────────── +INFO     Running pytest for module 'samtools/view' diff --git a/docs/images/nf-core-modules-update.svg b/docs/images/nf-core-modules-update.svg index 641fc97ac7..d1fa771510 100644 --- a/docs/images/nf-core-modules-update.svg +++ b/docs/images/nf-core-modules-update.svg @@ -19,77 +19,76 @@ font-weight: 700; } - .terminal-542272369-matrix { + .terminal-3977922886-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-542272369-title { + .terminal-3977922886-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-542272369-r1 { fill: #c5c8c6 } -.terminal-542272369-r2 { fill: #98a84b } -.terminal-542272369-r3 { fill: #9a9b99 } -.terminal-542272369-r4 { fill: #608ab1 } -.terminal-542272369-r5 { fill: #d0b344 } -.terminal-542272369-r6 { fill: #868887 } + .terminal-3977922886-r1 { fill: #c5c8c6 } +.terminal-3977922886-r2 { fill: #98a84b } +.terminal-3977922886-r3 { fill: #9a9b99 } +.terminal-3977922886-r4 { fill: #608ab1 } +.terminal-3977922886-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -101,26 +100,26 @@ - + - - $ nf-core modules update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - - -INFO    'modules/nf-core/abacas' is already up to date                                update.py:165 -INFO    'modules/nf-core/custom/dumpsoftwareversions' is already up to date           update.py:165 -INFO    'modules/nf-core/fastqc' is already up to date                                update.py:165 -INFO    'modules/nf-core/multiqc' is already up to date                               update.py:165 -INFO     Updates complete ✨                                                           update.py:247 + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +INFO    'modules/nf-core/abacas' is already up to date                                              +INFO     Updating 'nf-core/custom/dumpsoftwareversions' +INFO     Updating 'nf-core/fastqc' +INFO    'modules/nf-core/multiqc' is already up to date                                             +INFO     Updates complete ✨                                                                         diff --git a/docs/images/nf-core-schema-build.svg b/docs/images/nf-core-schema-build.svg index db945fd020..90c012ed63 100644 --- a/docs/images/nf-core-schema-build.svg +++ b/docs/images/nf-core-schema-build.svg @@ -19,72 +19,72 @@ font-weight: 700; } - .terminal-520878211-matrix { + .terminal-3325086355-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-520878211-title { + .terminal-3325086355-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-520878211-r1 { fill: #c5c8c6 } -.terminal-520878211-r2 { fill: #98a84b } -.terminal-520878211-r3 { fill: #9a9b99 } -.terminal-520878211-r4 { fill: #608ab1 } -.terminal-520878211-r5 { fill: #d0b344 } -.terminal-520878211-r6 { fill: #98a84b;font-weight: bold } -.terminal-520878211-r7 { fill: #868887 } -.terminal-520878211-r8 { fill: #868887;font-weight: bold } -.terminal-520878211-r9 { fill: #4e707b;font-weight: bold } -.terminal-520878211-r10 { fill: #68a0b3;font-weight: bold } + .terminal-3325086355-r1 { fill: #c5c8c6 } +.terminal-3325086355-r2 { fill: #98a84b } +.terminal-3325086355-r3 { fill: #9a9b99 } +.terminal-3325086355-r4 { fill: #608ab1 } +.terminal-3325086355-r5 { fill: #d0b344 } +.terminal-3325086355-r6 { fill: #98a84b;font-weight: bold } +.terminal-3325086355-r7 { fill: #868887;font-weight: bold } +.terminal-3325086355-r8 { fill: #868887 } +.terminal-3325086355-r9 { fill: #4e707b;font-weight: bold } +.terminal-3325086355-r10 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,23 +96,23 @@ - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validationschema.py:237 -INFO    [✓] Pipeline schema looks valid(found 30 params)schema.py:95 -INFO     Writing schema with 31 params: './nextflow_schema.json'schema.py:173 + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 31 params) +INFO     Writing schema with 32 params: './nextflow_schema.json' diff --git a/docs/images/nf-core-schema-lint.svg b/docs/images/nf-core-schema-lint.svg index 179672a372..c7c6f38486 100644 --- a/docs/images/nf-core-schema-lint.svg +++ b/docs/images/nf-core-schema-lint.svg @@ -19,68 +19,68 @@ font-weight: 700; } - .terminal-4182908040-matrix { + .terminal-617173835-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4182908040-title { + .terminal-617173835-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4182908040-r1 { fill: #c5c8c6 } -.terminal-4182908040-r2 { fill: #98a84b } -.terminal-4182908040-r3 { fill: #9a9b99 } -.terminal-4182908040-r4 { fill: #608ab1 } -.terminal-4182908040-r5 { fill: #d0b344 } -.terminal-4182908040-r6 { fill: #98a84b;font-weight: bold } -.terminal-4182908040-r7 { fill: #868887 } -.terminal-4182908040-r8 { fill: #868887;font-weight: bold } -.terminal-4182908040-r9 { fill: #4e707b;font-weight: bold } + .terminal-617173835-r1 { fill: #c5c8c6 } +.terminal-617173835-r2 { fill: #98a84b } +.terminal-617173835-r3 { fill: #9a9b99 } +.terminal-617173835-r4 { fill: #608ab1 } +.terminal-617173835-r5 { fill: #d0b344 } +.terminal-617173835-r6 { fill: #98a84b;font-weight: bold } +.terminal-617173835-r7 { fill: #868887;font-weight: bold } +.terminal-617173835-r8 { fill: #868887 } +.terminal-617173835-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -92,22 +92,22 @@ - + - - $ nf-core schema lint nextflow_schema.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validationschema.py:237 -INFO    [✓] Pipeline schema looks valid(found 31 params)schema.py:95 + + $ nf-core schema lint nextflow_schema.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 32 params) diff --git a/docs/images/nf-core-schema-validate.svg b/docs/images/nf-core-schema-validate.svg index 755794c92b..d0afb57106 100644 --- a/docs/images/nf-core-schema-validate.svg +++ b/docs/images/nf-core-schema-validate.svg @@ -19,71 +19,71 @@ font-weight: 700; } - .terminal-2556505363-matrix { + .terminal-3174760220-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2556505363-title { + .terminal-3174760220-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2556505363-r1 { fill: #c5c8c6 } -.terminal-2556505363-r2 { fill: #98a84b } -.terminal-2556505363-r3 { fill: #9a9b99 } -.terminal-2556505363-r4 { fill: #608ab1 } -.terminal-2556505363-r5 { fill: #d0b344 } -.terminal-2556505363-r6 { fill: #98a84b;font-weight: bold } -.terminal-2556505363-r7 { fill: #868887 } -.terminal-2556505363-r8 { fill: #868887;font-weight: bold } -.terminal-2556505363-r9 { fill: #4e707b;font-weight: bold } + .terminal-3174760220-r1 { fill: #c5c8c6 } +.terminal-3174760220-r2 { fill: #98a84b } +.terminal-3174760220-r3 { fill: #9a9b99 } +.terminal-3174760220-r4 { fill: #608ab1 } +.terminal-3174760220-r5 { fill: #d0b344 } +.terminal-3174760220-r6 { fill: #98a84b;font-weight: bold } +.terminal-3174760220-r7 { fill: #868887;font-weight: bold } +.terminal-3174760220-r8 { fill: #868887 } +.terminal-3174760220-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -95,23 +95,23 @@ - + - - $ nf-core schema validate nf-core-rnaseq/workflow nf-params.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validationschema.py:237 -INFO    [✓] Pipeline schema looks valid(found 93 params)schema.py:95 -INFO    [✓] Input parameters look validschema.py:213 + + $ nf-core schema validate nf-core-rnaseq/workflow nf-params.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 93 params) +INFO    [✓] Input parameters look valid diff --git a/docs/images/nf-core-subworkflows-create-test.svg b/docs/images/nf-core-subworkflows-create-test.svg new file mode 100644 index 0000000000..20fc71e2e7 --- /dev/null +++ b/docs/images/nf-core-subworkflows-create-test.svg @@ -0,0 +1,167 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $ nf-core subworkflows create-test-yml bam_stats_samtools --no-prompts --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. + + + + diff --git a/docs/images/nf-core-subworkflows-create.svg b/docs/images/nf-core-subworkflows-create.svg new file mode 100644 index 0000000000..41c763ff7a --- /dev/null +++ b/docs/images/nf-core-subworkflows-create.svg @@ -0,0 +1,143 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot  --label process_low --meta  +--force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +Usage: nf-core subworkflows create [OPTIONS] subworkflow name                                       + +Try 'nf-core subworkflows create -h' for help. +╭─ Error ──────────────────────────────────────────────────────────────────────────────────────────╮ +│ No such option: --label Did you mean --help?                                                     │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + + + + + diff --git a/docs/images/nf-core-subworkflows-info.svg b/docs/images/nf-core-subworkflows-info.svg new file mode 100644 index 0000000000..b3c6b6ee42 --- /dev/null +++ b/docs/images/nf-core-subworkflows-info.svg @@ -0,0 +1,465 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $ nf-core subworkflows info bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ +│/opt/hostedtoolcache/Python/3.11.0/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/3.11.0/x64/lib/python3.11/site-packages/nf_core/__main__.py:105 in   │ +│run_nf_core│ +││ +│ 104 │   # Launch the click cli│ +│❱  105 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │ +│ 106 │ +││ +│/opt/hostedtoolcache/Python/3.11.0/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/3.11.0/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/3.11.0/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/3.11.0/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/3.11.0/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/3.11.0/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/3.11.0/x64/lib/python3.11/site-packages/click/core.py:760 in invoke│ +││ +│ 759 │   │   │   with ctx:                                                                     │ +│❱  760 │   │   │   │   return __callback(*args, **kwargs)                                        │ +│ 761 │ +││ +│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/click/decorators.py:26 in    │ +│new_func│ +││ +│ 25 │   defnew_func(*args, **kwargs):  # type: ignore│ +│❱  26 │   │   return f(get_current_context(), *args, **kwargs)                                   │ +│ 27 │ +││ +│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/nf_core/__main__.py:1087 in  │ +│info│ +││ +│1086 │   │   )                                                                                 │ +│❱ 1087 │   │   stdout.print(subworkflow_info.get_component_info())                               │ +│1088 │   except (UserWarning, LookupError) as e:                                               │ +││ +│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/nf_core/components/info.py:1│ +│49 in get_component_info│ +││ +│148 │   │   │ +│❱ 149 │   │   returnself.generate_component_info_help()                                         │ +│150 │ +││ +│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/nf_core/components/info.py:2│ +│62 in generate_component_info_help│ +││ +│261 │   │   │   │   │   inputs_table.add_row(                                                  │ +│❱ 262 │   │   │   │   │   │   f"[orange1 on black] {key} [/][dim i] ({info['type']})",           │ +│263 │   │   │   │   │   │   Markdown(info["description"] if info["description"] else""),      │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +TypeError: 'NoneType' object is not subscriptable + + + + diff --git a/docs/images/nf-core-subworkflows-install.svg b/docs/images/nf-core-subworkflows-install.svg new file mode 100644 index 0000000000..cfb6a57f4c --- /dev/null +++ b/docs/images/nf-core-subworkflows-install.svg @@ -0,0 +1,167 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $ nf-core subworkflows install bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. + + + + diff --git a/docs/images/nf-core-subworkflows-list-local.svg b/docs/images/nf-core-subworkflows-list-local.svg new file mode 100644 index 0000000000..10b3198e2d --- /dev/null +++ b/docs/images/nf-core-subworkflows-list-local.svg @@ -0,0 +1,168 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $ nf-core subworkflows list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +[..truncated..] + + + + diff --git a/docs/images/nf-core-subworkflows-list-remote.svg b/docs/images/nf-core-subworkflows-list-remote.svg new file mode 100644 index 0000000000..966ce82802 --- /dev/null +++ b/docs/images/nf-core-subworkflows-list-remote.svg @@ -0,0 +1,169 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $ nf-core subworkflows list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Subworkflow Name                            ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ bam_dedup_stats_samtools_umitools            │ +│ bam_markduplicates_picard                    │ +│ bam_qc_picard                                │ +│ bam_rseqc                                    │ +│ bam_sort_stats_samtools                      │ +│ bam_stats_samtools                           │ +│ bcl_demultiplex                              │ +│ bed_scatter_bedtools                         │ +│ bedgraph_bedclip_bedgraphtobigwig            │ +[..truncated..] + + + + diff --git a/docs/images/nf-core-subworkflows-remove.svg b/docs/images/nf-core-subworkflows-remove.svg new file mode 100644 index 0000000000..d6667f8e68 --- /dev/null +++ b/docs/images/nf-core-subworkflows-remove.svg @@ -0,0 +1,167 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $ nf-core subworkflows remove bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. + + + + diff --git a/docs/images/nf-core-subworkflows-test.svg b/docs/images/nf-core-subworkflows-test.svg new file mode 100644 index 0000000000..a407a2844d --- /dev/null +++ b/docs/images/nf-core-subworkflows-test.svg @@ -0,0 +1,167 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $ nf-core subworkflows test bam_rseqc --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. + + + + diff --git a/docs/images/nf-core-subworkflows-update.svg b/docs/images/nf-core-subworkflows-update.svg new file mode 100644 index 0000000000..c83f453da6 --- /dev/null +++ b/docs/images/nf-core-subworkflows-update.svg @@ -0,0 +1,167 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $ nf-core subworkflows update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. + + + + diff --git a/docs/images/nf-core-sync.svg b/docs/images/nf-core-sync.svg index dcd7d1790b..c607247f3c 100644 --- a/docs/images/nf-core-sync.svg +++ b/docs/images/nf-core-sync.svg @@ -19,73 +19,72 @@ font-weight: 700; } - .terminal-3476133111-matrix { + .terminal-1725630925-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3476133111-title { + .terminal-1725630925-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3476133111-r1 { fill: #c5c8c6 } -.terminal-3476133111-r2 { fill: #98a84b } -.terminal-3476133111-r3 { fill: #9a9b99 } -.terminal-3476133111-r4 { fill: #608ab1 } -.terminal-3476133111-r5 { fill: #d0b344 } -.terminal-3476133111-r6 { fill: #98729f } -.terminal-3476133111-r7 { fill: #ff2c7a } -.terminal-3476133111-r8 { fill: #868887 } + .terminal-1725630925-r1 { fill: #c5c8c6 } +.terminal-1725630925-r2 { fill: #98a84b } +.terminal-1725630925-r3 { fill: #9a9b99 } +.terminal-1725630925-r4 { fill: #608ab1 } +.terminal-1725630925-r5 { fill: #d0b344 } +.terminal-1725630925-r6 { fill: #98729f } +.terminal-1725630925-r7 { fill: #ff2c7a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -97,24 +96,24 @@ - + - - $ nf-core sync - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.6 - https://nf-co.re - - -INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthingsync.py:95 -INFO     Original pipeline repository branch is 'master'sync.py:149 -INFO     Deleting all files in 'TEMPLATE' branch                                         sync.py:205 -INFO     Making a new template pipeline using pipeline variables                         sync.py:223 + + $ nf-core sync + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7 - 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                                     From eecf1c7079ef89e918a7493fb2228ac2fc63e5e0 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 8 Dec 2022 13:07:18 +0000 Subject: [PATCH 2/4] Generate new screengrabs with rich-codex --- docs/images/nf-core-bump-version.svg | 88 ++-- docs/images/nf-core-create.svg | 126 ++--- docs/images/nf-core-download.svg | 86 ++-- docs/images/nf-core-launch-rnaseq.svg | 82 ++-- docs/images/nf-core-licences.svg | 130 +++--- docs/images/nf-core-lint.svg | 178 +++---- docs/images/nf-core-list-rna.svg | 118 ++--- docs/images/nf-core-list-stars.svg | 104 ++--- docs/images/nf-core-list.svg | 108 ++--- docs/images/nf-core-modules-bump-version.svg | 106 ++--- docs/images/nf-core-modules-create-test.svg | 98 ++-- docs/images/nf-core-modules-create.svg | 132 ++---- docs/images/nf-core-modules-info.svg | 206 ++++----- docs/images/nf-core-modules-install.svg | 86 ++-- docs/images/nf-core-modules-lint.svg | 112 ++--- docs/images/nf-core-modules-list-local.svg | 130 +++--- docs/images/nf-core-modules-list-remote.svg | 132 +++--- docs/images/nf-core-modules-mulled.svg | 78 ++-- docs/images/nf-core-modules-patch.svg | 72 +-- docs/images/nf-core-modules-remove.svg | 70 +-- docs/images/nf-core-modules-test.svg | 74 +-- docs/images/nf-core-modules-update.svg | 86 ++-- docs/images/nf-core-schema-build.svg | 84 ++-- docs/images/nf-core-schema-lint.svg | 78 ++-- docs/images/nf-core-schema-validate.svg | 82 ++-- .../nf-core-subworkflows-create-test.svg | 128 ++--- docs/images/nf-core-subworkflows-create.svg | 108 ++--- docs/images/nf-core-subworkflows-info.svg | 436 +++++++++--------- docs/images/nf-core-subworkflows-install.svg | 128 ++--- .../nf-core-subworkflows-list-local.svg | 130 +++--- .../nf-core-subworkflows-list-remote.svg | 132 +++--- docs/images/nf-core-subworkflows-remove.svg | 128 ++--- docs/images/nf-core-subworkflows-test.svg | 128 ++--- docs/images/nf-core-subworkflows-update.svg | 128 ++--- docs/images/nf-core-sync.svg | 82 ++-- 35 files changed, 2066 insertions(+), 2108 deletions(-) diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg index 0dc1616cb8..d63cc442c5 100644 --- a/docs/images/nf-core-bump-version.svg +++ b/docs/images/nf-core-bump-version.svg @@ -19,77 +19,77 @@ font-weight: 700; } - .terminal-456906266-matrix { + .terminal-2897532537-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-456906266-title { + .terminal-2897532537-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-456906266-r1 { fill: #c5c8c6 } -.terminal-456906266-r2 { fill: #98a84b } -.terminal-456906266-r3 { fill: #9a9b99 } -.terminal-456906266-r4 { fill: #608ab1 } -.terminal-456906266-r5 { fill: #d0b344 } -.terminal-456906266-r6 { fill: #cc555a } + .terminal-2897532537-r1 { fill: #c5c8c6 } +.terminal-2897532537-r2 { fill: #98a84b } +.terminal-2897532537-r3 { fill: #9a9b99 } +.terminal-2897532537-r4 { fill: #608ab1 } +.terminal-2897532537-r5 { fill: #d0b344 } +.terminal-2897532537-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -101,26 +101,26 @@ - + - - $ nf-core bump-version 1.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - 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' + + diff --git a/docs/images/nf-core-create.svg b/docs/images/nf-core-create.svg index 4c7e243fff..78343c2d34 100644 --- a/docs/images/nf-core-create.svg +++ b/docs/images/nf-core-create.svg @@ -19,104 +19,104 @@ font-weight: 700; } - .terminal-1507512876-matrix { + .terminal-3886862987-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1507512876-title { + .terminal-3886862987-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1507512876-r1 { fill: #c5c8c6 } -.terminal-1507512876-r2 { fill: #98a84b } -.terminal-1507512876-r3 { fill: #9a9b99 } -.terminal-1507512876-r4 { fill: #608ab1 } -.terminal-1507512876-r5 { fill: #d0b344 } -.terminal-1507512876-r6 { fill: #98729f } -.terminal-1507512876-r7 { fill: #ff2c7a } -.terminal-1507512876-r8 { fill: #98a84b;font-weight: bold } -.terminal-1507512876-r9 { fill: #1984e9;text-decoration: underline; } + .terminal-3886862987-r1 { fill: #c5c8c6 } +.terminal-3886862987-r2 { fill: #98a84b } +.terminal-3886862987-r3 { fill: #9a9b99 } +.terminal-3886862987-r4 { fill: #608ab1 } +.terminal-3886862987-r5 { fill: #d0b344 } +.terminal-3886862987-r6 { fill: #98729f } +.terminal-3886862987-r7 { fill: #ff2c7a } +.terminal-3886862987-r8 { fill: #98a84b;font-weight: bold } +.terminal-3886862987-r9 { fill: #1984e9;text-decoration: underline; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -128,34 +128,34 @@ - + - - $ 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 - 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 2.7.1 - 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 diff --git a/docs/images/nf-core-download.svg b/docs/images/nf-core-download.svg index 6b19cc6433..4db5b62de9 100644 --- a/docs/images/nf-core-download.svg +++ b/docs/images/nf-core-download.svg @@ -19,76 +19,76 @@ font-weight: 700; } - .terminal-3721474111-matrix { + .terminal-405352606-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3721474111-title { + .terminal-405352606-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3721474111-r1 { fill: #c5c8c6 } -.terminal-3721474111-r2 { fill: #98a84b } -.terminal-3721474111-r3 { fill: #9a9b99 } -.terminal-3721474111-r4 { fill: #608ab1 } -.terminal-3721474111-r5 { fill: #d0b344 } + .terminal-405352606-r1 { fill: #c5c8c6 } +.terminal-405352606-r2 { fill: #98a84b } +.terminal-405352606-r3 { fill: #9a9b99 } +.terminal-405352606-r4 { fill: #608ab1 } +.terminal-405352606-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -c none - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - 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                                                 diff --git a/docs/images/nf-core-launch-rnaseq.svg b/docs/images/nf-core-launch-rnaseq.svg index 55a70279d9..52cfc344e2 100644 --- a/docs/images/nf-core-launch-rnaseq.svg +++ b/docs/images/nf-core-launch-rnaseq.svg @@ -19,72 +19,72 @@ font-weight: 700; } - .terminal-1175629223-matrix { + .terminal-3090263558-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1175629223-title { + .terminal-3090263558-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1175629223-r1 { fill: #c5c8c6 } -.terminal-1175629223-r2 { fill: #98a84b } -.terminal-1175629223-r3 { fill: #9a9b99 } -.terminal-1175629223-r4 { fill: #608ab1 } -.terminal-1175629223-r5 { fill: #d0b344 } -.terminal-1175629223-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1175629223-r7 { fill: #68a0b3;font-weight: bold } + .terminal-3090263558-r1 { fill: #c5c8c6 } +.terminal-3090263558-r2 { fill: #98a84b } +.terminal-3090263558-r3 { fill: #9a9b99 } +.terminal-3090263558-r4 { fill: #608ab1 } +.terminal-3090263558-r5 { fill: #d0b344 } +.terminal-3090263558-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3090263558-r7 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,24 +96,24 @@ - + - - $ nf-core launch rnaseq -r 3.8.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - 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) diff --git a/docs/images/nf-core-licences.svg b/docs/images/nf-core-licences.svg index db45603a7b..38d2266df9 100644 --- a/docs/images/nf-core-licences.svg +++ b/docs/images/nf-core-licences.svg @@ -19,108 +19,108 @@ font-weight: 700; } - .terminal-2422327830-matrix { + .terminal-3614362229-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2422327830-title { + .terminal-3614362229-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2422327830-r1 { fill: #c5c8c6 } -.terminal-2422327830-r2 { fill: #98a84b } -.terminal-2422327830-r3 { fill: #9a9b99 } -.terminal-2422327830-r4 { fill: #608ab1 } -.terminal-2422327830-r5 { fill: #d0b344 } -.terminal-2422327830-r6 { fill: #68a0b3;font-weight: bold } -.terminal-2422327830-r7 { fill: #c5c8c6;font-weight: bold } + .terminal-3614362229-r1 { fill: #c5c8c6 } +.terminal-3614362229-r2 { fill: #98a84b } +.terminal-3614362229-r3 { fill: #9a9b99 } +.terminal-3614362229-r4 { fill: #608ab1 } +.terminal-3614362229-r5 { fill: #d0b344 } +.terminal-3614362229-r6 { fill: #68a0b3;font-weight: bold } +.terminal-3614362229-r7 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,36 +132,36 @@ - + - - $ nf-core licences deepvariant - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - 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   │ +└──────────────┴─────────┴─────────┘ diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg index b255a7c4de..6ba942292b 100644 --- a/docs/images/nf-core-lint.svg +++ b/docs/images/nf-core-lint.svg @@ -19,142 +19,142 @@ font-weight: 700; } - .terminal-2054603030-matrix { + .terminal-2633876114-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2054603030-title { + .terminal-2633876114-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2054603030-r1 { fill: #c5c8c6 } -.terminal-2054603030-r2 { fill: #98a84b } -.terminal-2054603030-r3 { fill: #9a9b99 } -.terminal-2054603030-r4 { fill: #608ab1 } -.terminal-2054603030-r5 { fill: #d0b344 } -.terminal-2054603030-r6 { fill: #98729f } -.terminal-2054603030-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-2054603030-r8 { fill: #1984e9 } -.terminal-2054603030-r9 { fill: #d0b344;font-weight: bold } -.terminal-2054603030-r10 { fill: #8d7b39 } -.terminal-2054603030-r11 { fill: #cc555a } + .terminal-2633876114-r1 { fill: #c5c8c6 } +.terminal-2633876114-r2 { fill: #98a84b } +.terminal-2633876114-r3 { fill: #9a9b99 } +.terminal-2633876114-r4 { fill: #608ab1 } +.terminal-2633876114-r5 { fill: #d0b344 } +.terminal-2633876114-r6 { fill: #98729f } +.terminal-2633876114-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2633876114-r8 { fill: #1984e9 } +.terminal-2633876114-r9 { fill: #d0b344;font-weight: bold } +.terminal-2633876114-r10 { fill: #8d7b39 } +.terminal-2633876114-r11 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -166,46 +166,46 @@ - + - - $ nf-core lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - - -INFO     Testing pipeline: . - - -╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ -││ -│pipeline_todos: pipeline_todos│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - -╭─[!] 2 Module Test Warnings─────────────────────────────────────────────────────────────────────╮ -│                                           ╷                          ╷                           │ -│Module name                              │File path               │Test message             │ -│╶──────────────────────────────────────────┼──────────────────────────┼──────────────────────────╴│ -│custom/dumpsoftwareversions│modules/nf-core/custom/…│New version available│ -│fastqc│modules/nf-core/fastqc  │New version available│ -│                                           ╵                          ╵                           │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────╮ -│LINT RESULTS SUMMARY │ -├───────────────────────┤ -│[✔] 178 Tests Passed│ -│[?]   1 Test Ignored│ -│[!]   2 Test Warnings│ -│[✗]   0 Tests Failed│ -╰───────────────────────╯ + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + + +INFO     Testing pipeline: . + + +╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ +││ +│pipeline_todos: pipeline_todos│ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + +╭─[!] 2 Module Test Warnings─────────────────────────────────────────────────────────────────────╮ +│                                           ╷                          ╷                           │ +│Module name                              │File path               │Test message             │ +│╶──────────────────────────────────────────┼──────────────────────────┼──────────────────────────╴│ +│custom/dumpsoftwareversions│modules/nf-core/custom/…│New version available│ +│fastqc│modules/nf-core/fastqc  │New version available│ +│                                           ╵                          ╵                           │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭───────────────────────╮ +│LINT RESULTS SUMMARY │ +├───────────────────────┤ +│[✔] 178 Tests Passed│ +│[?]   1 Test Ignored│ +│[!]   2 Test Warnings│ +│[✗]   0 Tests Failed│ +╰───────────────────────╯ diff --git a/docs/images/nf-core-list-rna.svg b/docs/images/nf-core-list-rna.svg index 0dfaae8459..40830b3176 100644 --- a/docs/images/nf-core-list-rna.svg +++ b/docs/images/nf-core-list-rna.svg @@ -19,99 +19,99 @@ font-weight: 700; } - .terminal-1440873036-matrix { + .terminal-3770022571-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1440873036-title { + .terminal-3770022571-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1440873036-r1 { fill: #c5c8c6 } -.terminal-1440873036-r2 { fill: #98a84b } -.terminal-1440873036-r3 { fill: #9a9b99 } -.terminal-1440873036-r4 { fill: #608ab1 } -.terminal-1440873036-r5 { fill: #d0b344 } -.terminal-1440873036-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1440873036-r7 { fill: #868887 } + .terminal-3770022571-r1 { fill: #c5c8c6 } +.terminal-3770022571-r2 { fill: #98a84b } +.terminal-3770022571-r3 { fill: #9a9b99 } +.terminal-3770022571-r4 { fill: #608ab1 } +.terminal-3770022571-r5 { fill: #d0b344 } +.terminal-3770022571-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3770022571-r7 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -123,33 +123,33 @@ - + - - $ nf-core list rna rna-seq - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ smrnaseq             │    44 │          2.1.0 │ 1 months ago │           - │ -                   │ -│ rnaseq               │   538 │            3.9 │ 2 months ago │           - │ -                   │ -│ rnafusion            │    83 │          2.1.0 │ 5 months ago │           - │ -                   │ -│ dualrnaseq           │     8 │          1.0.0 │  2 years ago │           - │ -                   │ -│ circrna              │    24 │            dev │            - │           - │ -                   │ -│ lncpipe              │    23 │            dev │            - │           - │ -                   │ -│ scflow               │    14 │            dev │            - │           - │ -                   │ -│ spatialtranscriptom… │    12 │            dev │            - │           - │ -                   │ -└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ + + $ nf-core list rna rna-seq + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ smrnaseq             │    44 │          2.1.0 │ 1 months ago │           - │ -                   │ +│ rnaseq               │   538 │            3.9 │ 2 months ago │           - │ -                   │ +│ rnafusion            │    83 │          2.1.0 │ 5 months ago │           - │ -                   │ +│ dualrnaseq           │     8 │          1.0.0 │  2 years ago │           - │ -                   │ +│ circrna              │    24 │            dev │            - │           - │ -                   │ +│ lncpipe              │    23 │            dev │            - │           - │ -                   │ +│ scflow               │    14 │            dev │            - │           - │ -                   │ +│ spatialtranscriptom… │    12 │            dev │            - │           - │ -                   │ +└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg index 80d81c4dcd..af68101512 100644 --- a/docs/images/nf-core-list-stars.svg +++ b/docs/images/nf-core-list-stars.svg @@ -19,88 +19,88 @@ font-weight: 700; } - .terminal-2329934618-matrix { + .terminal-4159699833-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2329934618-title { + .terminal-4159699833-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2329934618-r1 { fill: #c5c8c6 } -.terminal-2329934618-r2 { fill: #98a84b } -.terminal-2329934618-r3 { fill: #9a9b99 } -.terminal-2329934618-r4 { fill: #608ab1 } -.terminal-2329934618-r5 { fill: #d0b344 } -.terminal-2329934618-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2329934618-r7 { fill: #868887 } -.terminal-2329934618-r8 { fill: #868887;font-style: italic; } + .terminal-4159699833-r1 { fill: #c5c8c6 } +.terminal-4159699833-r2 { fill: #98a84b } +.terminal-4159699833-r3 { fill: #9a9b99 } +.terminal-4159699833-r4 { fill: #608ab1 } +.terminal-4159699833-r5 { fill: #d0b344 } +.terminal-4159699833-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-4159699833-r7 { fill: #868887 } +.terminal-4159699833-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -112,29 +112,29 @@ - + - - $ nf-core list -s stars - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq               │   538 │            3.9 │ 2 months ago │           - │ -                   │ -│ sarek                │   210 │          3.1.1 │  2 weeks ago │           - │ -                   │ -│ chipseq              │   133 │          2.0.0 │ 2 months ago │           - │ -                   │ -│ atacseq              │   123 │            2.0 │   1 week ago │           - │ -                   │ -[..truncated..] + + $ nf-core list -s stars + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq               │   538 │            3.9 │ 2 months ago │           - │ -                   │ +│ sarek                │   210 │          3.1.1 │  2 weeks ago │           - │ -                   │ +│ chipseq              │   133 │          2.0.0 │ 2 months ago │           - │ -                   │ +│ atacseq              │   123 │            2.0 │   1 week ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg index efd90f47f8..24bc71baf4 100644 --- a/docs/images/nf-core-list.svg +++ b/docs/images/nf-core-list.svg @@ -19,91 +19,91 @@ font-weight: 700; } - .terminal-2923789563-matrix { + .terminal-3135274331-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2923789563-title { + .terminal-3135274331-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2923789563-r1 { fill: #c5c8c6 } -.terminal-2923789563-r2 { fill: #98a84b } -.terminal-2923789563-r3 { fill: #9a9b99 } -.terminal-2923789563-r4 { fill: #608ab1 } -.terminal-2923789563-r5 { fill: #d0b344 } -.terminal-2923789563-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2923789563-r7 { fill: #868887 } -.terminal-2923789563-r8 { fill: #868887;font-style: italic; } + .terminal-3135274331-r1 { fill: #c5c8c6 } +.terminal-3135274331-r2 { fill: #98a84b } +.terminal-3135274331-r3 { fill: #9a9b99 } +.terminal-3135274331-r4 { fill: #608ab1 } +.terminal-3135274331-r5 { fill: #d0b344 } +.terminal-3135274331-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3135274331-r7 { fill: #868887 } +.terminal-3135274331-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +115,30 @@ - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ ampliseq             │   101 │          2.4.1 │ 20 hours ago │           - │ -                   │ -│ airrflow             │    24 │          2.4.0 │   2 days ago │           - │ -                   │ -│ mhcquant             │    21 │          2.4.0 │   6 days ago │           - │ -                   │ -│ atacseq              │   123 │            2.0 │   1 week ago │           - │ -                   │ -│ methylseq            │    95 │          2.2.0 │  1 weeks ago │           - │ -                   │ -[..truncated..] + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ ampliseq             │   101 │          2.4.1 │ 21 hours ago │           - │ -                   │ +│ airrflow             │    24 │          2.4.0 │   2 days ago │           - │ -                   │ +│ mhcquant             │    21 │          2.4.0 │   6 days ago │           - │ -                   │ +│ atacseq              │   123 │            2.0 │   1 week ago │           - │ -                   │ +│ methylseq            │    95 │          2.2.0 │  1 weeks ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index 9f760347a3..bdd738ba03 100644 --- a/docs/images/nf-core-modules-bump-version.svg +++ b/docs/images/nf-core-modules-bump-version.svg @@ -19,90 +19,90 @@ font-weight: 700; } - .terminal-824833976-matrix { + .terminal-1795029015-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-824833976-title { + .terminal-1795029015-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-824833976-r1 { fill: #c5c8c6 } -.terminal-824833976-r2 { fill: #98a84b } -.terminal-824833976-r3 { fill: #9a9b99 } -.terminal-824833976-r4 { fill: #608ab1 } -.terminal-824833976-r5 { fill: #d0b344 } -.terminal-824833976-r6 { fill: #98a84b;font-weight: bold } -.terminal-824833976-r7 { fill: #c5c8c6;font-weight: bold } + .terminal-1795029015-r1 { fill: #c5c8c6 } +.terminal-1795029015-r2 { fill: #98a84b } +.terminal-1795029015-r3 { fill: #9a9b99 } +.terminal-1795029015-r4 { fill: #608ab1 } +.terminal-1795029015-r5 { fill: #d0b344 } +.terminal-1795029015-r6 { fill: #98a84b;font-weight: bold } +.terminal-1795029015-r7 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -114,30 +114,30 @@ - + - - $ nf-core modules bump-versions fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - https://nf-co.re + + + + +╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ +│[!] 1 Module version up to date.│ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ +│Module name                             │Update Message                                       │ +├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ +│ fastqc                                   │ Module version up to date: fastqc                     │ +╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ diff --git a/docs/images/nf-core-modules-create-test.svg b/docs/images/nf-core-modules-create-test.svg index a9bf5835bc..ab9e254f37 100644 --- a/docs/images/nf-core-modules-create-test.svg +++ b/docs/images/nf-core-modules-create-test.svg @@ -19,84 +19,84 @@ font-weight: 700; } - .terminal-1793760250-matrix { + .terminal-1810277116-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1793760250-title { + .terminal-1810277116-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1793760250-r1 { fill: #c5c8c6 } -.terminal-1793760250-r2 { fill: #98a84b } -.terminal-1793760250-r3 { fill: #9a9b99 } -.terminal-1793760250-r4 { fill: #608ab1 } -.terminal-1793760250-r5 { fill: #d0b344 } -.terminal-1793760250-r6 { fill: #ff2c7a } -.terminal-1793760250-r7 { fill: #98729f } + .terminal-1810277116-r1 { fill: #c5c8c6 } +.terminal-1810277116-r2 { fill: #98a84b } +.terminal-1810277116-r3 { fill: #9a9b99 } +.terminal-1810277116-r4 { fill: #608ab1 } +.terminal-1810277116-r5 { fill: #d0b344 } +.terminal-1810277116-r6 { fill: #ff2c7a } +.terminal-1810277116-r7 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -108,28 +108,28 @@ - + - - $ nf-core modules create-test-yml fastqc --no-prompts --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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' -INFO     Running 'fastqc' test with command:                                                         -nextflow run ./tests/modules/nf-core/fastqc -entry test_fastqc -c  -./tests/config/nextflow.config -c ./tests/modules/nf-core/fastqc/nextflow.config --outdir  -/tmp/tmpk231usbb -work-dir /tmp/tmpvt2u8pj3 + + $ nf-core modules create-test-yml fastqc --no-prompts --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - 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/tmplzj5q_cr -work-dir /tmp/tmpwkq3pr51 diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index 90626c9a55..82c008269b 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 2.7 - 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' -INFO     Using Docker container: 'quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1' -INFO     Using Singularity container:                                                                -'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--hdfd78af_1' -INFO     Created / edited following files:                                                           -           ./modules/nf-core/fastqc/main.nf -           ./modules/nf-core/fastqc/meta.yml -           ./tests/modules/nf-core/fastqc/main.nf -           ./tests/modules/nf-core/fastqc/test.yml -           ./tests/modules/nf-core/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 2.7.1 - 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' diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg index b22069ca8c..b3f667942c 100644 --- a/docs/images/nf-core-modules-info.svg +++ b/docs/images/nf-core-modules-info.svg @@ -19,163 +19,163 @@ font-weight: 700; } - .terminal-377483768-matrix { + .terminal-2882269783-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-377483768-title { + .terminal-2882269783-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-377483768-r1 { fill: #c5c8c6 } -.terminal-377483768-r2 { fill: #98a84b } -.terminal-377483768-r3 { fill: #9a9b99 } -.terminal-377483768-r4 { fill: #608ab1 } -.terminal-377483768-r5 { fill: #d0b344 } -.terminal-377483768-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-377483768-r7 { fill: #98a84b;font-weight: bold } -.terminal-377483768-r8 { fill: #868887 } -.terminal-377483768-r9 { fill: #d08442 } -.terminal-377483768-r10 { fill: #868887;font-style: italic; } -.terminal-377483768-r11 { fill: #98729f } + .terminal-2882269783-r1 { fill: #c5c8c6 } +.terminal-2882269783-r2 { fill: #98a84b } +.terminal-2882269783-r3 { fill: #9a9b99 } +.terminal-2882269783-r4 { fill: #608ab1 } +.terminal-2882269783-r5 { fill: #d0b344 } +.terminal-2882269783-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-2882269783-r7 { fill: #98a84b;font-weight: bold } +.terminal-2882269783-r8 { fill: #868887 } +.terminal-2882269783-r9 { fill: #d08442 } +.terminal-2882269783-r10 { fill: #868887;font-style: italic; } +.terminal-2882269783-r11 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -187,53 +187,53 @@ - + - - $ nf-core modules info abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - https://nf-co.re + + + +╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ +│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ +│ 🔧 Tools: abacas                                                                                 │ +│ 📖 Description: contiguate draft genome assembly                                                 │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +                  ╷                                                                   ╷              +📥 Inputs        │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} +                  ╵                                                                   ╵              +                  ╷                                                                   ╷              +📤 Outputs       │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + results  (files)│List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* +                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ +                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ +                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ +                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + versions  (file)│File containing software versions                                  │versions.yml +                  ╵                                                                   ╵              + + 💻  Installation command: nf-core modules install abacas + diff --git a/docs/images/nf-core-modules-install.svg b/docs/images/nf-core-modules-install.svg index 4a53bd06c8..fa6c7b941c 100644 --- a/docs/images/nf-core-modules-install.svg +++ b/docs/images/nf-core-modules-install.svg @@ -19,76 +19,76 @@ font-weight: 700; } - .terminal-2071432195-matrix { + .terminal-3882716258-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2071432195-title { + .terminal-3882716258-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2071432195-r1 { fill: #c5c8c6 } -.terminal-2071432195-r2 { fill: #98a84b } -.terminal-2071432195-r3 { fill: #9a9b99 } -.terminal-2071432195-r4 { fill: #608ab1 } -.terminal-2071432195-r5 { fill: #d0b344 } + .terminal-3882716258-r1 { fill: #c5c8c6 } +.terminal-3882716258-r2 { fill: #98a84b } +.terminal-3882716258-r3 { fill: #9a9b99 } +.terminal-3882716258-r4 { fill: #608ab1 } +.terminal-3882716258-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core modules install abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - https://nf-co.re + + + +INFO     Installing 'abacas' +INFO     Use the following statement to include this module:                                         + + include { ABACAS } from '../modules/nf-core/abacas/main'                                            + diff --git a/docs/images/nf-core-modules-lint.svg b/docs/images/nf-core-modules-lint.svg index 0531cdfe79..f63cf77d39 100644 --- a/docs/images/nf-core-modules-lint.svg +++ b/docs/images/nf-core-modules-lint.svg @@ -19,94 +19,94 @@ font-weight: 700; } - .terminal-2882701330-matrix { + .terminal-3569125489-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2882701330-title { + .terminal-3569125489-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2882701330-r1 { fill: #c5c8c6 } -.terminal-2882701330-r2 { fill: #98a84b } -.terminal-2882701330-r3 { fill: #9a9b99 } -.terminal-2882701330-r4 { fill: #608ab1 } -.terminal-2882701330-r5 { fill: #d0b344 } -.terminal-2882701330-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2882701330-r7 { fill: #98a84b;font-weight: bold } -.terminal-2882701330-r8 { fill: #cc555a } + .terminal-3569125489-r1 { fill: #c5c8c6 } +.terminal-3569125489-r2 { fill: #98a84b } +.terminal-3569125489-r3 { fill: #9a9b99 } +.terminal-3569125489-r4 { fill: #608ab1 } +.terminal-3569125489-r5 { fill: #d0b344 } +.terminal-3569125489-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3569125489-r7 { fill: #98a84b;font-weight: bold } +.terminal-3569125489-r8 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -118,31 +118,31 @@ - + - - $ nf-core modules lint multiqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - https://nf-co.re + + + +INFO     Linting modules repo: '.' +INFO     Linting module: 'multiqc' + +╭───────────────────────╮ +│LINT RESULTS SUMMARY│ +├───────────────────────┤ +│[✔]  23 Tests Passed │ +│[!]   0 Test Warnings│ +│[✗]   0 Tests Failed │ +╰───────────────────────╯ diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index 0d5cdf6f2f..c2cbe2b236 100644 --- a/docs/images/nf-core-modules-list-local.svg +++ b/docs/images/nf-core-modules-list-local.svg @@ -19,108 +19,108 @@ font-weight: 700; } - .terminal-2639661206-matrix { + .terminal-801966325-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2639661206-title { + .terminal-801966325-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2639661206-r1 { fill: #c5c8c6 } -.terminal-2639661206-r2 { fill: #98a84b } -.terminal-2639661206-r3 { fill: #9a9b99 } -.terminal-2639661206-r4 { fill: #608ab1 } -.terminal-2639661206-r5 { fill: #d0b344 } -.terminal-2639661206-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2639661206-r7 { fill: #868887;font-style: italic; } + .terminal-801966325-r1 { fill: #c5c8c6 } +.terminal-801966325-r2 { fill: #98a84b } +.terminal-801966325-r3 { fill: #9a9b99 } +.terminal-801966325-r4 { fill: #608ab1 } +.terminal-801966325-r5 { fill: #d0b344 } +.terminal-801966325-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-801966325-r7 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,36 +132,36 @@ - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - - -INFO     Modules installed in '.':                                                                   - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -┃Module Name        ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ custom/dumpsoftwar… │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ -│                     │                    │                     │ nf-core/modules    │            │ -│                     │                    │                     │ repo (#2141)       │            │ -│ fastqc              │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ -│                     │                    │                     │ nf-core/modules    │            │ -│                     │                    │                     │ repo (#2141)       │            │ -│ multiqc             │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ -│                     │                    │                     │ nf-core/modules    │            │ -│                     │                    │                     │ repo (#2141)       │            │ -[..truncated..] + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + + +INFO     Modules installed in '.':                                                                   + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +┃Module Name        ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ custom/dumpsoftwar… │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ +│                     │                    │                     │ nf-core/modules    │            │ +│                     │                    │                     │ repo (#2141)       │            │ +│ fastqc              │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ +│                     │                    │                     │ nf-core/modules    │            │ +│                     │                    │                     │ repo (#2141)       │            │ +│ multiqc             │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ +│                     │                    │                     │ nf-core/modules    │            │ +│                     │                    │                     │ repo (#2141)       │            │ +[..truncated..] diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index 0f37822110..701b00db57 100644 --- a/docs/images/nf-core-modules-list-remote.svg +++ b/docs/images/nf-core-modules-list-remote.svg @@ -19,109 +19,109 @@ font-weight: 700; } - .terminal-3342753500-matrix { + .terminal-3298778939-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3342753500-title { + .terminal-3298778939-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3342753500-r1 { fill: #c5c8c6 } -.terminal-3342753500-r2 { fill: #98a84b } -.terminal-3342753500-r3 { fill: #9a9b99 } -.terminal-3342753500-r4 { fill: #608ab1 } -.terminal-3342753500-r5 { fill: #d0b344 } -.terminal-3342753500-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-3342753500-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-3342753500-r8 { fill: #868887;font-style: italic; } + .terminal-3298778939-r1 { fill: #c5c8c6 } +.terminal-3298778939-r2 { fill: #98a84b } +.terminal-3298778939-r3 { fill: #9a9b99 } +.terminal-3298778939-r4 { fill: #608ab1 } +.terminal-3298778939-r5 { fill: #d0b344 } +.terminal-3298778939-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-3298778939-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-3298778939-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core modules list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - 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..] diff --git a/docs/images/nf-core-modules-mulled.svg b/docs/images/nf-core-modules-mulled.svg index 5373182936..b6ead66b4b 100644 --- a/docs/images/nf-core-modules-mulled.svg +++ b/docs/images/nf-core-modules-mulled.svg @@ -19,69 +19,69 @@ font-weight: 700; } - .terminal-3390485959-matrix { + .terminal-1123202598-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3390485959-title { + .terminal-1123202598-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3390485959-r1 { fill: #c5c8c6 } -.terminal-3390485959-r2 { fill: #98a84b } -.terminal-3390485959-r3 { fill: #9a9b99 } -.terminal-3390485959-r4 { fill: #608ab1 } -.terminal-3390485959-r5 { fill: #d0b344 } -.terminal-3390485959-r6 { fill: #00823d;font-weight: bold } -.terminal-3390485959-r7 { fill: #68a0b3;font-weight: bold } + .terminal-1123202598-r1 { fill: #c5c8c6 } +.terminal-1123202598-r2 { fill: #98a84b } +.terminal-1123202598-r3 { fill: #9a9b99 } +.terminal-1123202598-r4 { fill: #608ab1 } +.terminal-1123202598-r5 { fill: #d0b344 } +.terminal-1123202598-r6 { fill: #00823d;font-weight: bold } +.terminal-1123202598-r7 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -93,23 +93,23 @@ - + - - $ nf-core modules mulled pysam==0.16.0.1 biopython==1.78 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - https://nf-co.re + + +INFO     Found docker image on quay.io! ✨                                                           +INFO     Mulled container hash:                                                                      +mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 diff --git a/docs/images/nf-core-modules-patch.svg b/docs/images/nf-core-modules-patch.svg index 3bc3f80ffc..f54bff1e97 100644 --- a/docs/images/nf-core-modules-patch.svg +++ b/docs/images/nf-core-modules-patch.svg @@ -19,65 +19,65 @@ font-weight: 700; } - .terminal-239277571-matrix { + .terminal-2789283426-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-239277571-title { + .terminal-2789283426-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-239277571-r1 { fill: #c5c8c6 } -.terminal-239277571-r2 { fill: #98a84b } -.terminal-239277571-r3 { fill: #9a9b99 } -.terminal-239277571-r4 { fill: #608ab1 } -.terminal-239277571-r5 { fill: #d0b344 } -.terminal-239277571-r6 { fill: #cc555a;font-weight: bold } + .terminal-2789283426-r1 { fill: #c5c8c6 } +.terminal-2789283426-r2 { fill: #98a84b } +.terminal-2789283426-r3 { fill: #9a9b99 } +.terminal-2789283426-r4 { fill: #608ab1 } +.terminal-2789283426-r5 { fill: #d0b344 } +.terminal-2789283426-r6 { fill: #cc555a;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -89,22 +89,22 @@ - + - - $ nf-core modules patch fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - https://nf-co.re + + + +ERROR    Module 'modules/nf-core/fastqc' is unchanged. No patch to compute                           diff --git a/docs/images/nf-core-modules-remove.svg b/docs/images/nf-core-modules-remove.svg index a2dc8099d4..e495def404 100644 --- a/docs/images/nf-core-modules-remove.svg +++ b/docs/images/nf-core-modules-remove.svg @@ -19,64 +19,64 @@ font-weight: 700; } - .terminal-3629854034-matrix { + .terminal-2407804337-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3629854034-title { + .terminal-2407804337-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3629854034-r1 { fill: #c5c8c6 } -.terminal-3629854034-r2 { fill: #98a84b } -.terminal-3629854034-r3 { fill: #9a9b99 } -.terminal-3629854034-r4 { fill: #608ab1 } -.terminal-3629854034-r5 { fill: #d0b344 } + .terminal-2407804337-r1 { fill: #c5c8c6 } +.terminal-2407804337-r2 { fill: #98a84b } +.terminal-2407804337-r3 { fill: #9a9b99 } +.terminal-2407804337-r4 { fill: #608ab1 } +.terminal-2407804337-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -88,22 +88,22 @@ - + - - $ nf-core modules remove abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - - -INFO     Removed files for 'abacas' and it's dependencies 'abacas'.                                  + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + + +INFO     Removed files for 'abacas' and it's dependencies 'abacas'.                                  diff --git a/docs/images/nf-core-modules-test.svg b/docs/images/nf-core-modules-test.svg index 92943a04a3..1ff788e24b 100644 --- a/docs/images/nf-core-modules-test.svg +++ b/docs/images/nf-core-modules-test.svg @@ -19,67 +19,67 @@ font-weight: 700; } - .terminal-53791440-matrix { + .terminal-367250223-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-53791440-title { + .terminal-367250223-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-53791440-r1 { fill: #c5c8c6 } -.terminal-53791440-r2 { fill: #98a84b } -.terminal-53791440-r3 { fill: #9a9b99 } -.terminal-53791440-r4 { fill: #608ab1 } -.terminal-53791440-r5 { fill: #d0b344 } + .terminal-367250223-r1 { fill: #c5c8c6 } +.terminal-367250223-r2 { fill: #98a84b } +.terminal-367250223-r3 { fill: #9a9b99 } +.terminal-367250223-r4 { fill: #608ab1 } +.terminal-367250223-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -91,23 +91,23 @@ - + - - $ nf-core modules test samtools/view --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - https://nf-co.re + + + +────────────────────────────────────────── samtools/view ─────────────────────────────────────────── +INFO     Running pytest for module 'samtools/view' diff --git a/docs/images/nf-core-modules-update.svg b/docs/images/nf-core-modules-update.svg index d1fa771510..34ee63f06e 100644 --- a/docs/images/nf-core-modules-update.svg +++ b/docs/images/nf-core-modules-update.svg @@ -19,76 +19,76 @@ font-weight: 700; } - .terminal-3977922886-matrix { + .terminal-586434981-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3977922886-title { + .terminal-586434981-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3977922886-r1 { fill: #c5c8c6 } -.terminal-3977922886-r2 { fill: #98a84b } -.terminal-3977922886-r3 { fill: #9a9b99 } -.terminal-3977922886-r4 { fill: #608ab1 } -.terminal-3977922886-r5 { fill: #d0b344 } + .terminal-586434981-r1 { fill: #c5c8c6 } +.terminal-586434981-r2 { fill: #98a84b } +.terminal-586434981-r3 { fill: #9a9b99 } +.terminal-586434981-r4 { fill: #608ab1 } +.terminal-586434981-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core modules update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - - -INFO    'modules/nf-core/abacas' is already up to date                                              -INFO     Updating 'nf-core/custom/dumpsoftwareversions' -INFO     Updating 'nf-core/fastqc' -INFO    'modules/nf-core/multiqc' is already up to date                                             -INFO     Updates complete ✨                                                                         + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + + +INFO    'modules/nf-core/abacas' is already up to date                                              +INFO     Updating 'nf-core/custom/dumpsoftwareversions' +INFO     Updating 'nf-core/fastqc' +INFO    'modules/nf-core/multiqc' is already up to date                                             +INFO     Updates complete ✨                                                                         diff --git a/docs/images/nf-core-schema-build.svg b/docs/images/nf-core-schema-build.svg index 90c012ed63..91b1c4482f 100644 --- a/docs/images/nf-core-schema-build.svg +++ b/docs/images/nf-core-schema-build.svg @@ -19,72 +19,72 @@ font-weight: 700; } - .terminal-3325086355-matrix { + .terminal-1763756786-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3325086355-title { + .terminal-1763756786-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3325086355-r1 { fill: #c5c8c6 } -.terminal-3325086355-r2 { fill: #98a84b } -.terminal-3325086355-r3 { fill: #9a9b99 } -.terminal-3325086355-r4 { fill: #608ab1 } -.terminal-3325086355-r5 { fill: #d0b344 } -.terminal-3325086355-r6 { fill: #98a84b;font-weight: bold } -.terminal-3325086355-r7 { fill: #868887;font-weight: bold } -.terminal-3325086355-r8 { fill: #868887 } -.terminal-3325086355-r9 { fill: #4e707b;font-weight: bold } -.terminal-3325086355-r10 { fill: #68a0b3;font-weight: bold } + .terminal-1763756786-r1 { fill: #c5c8c6 } +.terminal-1763756786-r2 { fill: #98a84b } +.terminal-1763756786-r3 { fill: #9a9b99 } +.terminal-1763756786-r4 { fill: #608ab1 } +.terminal-1763756786-r5 { fill: #d0b344 } +.terminal-1763756786-r6 { fill: #98a84b;font-weight: bold } +.terminal-1763756786-r7 { fill: #868887;font-weight: bold } +.terminal-1763756786-r8 { fill: #868887 } +.terminal-1763756786-r9 { fill: #4e707b;font-weight: bold } +.terminal-1763756786-r10 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,23 +96,23 @@ - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 31 params) -INFO     Writing schema with 32 params: './nextflow_schema.json' + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 31 params) +INFO     Writing schema with 32 params: './nextflow_schema.json' diff --git a/docs/images/nf-core-schema-lint.svg b/docs/images/nf-core-schema-lint.svg index c7c6f38486..9bb3f251e6 100644 --- a/docs/images/nf-core-schema-lint.svg +++ b/docs/images/nf-core-schema-lint.svg @@ -19,68 +19,68 @@ font-weight: 700; } - .terminal-617173835-matrix { + .terminal-953635754-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-617173835-title { + .terminal-953635754-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-617173835-r1 { fill: #c5c8c6 } -.terminal-617173835-r2 { fill: #98a84b } -.terminal-617173835-r3 { fill: #9a9b99 } -.terminal-617173835-r4 { fill: #608ab1 } -.terminal-617173835-r5 { fill: #d0b344 } -.terminal-617173835-r6 { fill: #98a84b;font-weight: bold } -.terminal-617173835-r7 { fill: #868887;font-weight: bold } -.terminal-617173835-r8 { fill: #868887 } -.terminal-617173835-r9 { fill: #4e707b;font-weight: bold } + .terminal-953635754-r1 { fill: #c5c8c6 } +.terminal-953635754-r2 { fill: #98a84b } +.terminal-953635754-r3 { fill: #9a9b99 } +.terminal-953635754-r4 { fill: #608ab1 } +.terminal-953635754-r5 { fill: #d0b344 } +.terminal-953635754-r6 { fill: #98a84b;font-weight: bold } +.terminal-953635754-r7 { fill: #868887;font-weight: bold } +.terminal-953635754-r8 { fill: #868887 } +.terminal-953635754-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -92,22 +92,22 @@ - + - - $ nf-core schema lint nextflow_schema.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 32 params) + + $ nf-core schema lint nextflow_schema.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 32 params) diff --git a/docs/images/nf-core-schema-validate.svg b/docs/images/nf-core-schema-validate.svg index d0afb57106..8cc98e50b9 100644 --- a/docs/images/nf-core-schema-validate.svg +++ b/docs/images/nf-core-schema-validate.svg @@ -19,71 +19,71 @@ font-weight: 700; } - .terminal-3174760220-matrix { + .terminal-2859597691-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3174760220-title { + .terminal-2859597691-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3174760220-r1 { fill: #c5c8c6 } -.terminal-3174760220-r2 { fill: #98a84b } -.terminal-3174760220-r3 { fill: #9a9b99 } -.terminal-3174760220-r4 { fill: #608ab1 } -.terminal-3174760220-r5 { fill: #d0b344 } -.terminal-3174760220-r6 { fill: #98a84b;font-weight: bold } -.terminal-3174760220-r7 { fill: #868887;font-weight: bold } -.terminal-3174760220-r8 { fill: #868887 } -.terminal-3174760220-r9 { fill: #4e707b;font-weight: bold } + .terminal-2859597691-r1 { fill: #c5c8c6 } +.terminal-2859597691-r2 { fill: #98a84b } +.terminal-2859597691-r3 { fill: #9a9b99 } +.terminal-2859597691-r4 { fill: #608ab1 } +.terminal-2859597691-r5 { fill: #d0b344 } +.terminal-2859597691-r6 { fill: #98a84b;font-weight: bold } +.terminal-2859597691-r7 { fill: #868887;font-weight: bold } +.terminal-2859597691-r8 { fill: #868887 } +.terminal-2859597691-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -95,23 +95,23 @@ - + - - $ nf-core schema validate nf-core-rnaseq/workflow nf-params.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 93 params) +INFO    [✓] Input parameters look valid diff --git a/docs/images/nf-core-subworkflows-create-test.svg b/docs/images/nf-core-subworkflows-create-test.svg index 20fc71e2e7..efe5f5bd5e 100644 --- a/docs/images/nf-core-subworkflows-create-test.svg +++ b/docs/images/nf-core-subworkflows-create-test.svg @@ -19,107 +19,107 @@ font-weight: 700; } - .terminal-788073991-matrix { + .terminal-374083174-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-788073991-title { + .terminal-374083174-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-788073991-r1 { fill: #c5c8c6 } -.terminal-788073991-r2 { fill: #98a84b } -.terminal-788073991-r3 { fill: #9a9b99 } -.terminal-788073991-r4 { fill: #608ab1 } -.terminal-788073991-r5 { fill: #d0b344 } -.terminal-788073991-r6 { fill: #cc555a } + .terminal-374083174-r1 { fill: #c5c8c6 } +.terminal-374083174-r2 { fill: #98a84b } +.terminal-374083174-r3 { fill: #9a9b99 } +.terminal-374083174-r4 { fill: #608ab1 } +.terminal-374083174-r5 { fill: #d0b344 } +.terminal-374083174-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -131,36 +131,36 @@ - + - - $ nf-core subworkflows create-test-yml bam_stats_samtools --no-prompts --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - - -WARNING 'repository_type' not defined in .nf-core.yml                                               -Warning: Input is not a terminal (fd=0). -? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - » Pipeline -   nf-core/modules - - - -        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - -Aborted. + + $ nf-core subworkflows create-test-yml bam_stats_samtools --no-prompts --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. diff --git a/docs/images/nf-core-subworkflows-create.svg b/docs/images/nf-core-subworkflows-create.svg index 41c763ff7a..9542f9758d 100644 --- a/docs/images/nf-core-subworkflows-create.svg +++ b/docs/images/nf-core-subworkflows-create.svg @@ -19,90 +19,90 @@ font-weight: 700; } - .terminal-4205435415-matrix { + .terminal-2185943670-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4205435415-title { + .terminal-2185943670-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4205435415-r1 { fill: #c5c8c6 } -.terminal-4205435415-r2 { fill: #98a84b } -.terminal-4205435415-r3 { fill: #9a9b99 } -.terminal-4205435415-r4 { fill: #608ab1 } -.terminal-4205435415-r5 { fill: #d0b344 } -.terminal-4205435415-r6 { fill: #68a0b3;font-weight: bold } -.terminal-4205435415-r7 { fill: #868887 } -.terminal-4205435415-r8 { fill: #4a637a } -.terminal-4205435415-r9 { fill: #4a637a;font-weight: bold } -.terminal-4205435415-r10 { fill: #cc555a } + .terminal-2185943670-r1 { fill: #c5c8c6 } +.terminal-2185943670-r2 { fill: #98a84b } +.terminal-2185943670-r3 { fill: #9a9b99 } +.terminal-2185943670-r4 { fill: #608ab1 } +.terminal-2185943670-r5 { fill: #d0b344 } +.terminal-2185943670-r6 { fill: #68a0b3;font-weight: bold } +.terminal-2185943670-r7 { fill: #868887 } +.terminal-2185943670-r8 { fill: #4a637a } +.terminal-2185943670-r9 { fill: #4a637a;font-weight: bold } +.terminal-2185943670-r10 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -114,29 +114,29 @@ - + - - $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot  --label process_low --meta  ---force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - - -Usage: nf-core subworkflows create [OPTIONS] subworkflow name                                       - -Try 'nf-core subworkflows create -h' for help. -╭─ Error ──────────────────────────────────────────────────────────────────────────────────────────╮ -│ No such option: --label Did you mean --help?                                                     │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - + + $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot  --label process_low --meta  +--force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + + +Usage: nf-core subworkflows create [OPTIONS] subworkflow name                                       + +Try 'nf-core subworkflows create -h' for help. +╭─ Error ──────────────────────────────────────────────────────────────────────────────────────────╮ +│ No such option: --label Did you mean --help?                                                     │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + diff --git a/docs/images/nf-core-subworkflows-info.svg b/docs/images/nf-core-subworkflows-info.svg index b3c6b6ee42..680dbfc817 100644 --- a/docs/images/nf-core-subworkflows-info.svg +++ b/docs/images/nf-core-subworkflows-info.svg @@ -19,333 +19,333 @@ font-weight: 700; } - .terminal-2903024194-matrix { + .terminal-1096786593-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2903024194-title { + .terminal-1096786593-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2903024194-r1 { fill: #c5c8c6 } -.terminal-2903024194-r2 { fill: #98a84b } -.terminal-2903024194-r3 { fill: #9a9b99 } -.terminal-2903024194-r4 { fill: #608ab1 } -.terminal-2903024194-r5 { fill: #d0b344 } -.terminal-2903024194-r6 { fill: #cc555a } -.terminal-2903024194-r7 { fill: #cc555a;font-weight: bold } -.terminal-2903024194-r8 { fill: #8a4346;font-weight: bold } -.terminal-2903024194-r9 { fill: #8d7b39 } -.terminal-2903024194-r10 { fill: #d0b344;font-weight: bold } -.terminal-2903024194-r11 { fill: #1984e9 } -.terminal-2903024194-r12 { fill: #00823d } -.terminal-2903024194-r13 { fill: #868887 } -.terminal-2903024194-r14 { fill: #398280 } -.terminal-2903024194-r15 { fill: #ff2c7a } -.terminal-2903024194-r16 { fill: #ff2627;font-weight: bold } + .terminal-1096786593-r1 { fill: #c5c8c6 } +.terminal-1096786593-r2 { fill: #98a84b } +.terminal-1096786593-r3 { fill: #9a9b99 } +.terminal-1096786593-r4 { fill: #608ab1 } +.terminal-1096786593-r5 { fill: #d0b344 } +.terminal-1096786593-r6 { fill: #cc555a } +.terminal-1096786593-r7 { fill: #cc555a;font-weight: bold } +.terminal-1096786593-r8 { fill: #8a4346;font-weight: bold } +.terminal-1096786593-r9 { fill: #8d7b39 } +.terminal-1096786593-r10 { fill: #d0b344;font-weight: bold } +.terminal-1096786593-r11 { fill: #1984e9 } +.terminal-1096786593-r12 { fill: #00823d } +.terminal-1096786593-r13 { fill: #868887 } +.terminal-1096786593-r14 { fill: #398280 } +.terminal-1096786593-r15 { fill: #ff2c7a } +.terminal-1096786593-r16 { fill: #ff2627;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -357,108 +357,108 @@ - + - - $ nf-core subworkflows info bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - - -╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ -│/opt/hostedtoolcache/Python/3.11.0/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/3.11.0/x64/lib/python3.11/site-packages/nf_core/__main__.py:105 in   │ -│run_nf_core│ -││ -│ 104 │   # Launch the click cli│ -│❱  105 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │ -│ 106 │ -││ -│/opt/hostedtoolcache/Python/3.11.0/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/3.11.0/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/3.11.0/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/3.11.0/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/3.11.0/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/3.11.0/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/3.11.0/x64/lib/python3.11/site-packages/click/core.py:760 in invoke│ -││ -│ 759 │   │   │   with ctx:                                                                     │ -│❱  760 │   │   │   │   return __callback(*args, **kwargs)                                        │ -│ 761 │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/click/decorators.py:26 in    │ -│new_func│ -││ -│ 25 │   defnew_func(*args, **kwargs):  # type: ignore│ -│❱  26 │   │   return f(get_current_context(), *args, **kwargs)                                   │ -│ 27 │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/nf_core/__main__.py:1087 in  │ -│info│ -││ -│1086 │   │   )                                                                                 │ -│❱ 1087 │   │   stdout.print(subworkflow_info.get_component_info())                               │ -│1088 │   except (UserWarning, LookupError) as e:                                               │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/nf_core/components/info.py:1│ -│49 in get_component_info│ -││ -│148 │   │   │ -│❱ 149 │   │   returnself.generate_component_info_help()                                         │ -│150 │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/nf_core/components/info.py:2│ -│62 in generate_component_info_help│ -││ -│261 │   │   │   │   │   inputs_table.add_row(                                                  │ -│❱ 262 │   │   │   │   │   │   f"[orange1 on black] {key} [/][dim i] ({info['type']})",           │ -│263 │   │   │   │   │   │   Markdown(info["description"] if info["description"] else""),      │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -TypeError: 'NoneType' object is not subscriptable + + $ nf-core subworkflows info bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + + +╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ +│/opt/hostedtoolcache/Python/3.11.0/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/3.11.0/x64/lib/python3.11/site-packages/nf_core/__main__.py:105 in   │ +│run_nf_core│ +││ +│ 104 │   # Launch the click cli│ +│❱  105 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │ +│ 106 │ +││ +│/opt/hostedtoolcache/Python/3.11.0/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/3.11.0/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/3.11.0/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/3.11.0/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/3.11.0/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/3.11.0/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/3.11.0/x64/lib/python3.11/site-packages/click/core.py:760 in invoke│ +││ +│ 759 │   │   │   with ctx:                                                                     │ +│❱  760 │   │   │   │   return __callback(*args, **kwargs)                                        │ +│ 761 │ +││ +│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/click/decorators.py:26 in    │ +│new_func│ +││ +│ 25 │   defnew_func(*args, **kwargs):  # type: ignore│ +│❱  26 │   │   return f(get_current_context(), *args, **kwargs)                                   │ +│ 27 │ +││ +│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/nf_core/__main__.py:1087 in  │ +│info│ +││ +│1086 │   │   )                                                                                 │ +│❱ 1087 │   │   stdout.print(subworkflow_info.get_component_info())                               │ +│1088 │   except (UserWarning, LookupError) as e:                                               │ +││ +│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/nf_core/components/info.py:1│ +│49 in get_component_info│ +││ +│148 │   │   │ +│❱ 149 │   │   returnself.generate_component_info_help()                                         │ +│150 │ +││ +│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/nf_core/components/info.py:2│ +│62 in generate_component_info_help│ +││ +│261 │   │   │   │   │   inputs_table.add_row(                                                  │ +│❱ 262 │   │   │   │   │   │   f"[orange1 on black] {key} [/][dim i] ({info['type']})",           │ +│263 │   │   │   │   │   │   Markdown(info["description"] if info["description"] else""),      │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +TypeError: 'NoneType' object is not subscriptable diff --git a/docs/images/nf-core-subworkflows-install.svg b/docs/images/nf-core-subworkflows-install.svg index cfb6a57f4c..4ad2943f2d 100644 --- a/docs/images/nf-core-subworkflows-install.svg +++ b/docs/images/nf-core-subworkflows-install.svg @@ -19,107 +19,107 @@ font-weight: 700; } - .terminal-2034106394-matrix { + .terminal-1152843897-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2034106394-title { + .terminal-1152843897-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2034106394-r1 { fill: #c5c8c6 } -.terminal-2034106394-r2 { fill: #98a84b } -.terminal-2034106394-r3 { fill: #9a9b99 } -.terminal-2034106394-r4 { fill: #608ab1 } -.terminal-2034106394-r5 { fill: #d0b344 } -.terminal-2034106394-r6 { fill: #cc555a } + .terminal-1152843897-r1 { fill: #c5c8c6 } +.terminal-1152843897-r2 { fill: #98a84b } +.terminal-1152843897-r3 { fill: #9a9b99 } +.terminal-1152843897-r4 { fill: #608ab1 } +.terminal-1152843897-r5 { fill: #d0b344 } +.terminal-1152843897-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -131,36 +131,36 @@ - + - - $ nf-core subworkflows install bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - - -WARNING 'repository_type' not defined in .nf-core.yml                                               -Warning: Input is not a terminal (fd=0). -? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - » Pipeline -   nf-core/modules - - - -        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - -Aborted. + + $ nf-core subworkflows install bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. diff --git a/docs/images/nf-core-subworkflows-list-local.svg b/docs/images/nf-core-subworkflows-list-local.svg index 10b3198e2d..3338be6182 100644 --- a/docs/images/nf-core-subworkflows-list-local.svg +++ b/docs/images/nf-core-subworkflows-list-local.svg @@ -19,108 +19,108 @@ font-weight: 700; } - .terminal-1218770405-matrix { + .terminal-85784132-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1218770405-title { + .terminal-85784132-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1218770405-r1 { fill: #c5c8c6 } -.terminal-1218770405-r2 { fill: #98a84b } -.terminal-1218770405-r3 { fill: #9a9b99 } -.terminal-1218770405-r4 { fill: #608ab1 } -.terminal-1218770405-r5 { fill: #d0b344 } -.terminal-1218770405-r6 { fill: #cc555a } -.terminal-1218770405-r7 { fill: #868887;font-style: italic; } + .terminal-85784132-r1 { fill: #c5c8c6 } +.terminal-85784132-r2 { fill: #98a84b } +.terminal-85784132-r3 { fill: #9a9b99 } +.terminal-85784132-r4 { fill: #608ab1 } +.terminal-85784132-r5 { fill: #d0b344 } +.terminal-85784132-r6 { fill: #cc555a } +.terminal-85784132-r7 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,36 +132,36 @@ - + - - $ nf-core subworkflows list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - - -WARNING 'repository_type' not defined in .nf-core.yml                                               -Warning: Input is not a terminal (fd=0). -? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - » Pipeline -   nf-core/modules - - - -        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - -[..truncated..] + + $ nf-core subworkflows list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +[..truncated..] diff --git a/docs/images/nf-core-subworkflows-list-remote.svg b/docs/images/nf-core-subworkflows-list-remote.svg index 966ce82802..9c60556afe 100644 --- a/docs/images/nf-core-subworkflows-list-remote.svg +++ b/docs/images/nf-core-subworkflows-list-remote.svg @@ -19,109 +19,109 @@ font-weight: 700; } - .terminal-649478967-matrix { + .terminal-4078322582-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-649478967-title { + .terminal-4078322582-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-649478967-r1 { fill: #c5c8c6 } -.terminal-649478967-r2 { fill: #98a84b } -.terminal-649478967-r3 { fill: #9a9b99 } -.terminal-649478967-r4 { fill: #608ab1 } -.terminal-649478967-r5 { fill: #d0b344 } -.terminal-649478967-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-649478967-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-649478967-r8 { fill: #868887;font-style: italic; } + .terminal-4078322582-r1 { fill: #c5c8c6 } +.terminal-4078322582-r2 { fill: #98a84b } +.terminal-4078322582-r3 { fill: #9a9b99 } +.terminal-4078322582-r4 { fill: #608ab1 } +.terminal-4078322582-r5 { fill: #d0b344 } +.terminal-4078322582-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-4078322582-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-4078322582-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core subworkflows list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - - -INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Subworkflow Name                            ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ bam_dedup_stats_samtools_umitools            │ -│ bam_markduplicates_picard                    │ -│ bam_qc_picard                                │ -│ bam_rseqc                                    │ -│ bam_sort_stats_samtools                      │ -│ bam_stats_samtools                           │ -│ bcl_demultiplex                              │ -│ bed_scatter_bedtools                         │ -│ bedgraph_bedclip_bedgraphtobigwig            │ -[..truncated..] + + $ nf-core subworkflows list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + + +INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Subworkflow Name                            ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ bam_dedup_stats_samtools_umitools            │ +│ bam_markduplicates_picard                    │ +│ bam_qc_picard                                │ +│ bam_rseqc                                    │ +│ bam_sort_stats_samtools                      │ +│ bam_stats_samtools                           │ +│ bcl_demultiplex                              │ +│ bed_scatter_bedtools                         │ +│ bedgraph_bedclip_bedgraphtobigwig            │ +[..truncated..] diff --git a/docs/images/nf-core-subworkflows-remove.svg b/docs/images/nf-core-subworkflows-remove.svg index d6667f8e68..d6a95b7b77 100644 --- a/docs/images/nf-core-subworkflows-remove.svg +++ b/docs/images/nf-core-subworkflows-remove.svg @@ -19,107 +19,107 @@ font-weight: 700; } - .terminal-1454309282-matrix { + .terminal-559218704-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1454309282-title { + .terminal-559218704-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1454309282-r1 { fill: #c5c8c6 } -.terminal-1454309282-r2 { fill: #98a84b } -.terminal-1454309282-r3 { fill: #9a9b99 } -.terminal-1454309282-r4 { fill: #608ab1 } -.terminal-1454309282-r5 { fill: #d0b344 } -.terminal-1454309282-r6 { fill: #cc555a } + .terminal-559218704-r1 { fill: #c5c8c6 } +.terminal-559218704-r2 { fill: #98a84b } +.terminal-559218704-r3 { fill: #9a9b99 } +.terminal-559218704-r4 { fill: #608ab1 } +.terminal-559218704-r5 { fill: #d0b344 } +.terminal-559218704-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -131,36 +131,36 @@ - + - - $ nf-core subworkflows remove bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - - -WARNING 'repository_type' not defined in .nf-core.yml                                               -Warning: Input is not a terminal (fd=0). -? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - » Pipeline -   nf-core/modules - - - -        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - -Aborted. + + $ nf-core subworkflows remove bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. diff --git a/docs/images/nf-core-subworkflows-test.svg b/docs/images/nf-core-subworkflows-test.svg index a407a2844d..0e3904fc3c 100644 --- a/docs/images/nf-core-subworkflows-test.svg +++ b/docs/images/nf-core-subworkflows-test.svg @@ -19,107 +19,107 @@ font-weight: 700; } - .terminal-3187868540-matrix { + .terminal-2420114395-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3187868540-title { + .terminal-2420114395-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3187868540-r1 { fill: #c5c8c6 } -.terminal-3187868540-r2 { fill: #98a84b } -.terminal-3187868540-r3 { fill: #9a9b99 } -.terminal-3187868540-r4 { fill: #608ab1 } -.terminal-3187868540-r5 { fill: #d0b344 } -.terminal-3187868540-r6 { fill: #cc555a } + .terminal-2420114395-r1 { fill: #c5c8c6 } +.terminal-2420114395-r2 { fill: #98a84b } +.terminal-2420114395-r3 { fill: #9a9b99 } +.terminal-2420114395-r4 { fill: #608ab1 } +.terminal-2420114395-r5 { fill: #d0b344 } +.terminal-2420114395-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -131,36 +131,36 @@ - + - - $ nf-core subworkflows test bam_rseqc --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - - -WARNING 'repository_type' not defined in .nf-core.yml                                               -Warning: Input is not a terminal (fd=0). -? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - » Pipeline -   nf-core/modules - - - -        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - -Aborted. + + $ nf-core subworkflows test bam_rseqc --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. diff --git a/docs/images/nf-core-subworkflows-update.svg b/docs/images/nf-core-subworkflows-update.svg index c83f453da6..cee91fa471 100644 --- a/docs/images/nf-core-subworkflows-update.svg +++ b/docs/images/nf-core-subworkflows-update.svg @@ -19,107 +19,107 @@ font-weight: 700; } - .terminal-2269839890-matrix { + .terminal-1454637681-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2269839890-title { + .terminal-1454637681-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2269839890-r1 { fill: #c5c8c6 } -.terminal-2269839890-r2 { fill: #98a84b } -.terminal-2269839890-r3 { fill: #9a9b99 } -.terminal-2269839890-r4 { fill: #608ab1 } -.terminal-2269839890-r5 { fill: #d0b344 } -.terminal-2269839890-r6 { fill: #cc555a } + .terminal-1454637681-r1 { fill: #c5c8c6 } +.terminal-1454637681-r2 { fill: #98a84b } +.terminal-1454637681-r3 { fill: #9a9b99 } +.terminal-1454637681-r4 { fill: #608ab1 } +.terminal-1454637681-r5 { fill: #d0b344 } +.terminal-1454637681-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -131,36 +131,36 @@ - + - - $ nf-core subworkflows update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - https://nf-co.re - - - -WARNING 'repository_type' not defined in .nf-core.yml                                               -Warning: Input is not a terminal (fd=0). -? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - » Pipeline -   nf-core/modules - - - -        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - -Aborted. + + $ nf-core subworkflows update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.1 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. diff --git a/docs/images/nf-core-sync.svg b/docs/images/nf-core-sync.svg index c607247f3c..2f22643569 100644 --- a/docs/images/nf-core-sync.svg +++ b/docs/images/nf-core-sync.svg @@ -19,72 +19,72 @@ font-weight: 700; } - .terminal-1725630925-matrix { + .terminal-739183148-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1725630925-title { + .terminal-739183148-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1725630925-r1 { fill: #c5c8c6 } -.terminal-1725630925-r2 { fill: #98a84b } -.terminal-1725630925-r3 { fill: #9a9b99 } -.terminal-1725630925-r4 { fill: #608ab1 } -.terminal-1725630925-r5 { fill: #d0b344 } -.terminal-1725630925-r6 { fill: #98729f } -.terminal-1725630925-r7 { fill: #ff2c7a } + .terminal-739183148-r1 { fill: #c5c8c6 } +.terminal-739183148-r2 { fill: #98a84b } +.terminal-739183148-r3 { fill: #9a9b99 } +.terminal-739183148-r4 { fill: #608ab1 } +.terminal-739183148-r5 { fill: #d0b344 } +.terminal-739183148-r6 { fill: #98729f } +.terminal-739183148-r7 { fill: #ff2c7a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,24 +96,24 @@ - + - - $ nf-core sync - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7 - 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 2.7.1 - 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                                     From 46317bdcacd3321c23ed43e45345ee2e770d7f20 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 8 Dec 2022 17:52:37 +0100 Subject: [PATCH 3/4] fix github_output syntax --- nf_core/pipeline-template/.github/workflows/fix-linting.yml | 4 ++-- .../pipeline-template/.github/workflows/linting_comment.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml index 4c586a0929..f3dc3e50fe 100644 --- a/nf_core/pipeline-template/.github/workflows/fix-linting.yml +++ b/nf_core/pipeline-template/.github/workflows/fix-linting.yml @@ -34,9 +34,9 @@ jobs: id: prettier_status run: | if prettier --check ${GITHUB_WORKSPACE}; then - echo "name=result::pass" >> $GITHUB_OUTPUT + echo "result=pass" >> $GITHUB_OUTPUT else - echo "name=result::fail" >> $GITHUB_OUTPUT + echo "result=fail" >> $GITHUB_OUTPUT fi - name: Run 'prettier --write' diff --git a/nf_core/pipeline-template/.github/workflows/linting_comment.yml b/nf_core/pipeline-template/.github/workflows/linting_comment.yml index 585b933f1c..09f8c423e5 100644 --- a/nf_core/pipeline-template/.github/workflows/linting_comment.yml +++ b/nf_core/pipeline-template/.github/workflows/linting_comment.yml @@ -18,7 +18,7 @@ jobs: - name: Get PR number id: pr_number - run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT + run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment uses: marocchino/sticky-pull-request-comment@v2 From 78d4a25ee2d48c9177a3155c779a2699aa07d378 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 8 Dec 2022 17:55:42 +0100 Subject: [PATCH 4/4] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7894ed3d65..fd09bbde70 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,8 @@ ### Template +- Fix the syntax of github_output in GitHub actions ([#2114](https://github.com/nf-core/tools/pull/2114)) + ### Linting ### Modules