From f2a2710070ebd840d2f1d2cd9061ea8cec1de86a Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 23 Feb 2023 11:55:14 +0000 Subject: [PATCH 1/2] Generate new screengrabs with rich-codex --- docs/images/nf-core-bump-version.svg | 101 ++++----- docs/images/nf-core-create.svg | 145 +++++++------ docs/images/nf-core-download-tree.svg | 146 ++++++------- docs/images/nf-core-download.svg | 99 ++++----- docs/images/nf-core-launch-rnaseq.svg | 95 +++++---- docs/images/nf-core-licences.svg | 143 +++++++------ docs/images/nf-core-list-rna.svg | 129 ++++++------ docs/images/nf-core-list-stars.svg | 105 ++++----- docs/images/nf-core-list.svg | 109 +++++----- docs/images/nf-core-modules-bump-version.svg | 117 +++++----- docs/images/nf-core-modules-create.svg | 137 ++++++------ docs/images/nf-core-modules-info.svg | 211 ++++--------------- docs/images/nf-core-modules-install.svg | 83 ++++---- docs/images/nf-core-modules-lint.svg | 160 ++++---------- docs/images/nf-core-modules-list-local.svg | 133 ++++++------ docs/images/nf-core-modules-list-remote.svg | 133 ++++++------ docs/images/nf-core-modules-mulled.svg | 91 ++++---- docs/images/nf-core-modules-patch.svg | 157 +++++++------- docs/images/nf-core-modules-remove.svg | 84 ++++---- docs/images/nf-core-modules-test.svg | 90 ++++---- docs/images/nf-core-modules-update.svg | 100 ++++----- docs/images/nf-core-schema-build.svg | 95 +++++---- docs/images/nf-core-schema-lint.svg | 105 ++++----- docs/images/nf-core-schema-validate.svg | 93 ++++---- docs/images/nf-core-sync.svg | 95 +++++---- 25 files changed, 1427 insertions(+), 1529 deletions(-) diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg index 6e8b89d1c..41d7b74f8 100644 --- a/docs/images/nf-core-bump-version.svg +++ b/docs/images/nf-core-bump-version.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core bump-version 1.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Changing version number from '1.0dev' to '1.1'bump_version.py:35 -INFO     Updated version in 'nextflow.config'bump_version.py:164 - - version         = '1.0dev' - + version = '1.1' - - + + $ nf-core bump-version 1.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO     Changing version number from '1.0dev' to '1.1'bump_version.py:35 +INFO     Updated version in 'nextflow.config'bump_version.py:164 + - version         = '1.0dev' + + version = '1.1' + + diff --git a/docs/images/nf-core-create.svg b/docs/images/nf-core-create.svg index a453d8c57..ca414a5c5 100644 --- a/docs/images/nf-core-create.svg +++ b/docs/images/nf-core-create.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - - - - $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique"  --a "Big Steve" --plain - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Creating new nf-core pipeline: 'nf-core/nextbigthing'create.py:226 -INFO     Initialising pipeline git repository                                          create.py:518 -INFO     Done. Remember to add a remote and push to GitHub:                            create.py:525 - cd /home/runner/work/tools/tools/tmp/nf-core-nextbigthing - git remote add origin git@github.com:USERNAME/REPO_NAME.git  - git push --all origin                                        -INFO     This will also push your newly created dev branch and the TEMPLATE branch for create.py:531 -         syncing.                                                                       -INFO    !!!!!! IMPORTANT !!!!!!create.py:217 - -If you are interested in adding your pipeline to the nf-core community, -PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE! - -Please read: https://nf-co.re/developers/adding_pipelines#join-the-community + + + + $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique"  +-a "Big Steve" --plain + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO     Creating new nf-core pipeline: 'nf-core/nextbigthing'create.py:226 +INFO     Initialising pipeline git repository                                          create.py:518 +INFO     Done. Remember to add a remote and push to GitHub:                            create.py:525 + cd /home/runner/work/tools/tools/tmp/nf-core-nextbigthing + git remote add origin git@github.com:USERNAME/REPO_NAME.git  + git push --all origin                                        +INFO     This will also push your newly created dev branch and the TEMPLATE branch for create.py:531 +         syncing.                                                                       +INFO    !!!!!! IMPORTANT !!!!!!create.py:217 + +If you are interested in adding your pipeline to the nf-core community, +PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE! + +Please read: https://nf-co.re/developers/adding_pipelines#join-the-community diff --git a/docs/images/nf-core-download-tree.svg b/docs/images/nf-core-download-tree.svg index 24a0f671f..a06c743fd 100644 --- a/docs/images/nf-core-download-tree.svg +++ b/docs/images/nf-core-download-tree.svg @@ -19,123 +19,123 @@ font-weight: 700; } - .terminal-187724284-matrix { + .terminal-3113317903-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-187724284-title { + .terminal-3113317903-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-187724284-r1 { fill: #c5c8c6 } + .terminal-3113317903-r1 { fill: #c5c8c6 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -147,43 +147,43 @@ - + - - $ tree -L 2 nf-core-rnaseq/ -nf-core-rnaseq/ -├── configs -│   ├── CITATION.cff -│   ├── LICENSE -│   ├── README.md -│   ├── bin -│   ├── conf -│   ├── configtest.nf -│   ├── docs -│   ├── nextflow.config -│   ├── nfcore_custom.config -│   └── pipeline -└── workflow -    ├── CHANGELOG.md -    ├── CITATIONS.md -    ├── CODE_OF_CONDUCT.md -    ├── LICENSE -    ├── README.md -    ├── assets -    ├── bin -    ├── conf -    ├── docs -    ├── lib -    ├── main.nf -    ├── modules -    ├── modules.json -    ├── nextflow.config -    ├── nextflow_schema.json -    ├── subworkflows -    ├── tower.yml -    └── workflows - -14 directories, 16 files + + $ tree -L 2 nf-core-rnaseq/ +nf-core-rnaseq/ +├── configs +│   ├── CITATION.cff +│   ├── LICENSE +│   ├── README.md +│   ├── bin +│   ├── conf +│   ├── configtest.nf +│   ├── docs +│   ├── nextflow.config +│   ├── nfcore_custom.config +│   └── pipeline +└── workflow +    ├── CHANGELOG.md +    ├── CITATIONS.md +    ├── CODE_OF_CONDUCT.md +    ├── LICENSE +    ├── README.md +    ├── assets +    ├── bin +    ├── conf +    ├── docs +    ├── lib +    ├── main.nf +    ├── modules +    ├── modules.json +    ├── nextflow.config +    ├── nextflow_schema.json +    ├── subworkflows +    ├── tower.yml +    └── workflows + +14 directories, 16 files diff --git a/docs/images/nf-core-download.svg b/docs/images/nf-core-download.svg index 5502d4fc4..cf54cf6ef 100644 --- a/docs/images/nf-core-download.svg +++ b/docs/images/nf-core-download.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -c none - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Saving 'nf-core/rnaseq'download.py:158 -          Pipeline revision: '3.8' -          Pull containers: 'none' -          Output directory: 'nf-core-rnaseq' -INFO     Downloading workflow files from GitHub                                      download.py:161 -INFO     Downloading centralised configs from GitHub                                 download.py:165 + + $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -c none + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO     Saving 'nf-core/rnaseq'download.py:158 +          Pipeline revision: '3.8' +          Pull containers: 'none' +          Output directory: 'nf-core-rnaseq' +INFO     Downloading workflow files from GitHub                                      download.py:161 +INFO     Downloading centralised configs from GitHub                                 download.py:165 diff --git a/docs/images/nf-core-launch-rnaseq.svg b/docs/images/nf-core-launch-rnaseq.svg index 96ecbd342..1250c9d5f 100644 --- a/docs/images/nf-core-launch-rnaseq.svg +++ b/docs/images/nf-core-launch-rnaseq.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core launch rnaseq -r 3.8.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     NOTE: This tool ignores any pipeline parameter defaults overwritten by        launch.py:131 -         Nextflow config files or profiles                                              - -INFO     Downloading workflow: nf-core/rnaseq (3.8.1)list.py:67 + + $ nf-core launch rnaseq -r 3.8.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO     NOTE: This tool ignores any pipeline parameter defaults overwritten by        launch.py:131 +         Nextflow config files or profiles                                              + +INFO     Downloading workflow: nf-core/rnaseq (3.8.1)list.py:67 diff --git a/docs/images/nf-core-licences.svg b/docs/images/nf-core-licences.svg index 5f84e722e..3a4d3015b 100644 --- a/docs/images/nf-core-licences.svg +++ b/docs/images/nf-core-licences.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core licences deepvariant - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Fetching licence information for 8 tools                                     licences.py:77 -INFO     Warning: This tool only prints licence information for the software tools    licences.py:98 -         packaged using conda.                                                         -INFO     The pipeline may use other software and dependencies not described here.     licences.py:99 -┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓ -┃Package Name┃Version┃Licence┃ -┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩ -│ lbzip2       │ 2.5     │ GPL v3  │ -│ deepvariant  │ 0.7.0   │ MIT     │ -│ htslib       │ 1.9     │ MIT     │ -│ picard       │ 2.18.7  │ MIT     │ -│ pip          │ 10.0.1  │ MIT     │ -│ samtools     │ 1.9     │ MIT     │ -│ python       │ 2.7.15  │ PSF     │ -│ bzip2        │ 1.0.6   │ bzip2   │ -└──────────────┴─────────┴─────────┘ + + $ nf-core licences deepvariant + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO     Fetching licence information for 8 tools                                     licences.py:77 +INFO     Warning: This tool only prints licence information for the software tools    licences.py:98 +         packaged using conda.                                                         +INFO     The pipeline may use other software and dependencies not described here.     licences.py:99 +┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓ +┃Package Name┃Version┃Licence┃ +┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩ +│ lbzip2       │ 2.5     │ GPL v3  │ +│ deepvariant  │ 0.7.0   │ MIT     │ +│ htslib       │ 1.9     │ MIT     │ +│ picard       │ 2.18.7  │ MIT     │ +│ pip          │ 10.0.1  │ MIT     │ +│ samtools     │ 1.9     │ MIT     │ +│ python       │ 2.7.15  │ PSF     │ +│ bzip2        │ 1.0.6   │ bzip2   │ +└──────────────┴─────────┴─────────┘ diff --git a/docs/images/nf-core-list-rna.svg b/docs/images/nf-core-list-rna.svg index cbd098b94..057546d4e 100644 --- a/docs/images/nf-core-list-rna.svg +++ b/docs/images/nf-core-list-rna.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core list rna rna-seq - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnafusion            │    76 │          2.1.0 │ 2 months ago │           - │ -                   │ -│ smrnaseq             │    42 │          2.0.0 │ 3 months ago │           - │ -                   │ -│ rnaseq               │   501 │          3.8.1 │ 3 months ago │           - │ -                   │ -│ dualrnaseq           │     7 │          1.0.0 │  2 years ago │           - │ -                   │ -│ circrna              │    19 │            dev │            - │           - │ -                   │ -│ lncpipe              │    23 │            dev │            - │           - │ -                   │ -│ scflow               │    12 │            dev │            - │           - │ -                   │ -│ spatialtranscriptom… │    10 │            dev │            - │           - │ -                   │ -└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ + + $ nf-core list rna rna-seq + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq               │   570 │         3.10.1 │ 2 months ago │           - │ -                   │ +│ smrnaseq             │    48 │          2.1.0 │ 4 months ago │           - │ -                   │ +│ rnafusion            │    89 │          2.1.0 │ 8 months ago │           - │ -                   │ +│ dualrnaseq           │     9 │          1.0.0 │  2 years ago │           - │ -                   │ +│ circrna              │    26 │            dev │            - │           - │ -                   │ +│ lncpipe              │    24 │            dev │            - │           - │ -                   │ +│ scflow               │    18 │            dev │            - │           - │ -                   │ +│ spatialtranscriptom… │    16 │            dev │            - │           - │ -                   │ +└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg index da3f02c7d..0524ecb02 100644 --- a/docs/images/nf-core-list-stars.svg +++ b/docs/images/nf-core-list-stars.svg @@ -19,88 +19,89 @@ font-weight: 700; } - .terminal-1473353797-matrix { + .terminal-3466505919-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1473353797-title { + .terminal-3466505919-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1473353797-r1 { fill: #c5c8c6 } -.terminal-1473353797-r2 { fill: #98a84b } -.terminal-1473353797-r3 { fill: #9a9b99 } -.terminal-1473353797-r4 { fill: #608ab1 } -.terminal-1473353797-r5 { fill: #d0b344 } -.terminal-1473353797-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1473353797-r7 { fill: #868887 } -.terminal-1473353797-r8 { fill: #868887;font-style: italic; } + .terminal-3466505919-r1 { fill: #c5c8c6 } +.terminal-3466505919-r2 { fill: #98a84b } +.terminal-3466505919-r3 { fill: #9a9b99 } +.terminal-3466505919-r4 { fill: #608ab1 } +.terminal-3466505919-r5 { fill: #d0b344 } +.terminal-3466505919-r6 { fill: #d08442;font-weight: bold } +.terminal-3466505919-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-3466505919-r8 { fill: #868887 } +.terminal-3466505919-r9 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -112,29 +113,29 @@ - + - - $ nf-core list -s stars - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq               │   501 │          3.8.1 │ 3 months ago │           - │ -                   │ -│ sarek                │   186 │          3.0.1 │  2 weeks ago │           - │ -                   │ -│ chipseq              │   121 │          1.2.2 │  1 years ago │           - │ -                   │ -│ atacseq              │   116 │          1.2.2 │ 4 months ago │           - │ -                   │ -[..truncated..] + + $ nf-core list -s stars + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq              │   570 │         3.10.1 │  2 months ago │           - │ -                   │ +│ sarek               │   227 │          3.1.2 │  2 months ago │           - │ -                   │ +│ chipseq             │   140 │          2.0.0 │  5 months ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg index c5e7e17dd..acc607561 100644 --- a/docs/images/nf-core-list.svg +++ b/docs/images/nf-core-list.svg @@ -19,91 +19,92 @@ font-weight: 700; } - .terminal-2711598360-matrix { + .terminal-4220727666-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2711598360-title { + .terminal-4220727666-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2711598360-r1 { fill: #c5c8c6 } -.terminal-2711598360-r2 { fill: #98a84b } -.terminal-2711598360-r3 { fill: #9a9b99 } -.terminal-2711598360-r4 { fill: #608ab1 } -.terminal-2711598360-r5 { fill: #d0b344 } -.terminal-2711598360-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2711598360-r7 { fill: #868887 } -.terminal-2711598360-r8 { fill: #868887;font-style: italic; } + .terminal-4220727666-r1 { fill: #c5c8c6 } +.terminal-4220727666-r2 { fill: #98a84b } +.terminal-4220727666-r3 { fill: #9a9b99 } +.terminal-4220727666-r4 { fill: #608ab1 } +.terminal-4220727666-r5 { fill: #d0b344 } +.terminal-4220727666-r6 { fill: #d08442;font-weight: bold } +.terminal-4220727666-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-4220727666-r8 { fill: #868887 } +.terminal-4220727666-r9 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +116,30 @@ - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ mag                  │    99 │          2.2.1 │   4 days ago │           - │ -                   │ -│ sarek                │   186 │          3.0.1 │  2 weeks ago │           - │ -                   │ -│ epitopeprediction    │    22 │          2.1.0 │  4 weeks ago │           - │ -                   │ -│ eager                │    71 │          2.4.5 │  4 weeks ago │           - │ -                   │ -│ viralrecon           │    74 │            2.5 │ 2 months ago │           - │ -                   │ -[..truncated..] + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ nascent             │     6 │          2.1.1 │    5 days ago │           - │ -                   │ +│ phyloplace          │     2 │          1.0.0 │    1 week ago │           - │ -                   │ +│ funcscan            │    21 │          1.0.0 │   1 weeks ago │           - │ -                   │ +│ proteinfold         │    15 │          1.0.0 │   2 weeks ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index e76e7a0a1..48049fcfb 100644 --- a/docs/images/nf-core-modules-bump-version.svg +++ b/docs/images/nf-core-modules-bump-version.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules bump-versions fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - - -╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ -│[!] 1 Module version up to date.│ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ -│Module name                             │Update Message                                       │ -├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ -│ fastqc                                   │ Module version up to date: fastqc                     │ -╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ + + $ nf-core modules bump-versions fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + + +╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ +│[!] 1 Module version up to date.│ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ +│Module name                             │Update Message                                       │ +├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ +│ fastqc                                   │ Module version up to date: fastqc                     │ +╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index 13e19b5e7..b485e9bc8 100644 --- a/docs/images/nf-core-modules-create.svg +++ b/docs/images/nf-core-modules-create.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Repository type: modulescreate.py:93 -INFO    Press enter to use default values (shown in brackets)or type your own create.py:97 -responses. ctrl+click underlined text to open links. -INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9'create.py:165 -INFO     Using Docker container: 'quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1'create.py:191 -INFO     Using Singularity container:                                                  create.py:192 -'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--hdfd78af_1' -INFO     Created / edited following files:                                             create.py:270 -           ./modules/fastqc/main.nf -           ./modules/fastqc/meta.yml -           ./tests/modules/fastqc/main.nf -           ./tests/modules/fastqc/test.yml -           ./tests/modules/fastqc/nextflow.config -           ./tests/config/pytest_modules.yml + + $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO     Repository type: modulescreate.py:93 +INFO    Press enter to use default values (shown in brackets)or type your own create.py:97 +responses. ctrl+click underlined text to open links. +INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9'create.py:165 +INFO     Using Docker container: 'quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1'create.py:191 +INFO     Using Singularity container:                                                  create.py:192 +'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--hdfd78af_1' +INFO     Created / edited following files:                                             create.py:270 +           ./modules/fastqc/main.nf +           ./modules/fastqc/meta.yml +           ./tests/modules/fastqc/main.nf +           ./tests/modules/fastqc/test.yml +           ./tests/modules/fastqc/nextflow.config +           ./tests/config/pytest_modules.yml diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg index 5c3a82569..46fc01463 100644 --- a/docs/images/nf-core-modules-info.svg +++ b/docs/images/nf-core-modules-info.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - $ nf-core modules info abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ -│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ -│ 🔧 Tools: abacas                                                                                 │ -│ 📖 Description: contiguate draft genome assembly                                                 │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -                  ╷                                                                   ╷              -📥 Inputs        │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} -                  ╵                                                                   ╵              -                  ╷                                                                   ╷              -📤 Outputs       │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - results  (files)│List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* -                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ -                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ -                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ -                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - versions  (file)│File containing software versions                                  │versions.yml -                  ╵                                                                   ╵              - - 💻  Installation command: nf-core modules install abacas - + + + + $ nf-core modules info abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +ERROR    Could not find module 'abacas'__main__.py:755 diff --git a/docs/images/nf-core-modules-install.svg b/docs/images/nf-core-modules-install.svg index ce016fe92..c987a2939 100644 --- a/docs/images/nf-core-modules-install.svg +++ b/docs/images/nf-core-modules-install.svg @@ -19,72 +19,73 @@ font-weight: 700; } - .terminal-2202046856-matrix { + .terminal-2052881942-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2202046856-title { + .terminal-2052881942-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2202046856-r1 { fill: #c5c8c6 } -.terminal-2202046856-r2 { fill: #98a84b } -.terminal-2202046856-r3 { fill: #9a9b99 } -.terminal-2202046856-r4 { fill: #608ab1 } -.terminal-2202046856-r5 { fill: #d0b344 } -.terminal-2202046856-r6 { fill: #868887 } -.terminal-2202046856-r7 { fill: #c5c8c6;font-weight: bold } + .terminal-2052881942-r1 { fill: #c5c8c6 } +.terminal-2052881942-r2 { fill: #98a84b } +.terminal-2052881942-r3 { fill: #9a9b99 } +.terminal-2052881942-r4 { fill: #608ab1 } +.terminal-2052881942-r5 { fill: #d0b344 } +.terminal-2052881942-r6 { fill: #d08442;font-weight: bold } +.terminal-2052881942-r7 { fill: #cc555a;font-weight: bold } +.terminal-2052881942-r8 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,24 +97,24 @@ - + - - $ nf-core modules install abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Installing 'abacas'install.py:116 -INFO     Include statement: include { ABACAS } from                                   install.py:125 -'../modules/nf-core/modules/abacas/main' + + $ nf-core modules install abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +ERROR    Module 'abacas' not found in list of available modules.                       install.py:63 +INFO     Use the command 'nf-core modules list' to view available software             install.py:64 diff --git a/docs/images/nf-core-modules-lint.svg b/docs/images/nf-core-modules-lint.svg index e74151121..bc95f77e2 100644 --- a/docs/images/nf-core-modules-lint.svg +++ b/docs/images/nf-core-modules-lint.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - $ nf-core modules lint multiqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Linting modules repo: '.'__init__.py:206 -INFO     Linting module: 'multiqc'__init__.py:210 - -╭─[!] 1 Module Test Warning ──────────────────────────────────────────────────────────────────────╮ -│                                           ╷                         ╷                            │ -│Module name                              │File path              │Test message              │ -│╶──────────────────────────────────────────┼─────────────────────────┼───────────────────────────╴│ -│multiqc│modules/multiqc/main.nf│Conda update: │ -│││bioconda::multiqc 1.10 -> │ -│││1.13a│ -│                                           ╵                         ╵                            │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭──────────────────────╮ -│LINT RESULTS SUMMARY│ -├──────────────────────┤ -│[✔]  22 Tests Passed│ -│[!]   1 Test Warning│ -│[✗]   0 Tests Failed│ -╰──────────────────────╯ + + + + $ nf-core modules lint multiqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +ERROR    Could not find the specified module: 'multiqc'__main__.py:715 diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index 61c394913..532289347 100644 --- a/docs/images/nf-core-modules-list-local.svg +++ b/docs/images/nf-core-modules-list-local.svg @@ -19,109 +19,110 @@ font-weight: 700; } - .terminal-578959072-matrix { + .terminal-1197768805-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-578959072-title { + .terminal-1197768805-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-578959072-r1 { fill: #c5c8c6 } -.terminal-578959072-r2 { fill: #98a84b } -.terminal-578959072-r3 { fill: #9a9b99 } -.terminal-578959072-r4 { fill: #608ab1 } -.terminal-578959072-r5 { fill: #d0b344 } -.terminal-578959072-r6 { fill: #868887 } -.terminal-578959072-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-578959072-r8 { fill: #868887;font-style: italic; } + .terminal-1197768805-r1 { fill: #c5c8c6 } +.terminal-1197768805-r2 { fill: #98a84b } +.terminal-1197768805-r3 { fill: #9a9b99 } +.terminal-1197768805-r4 { fill: #608ab1 } +.terminal-1197768805-r5 { fill: #d0b344 } +.terminal-1197768805-r6 { fill: #d08442;font-weight: bold } +.terminal-1197768805-r7 { fill: #868887 } +.terminal-1197768805-r8 { fill: #c5c8c6;font-weight: bold } +.terminal-1197768805-r9 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +134,36 @@ - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Modules installed in '.':                                                       list.py:124 - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -┃Module Name         ┃Repository     ┃Version SHA        ┃Message             ┃Date      ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ custom/dumpsoftware… │ nf-core/modules │ e745e167c1020928ef… │ Fix formatting in    │ 2022-02-15 │ -│                      │                 │                     │ yaml files, add      │            │ -│                      │                 │                     │ yamllint config      │            │ -│                      │                 │                     │ (#1279)              │            │ -│ fastqc               │ nf-core/modules │ e745e167c1020928ef… │ Fix formatting in    │ 2022-02-15 │ -│                      │                 │                     │ yaml files, add      │            │ -│                      │                 │                     │ yamllint config      │            │ -│                      │                 │                     │ (#1279)              │            │ -│ multiqc              │ nf-core/modules │ e745e167c1020928ef… │ Fix formatting in    │ 2022-02-15 │ -[..truncated..] + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +INFO     Modules installed in '.':                                                       list.py:124 + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +┃Module Name         ┃Repository     ┃Version SHA        ┃Message             ┃Date      ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ custom/dumpsoftware… │ nf-core/modules │ e745e167c1020928ef… │ Fix formatting in    │ 2022-02-15 │ +│                      │                 │                     │ yaml files, add      │            │ +│                      │                 │                     │ yamllint config      │            │ +│                      │                 │                     │ (#1279)              │            │ +│ fastqc               │ nf-core/modules │ e745e167c1020928ef… │ Fix formatting in    │ 2022-02-15 │ +│                      │                 │                     │ yaml files, add      │            │ +│                      │                 │                     │ yamllint config      │            │ +│                      │                 │                     │ (#1279)              │            │ +[..truncated..] diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index 96b91a83f..b26e5fc24 100644 --- a/docs/images/nf-core-modules-list-remote.svg +++ b/docs/images/nf-core-modules-list-remote.svg @@ -19,109 +19,110 @@ font-weight: 700; } - .terminal-277652753-matrix { + .terminal-1507654550-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-277652753-title { + .terminal-1507654550-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-277652753-r1 { fill: #c5c8c6 } -.terminal-277652753-r2 { fill: #98a84b } -.terminal-277652753-r3 { fill: #9a9b99 } -.terminal-277652753-r4 { fill: #608ab1 } -.terminal-277652753-r5 { fill: #d0b344 } -.terminal-277652753-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-277652753-r7 { fill: #868887 } -.terminal-277652753-r8 { fill: #868887;font-style: italic; } + .terminal-1507654550-r1 { fill: #c5c8c6 } +.terminal-1507654550-r2 { fill: #98a84b } +.terminal-1507654550-r3 { fill: #9a9b99 } +.terminal-1507654550-r4 { fill: #608ab1 } +.terminal-1507654550-r5 { fill: #d0b344 } +.terminal-1507654550-r6 { fill: #d08442;font-weight: bold } +.terminal-1507654550-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-1507654550-r8 { fill: #868887 } +.terminal-1507654550-r9 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +134,36 @@ - + - - $ nf-core modules list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Modules available from nf-core/modules (master):                                list.py:119 - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Module Name                             ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ abacas                                   │ -│ abricate/run                             │ -│ abricate/summary                         │ -│ adapterremoval                           │ -│ adapterremovalfixprefix                  │ -│ agrvate                                  │ -│ allelecounter                            │ -│ ampir                                    │ -│ amplify/predict                          │ -[..truncated..] + + $ nf-core modules list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +INFO     Modules available from nf-core/modules (master):                                list.py:119 + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Module Name                                                  ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ nf-core/abacas                                                │ +│ nf-core/abricate/run                                          │ +│ nf-core/abricate/summary                                      │ +│ nf-core/adapterremoval                                        │ +│ nf-core/adapterremovalfixprefix                               │ +│ nf-core/admixture                                             │ +│ nf-core/affy/justrma                                          │ +│ nf-core/agat/convertspgff2gtf                                 │ +[..truncated..] diff --git a/docs/images/nf-core-modules-mulled.svg b/docs/images/nf-core-modules-mulled.svg index b7ac11336..d03e7a665 100644 --- a/docs/images/nf-core-modules-mulled.svg +++ b/docs/images/nf-core-modules-mulled.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules mulled pysam==0.16.0.1 biopython==1.78 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Found docker image on quay.io! ✨                                              mulled.py:68 -INFO     Mulled container hash:                                                      __main__.py:826 -mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 + + $ nf-core modules mulled pysam==0.16.0.1 biopython==1.78 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO     Found docker image on quay.io! ✨                                              mulled.py:68 +INFO     Mulled container hash:                                                      __main__.py:826 +mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 diff --git a/docs/images/nf-core-modules-patch.svg b/docs/images/nf-core-modules-patch.svg index 8dea1566a..bad2028c3 100644 --- a/docs/images/nf-core-modules-patch.svg +++ b/docs/images/nf-core-modules-patch.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules patch fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Changes in module 'nf-core/modules/fastqc'modules_differ.py:252 -INFO    'modules/nf-core/modules/fastqc/meta.yml' is unchanged                modules_differ.py:257 -INFO     Changes in 'fastqc/main.nf':                                          modules_differ.py:266 - ---- modules/nf-core/modules/fastqc/main.nf -+++ modules/nf-core/modules/fastqc/main.nf -@@ -1,6 +1,6 @@ -process FASTQC {                                                                                   -    tag "$meta.id"                                                                                 --    label 'process_medium' -+    label 'process_low' - -    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)                                 -    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_  - - -INFO     Patch file of 'nf-core/modules/fastqc' written to                              patch.py:115 -'modules/nf-core/modules/fastqc/fastqc.diff' + + $ nf-core modules patch fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +INFO     Changes in module 'nf-core/modules/fastqc'modules_differ.py:252 +INFO    'modules/nf-core/modules/fastqc/meta.yml' is unchanged                modules_differ.py:257 +INFO     Changes in 'fastqc/main.nf':                                          modules_differ.py:266 + +--- modules/nf-core/modules/fastqc/main.nf ++++ modules/nf-core/modules/fastqc/main.nf +@@ -1,6 +1,6 @@ +process FASTQC {                                                                                   +    tag "$meta.id"                                                                                 +-    label 'process_medium' ++    label 'process_low' + +    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)                                 +    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_  + + +INFO     Patch file of 'nf-core/modules/fastqc' written to                              patch.py:115 +'modules/nf-core/modules/fastqc/fastqc.diff' diff --git a/docs/images/nf-core-modules-remove.svg b/docs/images/nf-core-modules-remove.svg index 1deb2efd3..17157949a 100644 --- a/docs/images/nf-core-modules-remove.svg +++ b/docs/images/nf-core-modules-remove.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules remove abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Removing abacas                                                                remove.py:52 + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +ERROR    Module directory does not exist: 'modules/nf-core/modules/abacas'remove.py:45 diff --git a/docs/images/nf-core-modules-test.svg b/docs/images/nf-core-modules-test.svg index 20b7f7bb7..89e562691 100644 --- a/docs/images/nf-core-modules-test.svg +++ b/docs/images/nf-core-modules-test.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - - - - $ nf-core modules test samtools/view --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -────────────────────────────────────────── samtools/view ─────────────────────────────────────────── -INFO     Running pytest for module 'samtools/view'module_test.py:184 + + + + $ nf-core modules test samtools/view --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +CRITICAL Cannot find directory 'modules/samtools/view'. Should be TOOL/SUBTOOL or    __main__.py:846 +         TOOL. Are you running the tests inside the nf-core/modules main directory?   diff --git a/docs/images/nf-core-modules-update.svg b/docs/images/nf-core-modules-update.svg index 20db55363..5d1a0ed52 100644 --- a/docs/images/nf-core-modules-update.svg +++ b/docs/images/nf-core-modules-update.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO    'nf-core/modules/abacas' is already up to date                                update.py:160 -INFO     Updating 'nf-core/modules/custom/dumpsoftwareversions'update.py:516 -INFO     Updating 'nf-core/modules/fastqc'update.py:516 -INFO     Updating 'nf-core/modules/multiqc'update.py:516 -INFO     Updates complete ✨                                                           update.py:242 + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +WARNING  Module 'custom/dumpsoftwareversions' does not exist in 'nf-core/modules'.     update.py:448 +         Skipping... +WARNING  Module 'fastqc' does not exist in 'nf-core/modules'. Skipping...update.py:448 +WARNING  Module 'multiqc' does not exist in 'nf-core/modules'. Skipping...update.py:448 +INFO     Updates complete ✨                                                           update.py:242 diff --git a/docs/images/nf-core-schema-build.svg b/docs/images/nf-core-schema-build.svg index bf05c1cb9..396cb52f1 100644 --- a/docs/images/nf-core-schema-build.svg +++ b/docs/images/nf-core-schema-build.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validationschema.py:237 -INFO    [✓] Pipeline schema looks valid(found 27 params)schema.py:95 -INFO     Writing schema with 30 params: './nextflow_schema.json'schema.py:173 + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO    [✓] Default parameters match schema validationschema.py:237 +INFO    [✓] Pipeline schema looks valid(found 27 params)schema.py:95 +INFO     Writing schema with 30 params: './nextflow_schema.json'schema.py:173 diff --git a/docs/images/nf-core-schema-lint.svg b/docs/images/nf-core-schema-lint.svg index 5dc2da7da..1551da73e 100644 --- a/docs/images/nf-core-schema-lint.svg +++ b/docs/images/nf-core-schema-lint.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core schema lint nextflow_schema.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validationschema.py:237 -INFO    [✗] Invalid default parameters found:schema.py:84 -  --fail_unrecognised_params: String should not be set to `false` -  --lenient_mode: String should not be set to `false` - -NOTE: Use null in config for no default. + + $ nf-core schema lint nextflow_schema.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO    [✓] Default parameters match schema validationschema.py:237 +INFO    [✗] Invalid default parameters found:schema.py:84 +  --fail_unrecognised_params: String should not be set to `false` +  --lenient_mode: String should not be set to `false` + +NOTE: Use null in config for no default. diff --git a/docs/images/nf-core-schema-validate.svg b/docs/images/nf-core-schema-validate.svg index 41376f5bd..55ad64204 100644 --- a/docs/images/nf-core-schema-validate.svg +++ b/docs/images/nf-core-schema-validate.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core schema validate nf-core-rnaseq/workflow nf-params.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validationschema.py:237 -INFO    [✓] Pipeline schema looks valid(found 93 params)schema.py:95 -INFO    [✓] Input parameters look validschema.py:213 + + $ nf-core schema validate nf-core-rnaseq/workflow nf-params.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO    [✓] Default parameters match schema validationschema.py:237 +INFO    [✓] Pipeline schema looks valid(found 93 params)schema.py:95 +INFO    [✓] Input parameters look validschema.py:213 diff --git a/docs/images/nf-core-sync.svg b/docs/images/nf-core-sync.svg index 1b6f3a9e8..71e9a6bf2 100644 --- a/docs/images/nf-core-sync.svg +++ b/docs/images/nf-core-sync.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core sync - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthingsync.py:95 -INFO     Original pipeline repository branch is 'master'sync.py:149 -INFO     Deleting all files in 'TEMPLATE' branch                                         sync.py:205 -INFO     Making a new template pipeline using pipeline variables                         sync.py:223 + + $ nf-core sync + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthingsync.py:95 +INFO     Original pipeline repository branch is 'master'sync.py:149 +INFO     Deleting all files in 'TEMPLATE' branch                                         sync.py:205 +INFO     Making a new template pipeline using pipeline variables                         sync.py:223 From 203712f4a0030deec426e69e636e6573022b6cb2 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 23 Feb 2023 12:02:58 +0000 Subject: [PATCH 2/2] Generate new screengrabs with rich-codex --- docs/images/nf-core-lint.svg | 498 ++++++++++++++----- docs/images/nf-core-modules-bump-version.svg | 118 ++--- docs/images/nf-core-modules-create-test.svg | 128 ++--- docs/images/nf-core-modules-create.svg | 136 ++--- 4 files changed, 508 insertions(+), 372 deletions(-) diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg index 6e0bf2af4..47acc16cc 100644 --- a/docs/images/nf-core-lint.svg +++ b/docs/images/nf-core-lint.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - $ nf-core lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Testing pipeline: .__init__.py:263 - - -╭─[?] 2 Pipeline Tests Ignored ───────────────────────────────────────────────────────────────────╮ -││ -│files_unchanged: File does not exist: lib/NfcoreSchema.groovy│ -│pipeline_todos: pipeline_todos│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─[✗] 3 Pipeline Tests Failed ────────────────────────────────────────────────────────────────────╮ -││ -│files_exist: File not found: lib/NfcoreSchema.groovy│ -│schema_params: Param fail_unrecognised_params from nextflow config not found in │ -│nextflow_schema.json│ -│schema_params: Param lenient_mode from nextflow config not found in nextflow_schema.json│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - -╭─[!] 5 Module Test Warnings ─────────────────────────────────────────────────────────────────────╮ -│                                           ╷                          ╷                           │ -│Module name                              │File path               │Test message             │ -│╶──────────────────────────────────────────┼──────────────────────────┼──────────────────────────╴│ -│custom/dumpsoftwareversions│modules/nf-core/modules…│New version available│ -│fastqc│modules/nf-core/modules…│New version available│ -│multiqc│modules/nf-core/modules…│New version available│ -│samplesheet_check│modules/local/sampleshe…│Process label unspecified│ -│samplesheet_check│modules/local/sampleshe…│when: condition has been │ -│││removed│ -│                                           ╵                          ╵                           │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────╮ -│LINT RESULTS SUMMARY │ -├───────────────────────┤ -│[✔] 166 Tests Passed│ -│[?]   2 Tests Ignored│ -│[!]   5 Test Warnings│ -│[✗]   3 Tests Failed│ -╰───────────────────────╯ + + + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ +│/opt/hostedtoolcache/Python/3.11.2/x64/bin/nf-core:8 in <module>│ +││ +│7 │   sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])                         │ +│❱ 8 │   sys.exit(run_nf_core())                                                                  │ +│9 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/nf_core/__main__.py:93 in    │ +│run_nf_core│ +││ +│  92 │   # Lanch the click cli│ +│❱   93 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │ +│  94 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/click/core.py:1130 in        │ +│__call__│ +││ +│1129 │   │   """Alias for :meth:`main`."""│ +│❱ 1130 │   │   returnself.main(*args, **kwargs)                                                 │ +│1131 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/rich_click/rich_group.py:21│ +│ in main│ +││ +│20 │   │   try:                                                                                │ +│❱ 21 │   │   │   rv = super().main(*args, standalone_mode=False, **kwargs)                       │ +│22 │   │   │   ifnot standalone_mode:                                                         │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/click/core.py:1055 in main│ +││ +│1054 │   │   │   │   withself.make_context(prog_name, args, **extra) as ctx:                  │ +│❱ 1055 │   │   │   │   │   rv = self.invoke(ctx)                                                 │ +│1056 │   │   │   │   │   ifnot standalone_mode:                                               │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/click/core.py:1657 in invoke│ +││ +│1656 │   │   │   │   with sub_ctx:                                                             │ +│❱ 1657 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │ +│1658 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/click/core.py:1404 in invoke│ +││ +│1403 │   │   ifself.callback isnotNone:                                                     │ +│❱ 1404 │   │   │   return ctx.invoke(self.callback, **ctx.params)                                │ +│1405 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/click/core.py:760 in invoke│ +││ +│ 759 │   │   │   with ctx:                                                                     │ +│❱  760 │   │   │   │   return __callback(*args, **kwargs)                                        │ +│ 761 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/nf_core/__main__.py:341 in   │ +│lint│ +││ +│ 340 │   try:                                                                                  │ +│❱  341 │   │   lint_obj, module_lint_obj = nf_core.lint.run_linting(                             │ +│ 342 │   │   │   dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown,     │ +│        json, hide_progress                                                                       │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/nf_core/lint/__init__.py:89│ +│ in run_linting│ +││ +│ 88 │   # Create the modules lint object│ +│❱  89 │   module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir,                        │ +│       hide_progress=hide_progress)                                                               │ +│ 90 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/nf_core/modules/lint/__init_│ +│_.py:105 in __init__│ +││ +│104 │   │   │   │   │   NFCoreModule(m, None, local_module_dir / m, self.repo_type,            │ +│       Path(self.dir), nf_core_module=False)                                                      │ +│❱ 105 │   │   │   │   │   for m inself.get_local_modules()                                      │ +│106 │   │   │   │   ]                                                                          │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/nf_core/modules/modules_comm│ +│and.py:52 in get_local_modules│ +││ +│ 51 │   │   local_module_dir = Path(self.dir, "modules", "local")                              │ +│❱  52 │   │   return [str(path.relative_to(local_module_dir)) for path in│ +│       local_module_dir.iterdir() if path.suffix == ".nf"]                                        │ +│ 53 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/site-packages/nf_core/modules/modules_comm│ +│and.py:52 in <listcomp>│ +││ +│ 51 │   │   local_module_dir = Path(self.dir, "modules", "local")                              │ +│❱  52 │   │   return [str(path.relative_to(local_module_dir)) for path in│ +│       local_module_dir.iterdir() if path.suffix == ".nf"]                                        │ +│ 53 │ +││ +│/opt/hostedtoolcache/Python/3.11.2/x64/lib/python3.11/pathlib.py:931 in iterdir│ +││ +│ 930 │   │   """│ +│❱  931 │   │   for name in os.listdir(self):                                                     │ +│ 932 │   │   │   yieldself._make_child_relpath(name)                                          │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +FileNotFoundError: [Errno 2] No such file or directory: 'modules/local' diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index 48049fcfb..94ba436bb 100644 --- a/docs/images/nf-core-modules-bump-version.svg +++ b/docs/images/nf-core-modules-bump-version.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - + - + - - $ nf-core modules bump-versions fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re -    There is a new version of nf-core/tools available! (2.7.2) - - - - -╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ -│[!] 1 Module version up to date.│ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ -│Module name                             │Update Message                                       │ -├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ -│ fastqc                                   │ Module version up to date: fastqc                     │ -╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ + + $ nf-core modules bump-versions fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + + +ERROR    Could not find the specified module: 'fastqc'__main__.py:780 diff --git a/docs/images/nf-core-modules-create-test.svg b/docs/images/nf-core-modules-create-test.svg index 5711bd843..3f72db085 100644 --- a/docs/images/nf-core-modules-create-test.svg +++ b/docs/images/nf-core-modules-create-test.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - $ nf-core modules create-test-yml fastqc --no-prompts --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Looking for test workflow entry points:                             test_yml_builder.py:123 -'tests/modules/fastqc/main.nf' -──────────────────────────────────────────────────────────────────────────────────────────────────── -INFO     Building test meta for entry point 'test_fastqc'test_yml_builder.py:157 -INFO     Setting env var '$PROFILE' to an empty string as not set.           test_yml_builder.py:301 -         Tests will run with Docker by default. To use Singularity set        -'export PROFILE=singularity' in your shell before running this       -         command.                                                             -INFO     Running 'fastqc' test with command:                                 test_yml_builder.py:325 -nextflow run ./tests/modules/fastqc -entry test_fastqc -c  -./tests/config/nextflow.config  -c  -./tests/modules/fastqc/nextflow.config --outdir /tmp/tmpzotojksy --work-dir /tmp/tmps14qhvf6 + + + + $ nf-core modules create-test-yml fastqc --no-prompts --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +CRITICAL Cannot find directory 'modules/fastqc'. Should be TOOL/SUBTOOL or TOOL      __main__.py:667 diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index b485e9bc8..662e5e596 100644 --- a/docs/images/nf-core-modules-create.svg +++ b/docs/images/nf-core-modules-create.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + - - $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re -    There is a new version of nf-core/tools available! (2.7.2) - - -INFO     Repository type: modulescreate.py:93 -INFO    Press enter to use default values (shown in brackets)or type your own create.py:97 -responses. ctrl+click underlined text to open links. -INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9'create.py:165 -INFO     Using Docker container: 'quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1'create.py:191 -INFO     Using Singularity container:                                                  create.py:192 -'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--hdfd78af_1' -INFO     Created / edited following files:                                             create.py:270 -           ./modules/fastqc/main.nf -           ./modules/fastqc/meta.yml -           ./tests/modules/fastqc/main.nf -           ./tests/modules/fastqc/test.yml -           ./tests/modules/fastqc/nextflow.config -           ./tests/config/pytest_modules.yml + + $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.7.2) + + +INFO     Repository type: modulescreate.py:93 +INFO    Press enter to use default values (shown in brackets)or type your own create.py:97 +responses. ctrl+click underlined text to open links. +INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9'create.py:165