From cd0ac0b5ee826304a0fd77792593735dd8fc2e58 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Tue, 30 Aug 2022 13:25:07 +0000 Subject: [PATCH] Generate new screengrabs with rich-codex --- docs/images/nf-core-bump-version.svg | 90 +++---- docs/images/nf-core-create.svg | 132 ++++----- docs/images/nf-core-download.svg | 88 +++--- docs/images/nf-core-launch-rnaseq.svg | 84 +++--- docs/images/nf-core-licences.svg | 132 ++++----- docs/images/nf-core-lint.svg | 270 ++++++++++--------- 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 | 126 ++++----- docs/images/nf-core-modules-create.svg | 130 +++++---- docs/images/nf-core-modules-info.svg | 226 ++++++++-------- docs/images/nf-core-modules-install.svg | 88 +++--- docs/images/nf-core-modules-lint.svg | 204 +++++++------- docs/images/nf-core-modules-list-local.svg | 137 +++++++--- docs/images/nf-core-modules-list-remote.svg | 132 ++++----- docs/images/nf-core-modules-mulled.svg | 80 +++--- docs/images/nf-core-modules-patch.svg | 150 ++++++++--- docs/images/nf-core-modules-remove.svg | 75 +++--- docs/images/nf-core-modules-test.svg | 76 +++--- docs/images/nf-core-modules-update.svg | 95 ++++--- docs/images/nf-core-schema-build.svg | 84 +++--- docs/images/nf-core-schema-lint.svg | 78 +++--- docs/images/nf-core-schema-validate.svg | 82 +++--- docs/images/nf-core-sync.svg | 84 +++--- 26 files changed, 1613 insertions(+), 1466 deletions(-) diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg index 6e8b89d1c2..a956d2c922 100644 --- a/docs/images/nf-core-bump-version.svg +++ b/docs/images/nf-core-bump-version.svg @@ -19,78 +19,78 @@ font-weight: 700; } - .terminal-1189121654-matrix { + .terminal-440110297-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1189121654-title { + .terminal-440110297-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1189121654-r1 { fill: #c5c8c6 } -.terminal-1189121654-r2 { fill: #98a84b } -.terminal-1189121654-r3 { fill: #9a9b99 } -.terminal-1189121654-r4 { fill: #608ab1 } -.terminal-1189121654-r5 { fill: #d0b344 } -.terminal-1189121654-r6 { fill: #868887 } -.terminal-1189121654-r7 { fill: #cc555a } + .terminal-440110297-r1 { fill: #c5c8c6 } +.terminal-440110297-r2 { fill: #98a84b } +.terminal-440110297-r3 { fill: #9a9b99 } +.terminal-440110297-r4 { fill: #608ab1 } +.terminal-440110297-r5 { fill: #d0b344 } +.terminal-440110297-r6 { fill: #868887 } +.terminal-440110297-r7 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -102,26 +102,26 @@ - + - - $ 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 - https://nf-co.re + + +INFO     Changing version number from '1.0dev' to '1.1'bump_version.py:35 +INFO     Updated version in 'nextflow.config'bump_version.py:164 + - version         = '1.0dev' + + version = '1.1' + + diff --git a/docs/images/nf-core-create.svg b/docs/images/nf-core-create.svg index 2158fb082e..96278a10cd 100644 --- a/docs/images/nf-core-create.svg +++ b/docs/images/nf-core-create.svg @@ -19,108 +19,108 @@ font-weight: 700; } - .terminal-2228597254-matrix { + .terminal-2135273577-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2228597254-title { + .terminal-2135273577-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2228597254-r1 { fill: #c5c8c6 } -.terminal-2228597254-r2 { fill: #98a84b } -.terminal-2228597254-r3 { fill: #9a9b99 } -.terminal-2228597254-r4 { fill: #608ab1 } -.terminal-2228597254-r5 { fill: #d0b344 } -.terminal-2228597254-r6 { fill: #868887 } -.terminal-2228597254-r7 { fill: #98729f } -.terminal-2228597254-r8 { fill: #ff2c7a } -.terminal-2228597254-r9 { fill: #98a84b;font-weight: bold } -.terminal-2228597254-r10 { fill: #1984e9;text-decoration: underline; } + .terminal-2135273577-r1 { fill: #c5c8c6 } +.terminal-2135273577-r2 { fill: #98a84b } +.terminal-2135273577-r3 { fill: #9a9b99 } +.terminal-2135273577-r4 { fill: #608ab1 } +.terminal-2135273577-r5 { fill: #d0b344 } +.terminal-2135273577-r6 { fill: #868887 } +.terminal-2135273577-r7 { fill: #98729f } +.terminal-2135273577-r8 { fill: #ff2c7a } +.terminal-2135273577-r9 { fill: #98a84b;font-weight: bold } +.terminal-2135273577-r10 { fill: #1984e9;text-decoration: underline; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,35 +132,35 @@ - + - - $ 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: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 2.5 - 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 diff --git a/docs/images/nf-core-download.svg b/docs/images/nf-core-download.svg index 5502d4fc46..9fd4ecc75a 100644 --- a/docs/images/nf-core-download.svg +++ b/docs/images/nf-core-download.svg @@ -19,77 +19,77 @@ font-weight: 700; } - .terminal-2172378614-matrix { + .terminal-3988708441-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2172378614-title { + .terminal-3988708441-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2172378614-r1 { fill: #c5c8c6 } -.terminal-2172378614-r2 { fill: #98a84b } -.terminal-2172378614-r3 { fill: #9a9b99 } -.terminal-2172378614-r4 { fill: #608ab1 } -.terminal-2172378614-r5 { fill: #d0b344 } -.terminal-2172378614-r6 { fill: #868887 } + .terminal-3988708441-r1 { fill: #c5c8c6 } +.terminal-3988708441-r2 { fill: #98a84b } +.terminal-3988708441-r3 { fill: #9a9b99 } +.terminal-3988708441-r4 { fill: #608ab1 } +.terminal-3988708441-r5 { fill: #d0b344 } +.terminal-3988708441-r6 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -101,26 +101,26 @@ - + - - $ 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 - https://nf-co.re + + +INFO     Saving 'nf-core/rnaseq'download.py:158 +          Pipeline revision: '3.8' +          Pull containers: 'none' +          Output directory: 'nf-core-rnaseq' +INFO     Downloading workflow files from GitHub                                      download.py:161 +INFO     Downloading centralised configs from GitHub                                 download.py:165 diff --git a/docs/images/nf-core-launch-rnaseq.svg b/docs/images/nf-core-launch-rnaseq.svg index 96ecbd3426..0815e2d7fe 100644 --- a/docs/images/nf-core-launch-rnaseq.svg +++ b/docs/images/nf-core-launch-rnaseq.svg @@ -19,73 +19,73 @@ font-weight: 700; } - .terminal-2229446587-matrix { + .terminal-2111743518-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2229446587-title { + .terminal-2111743518-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2229446587-r1 { fill: #c5c8c6 } -.terminal-2229446587-r2 { fill: #98a84b } -.terminal-2229446587-r3 { fill: #9a9b99 } -.terminal-2229446587-r4 { fill: #608ab1 } -.terminal-2229446587-r5 { fill: #d0b344 } -.terminal-2229446587-r6 { fill: #868887 } -.terminal-2229446587-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-2229446587-r8 { fill: #68a0b3;font-weight: bold } + .terminal-2111743518-r1 { fill: #c5c8c6 } +.terminal-2111743518-r2 { fill: #98a84b } +.terminal-2111743518-r3 { fill: #9a9b99 } +.terminal-2111743518-r4 { fill: #608ab1 } +.terminal-2111743518-r5 { fill: #d0b344 } +.terminal-2111743518-r6 { fill: #868887 } +.terminal-2111743518-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2111743518-r8 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -97,24 +97,24 @@ - + - - $ 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 - https://nf-co.re + + +INFO     NOTE: This tool ignores any pipeline parameter defaults overwritten by        launch.py:131 +         Nextflow config files or profiles                                              + +INFO     Downloading workflow: nf-core/rnaseq (3.8.1)list.py:67 diff --git a/docs/images/nf-core-licences.svg b/docs/images/nf-core-licences.svg index 5f84e722e9..df8efdc33f 100644 --- a/docs/images/nf-core-licences.svg +++ b/docs/images/nf-core-licences.svg @@ -19,109 +19,109 @@ font-weight: 700; } - .terminal-290135093-matrix { + .terminal-1746868888-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-290135093-title { + .terminal-1746868888-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-290135093-r1 { fill: #c5c8c6 } -.terminal-290135093-r2 { fill: #98a84b } -.terminal-290135093-r3 { fill: #9a9b99 } -.terminal-290135093-r4 { fill: #608ab1 } -.terminal-290135093-r5 { fill: #d0b344 } -.terminal-290135093-r6 { fill: #68a0b3;font-weight: bold } -.terminal-290135093-r7 { fill: #868887 } -.terminal-290135093-r8 { fill: #c5c8c6;font-weight: bold } + .terminal-1746868888-r1 { fill: #c5c8c6 } +.terminal-1746868888-r2 { fill: #98a84b } +.terminal-1746868888-r3 { fill: #9a9b99 } +.terminal-1746868888-r4 { fill: #608ab1 } +.terminal-1746868888-r5 { fill: #d0b344 } +.terminal-1746868888-r6 { fill: #68a0b3;font-weight: bold } +.terminal-1746868888-r7 { fill: #868887 } +.terminal-1746868888-r8 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ 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 - https://nf-co.re + + +INFO     Fetching licence information for 8 tools                                     licences.py:77 +INFO     Warning: This tool only prints licence information for the software tools    licences.py:98 +         packaged using conda.                                                         +INFO     The pipeline may use other software and dependencies not described here.     licences.py:99 +┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓ +┃Package Name┃Version┃Licence┃ +┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩ +│ lbzip2       │ 2.5     │ GPL v3  │ +│ deepvariant  │ 0.7.0   │ MIT     │ +│ htslib       │ 1.9     │ MIT     │ +│ picard       │ 2.18.7  │ MIT     │ +│ pip          │ 10.0.1  │ MIT     │ +│ samtools     │ 1.9     │ MIT     │ +│ python       │ 2.7.15  │ PSF     │ +│ bzip2        │ 1.0.6   │ bzip2   │ +└──────────────┴─────────┴─────────┘ diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg index 1f4b387b45..b7788b02ca 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 - - -Linting local modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━0 of 1 » samplesheet_check -Linting local modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » samplesheet_check - - -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━0 of 3 » custom/dumpsoftwareversions -Linting nf-core modules━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━1 of 3 » custom/dumpsoftwareversions -Linting nf-core modules━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━1 of 3 » custom/dumpsoftwareversions -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━2 of 3 » fastqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━2 of 3 » fastqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━3 of 3 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━3 of 3 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━3 of 3 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━3 of 3 » multiqc - - -╭─[?] 1 Pipeline Test Ignored ────────────────────────────────────────────────────────────────────╮ -││ -│pipeline_todos: pipeline_todos│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - -╭─[!] 5 Module Test Warnings ─────────────────────────────────────────────────────────────────────╮ -│                                           ╷                          ╷                           │ -│Module name                              │File path               │Test message             │ -│╶──────────────────────────────────────────┼──────────────────────────┼──────────────────────────╴│ -│custom/dumpsoftwareversions│modules/nf-core/modules…│New version available│ -│fastqc│modules/nf-core/modules…│New version available│ -│multiqc│modules/nf-core/modules…│New version available│ -│samplesheet_check│modules/local/sampleshe…│Process label unspecified│ -│samplesheet_check│modules/local/sampleshe…│when: condition has been │ -│││removed│ -│                                           ╵                          ╵                           │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────╮ -│LINT RESULTS SUMMARY │ -├───────────────────────┤ -│[✔] 169 Tests Passed│ -│[?]   1 Test Ignored│ -│[!]   5 Test Warnings│ -│[✗]   0 Tests Failed│ -╰───────────────────────╯ + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5 - https://nf-co.re + + + +INFO     Testing pipeline: .__init__.py:263 + + +Linting local modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━0 of 1 » samplesheet_check +Linting local modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » samplesheet_check + + +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━0 of 3 » custom/dumpsoftwareversions +Linting nf-core modules━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━1 of 3 » custom/dumpsoftwareversions +Linting nf-core modules━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━1 of 3 » custom/dumpsoftwareversions +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━2 of 3 » fastqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━2 of 3 » fastqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━2 of 3 » fastqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━3 of 3 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━3 of 3 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━3 of 3 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━3 of 3 » multiqc + + +╭─[?] 1 Pipeline Test Ignored ────────────────────────────────────────────────────────────────────╮ +││ +│pipeline_todos: pipeline_todos│ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + +╭─[!] 5 Module Test Warnings ─────────────────────────────────────────────────────────────────────╮ +│                                           ╷                          ╷                           │ +│Module name                              │File path               │Test message             │ +│╶──────────────────────────────────────────┼──────────────────────────┼──────────────────────────╴│ +│custom/dumpsoftwareversions│modules/nf-core/modules…│New version available│ +│fastqc│modules/nf-core/modules…│New version available│ +│multiqc│modules/nf-core/modules…│New version available│ +│samplesheet_check│modules/local/sampleshe…│Process label unspecified│ +│samplesheet_check│modules/local/sampleshe…│when: condition has been │ +│││removed│ +│                                           ╵                          ╵                           │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭───────────────────────╮ +│LINT RESULTS SUMMARY │ +├───────────────────────┤ +│[✔] 169 Tests Passed│ +│[?]   1 Test Ignored│ +│[!]   5 Test Warnings│ +│[✗]   0 Tests Failed│ +╰───────────────────────╯ diff --git a/docs/images/nf-core-list-rna.svg b/docs/images/nf-core-list-rna.svg index cbd098b947..def102c509 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-4236301330-matrix { + .terminal-2458374773-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4236301330-title { + .terminal-2458374773-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4236301330-r1 { fill: #c5c8c6 } -.terminal-4236301330-r2 { fill: #98a84b } -.terminal-4236301330-r3 { fill: #9a9b99 } -.terminal-4236301330-r4 { fill: #608ab1 } -.terminal-4236301330-r5 { fill: #d0b344 } -.terminal-4236301330-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-4236301330-r7 { fill: #868887 } + .terminal-2458374773-r1 { fill: #c5c8c6 } +.terminal-2458374773-r2 { fill: #98a84b } +.terminal-2458374773-r3 { fill: #9a9b99 } +.terminal-2458374773-r4 { fill: #608ab1 } +.terminal-2458374773-r5 { fill: #d0b344 } +.terminal-2458374773-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-2458374773-r7 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -123,33 +123,33 @@ - + - - $ 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 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnafusion            │    76 │          2.1.0 │ 2 months ago │           - │ -                   │ +│ smrnaseq             │    42 │          2.0.0 │ 3 months ago │           - │ -                   │ +│ rnaseq               │   501 │          3.8.1 │ 3 months ago │           - │ -                   │ +│ dualrnaseq           │     7 │          1.0.0 │  2 years ago │           - │ -                   │ +│ circrna              │    19 │            dev │            - │           - │ -                   │ +│ lncpipe              │    23 │            dev │            - │           - │ -                   │ +│ scflow               │    12 │            dev │            - │           - │ -                   │ +│ spatialtranscriptom… │    10 │            dev │            - │           - │ -                   │ +└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg index da3f02c7db..6b8aa5659b 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-1473353797-matrix { + .terminal-2850002601-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1473353797-title { + .terminal-2850002601-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-2850002601-r1 { fill: #c5c8c6 } +.terminal-2850002601-r2 { fill: #98a84b } +.terminal-2850002601-r3 { fill: #9a9b99 } +.terminal-2850002601-r4 { fill: #608ab1 } +.terminal-2850002601-r5 { fill: #d0b344 } +.terminal-2850002601-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-2850002601-r7 { fill: #868887 } +.terminal-2850002601-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -112,29 +112,29 @@ - + - - $ 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 - 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              │   122 │          1.2.2 │  1 years ago │           - │ -                   │ +│ atacseq              │   116 │          1.2.2 │ 4 months ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg index c5e7e17dd8..943cf41219 100644 --- a/docs/images/nf-core-list.svg +++ b/docs/images/nf-core-list.svg @@ -19,91 +19,91 @@ font-weight: 700; } - .terminal-2711598360-matrix { + .terminal-1258795901-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2711598360-title { + .terminal-1258795901-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-1258795901-r1 { fill: #c5c8c6 } +.terminal-1258795901-r2 { fill: #98a84b } +.terminal-1258795901-r3 { fill: #9a9b99 } +.terminal-1258795901-r4 { fill: #608ab1 } +.terminal-1258795901-r5 { fill: #d0b344 } +.terminal-1258795901-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1258795901-r7 { fill: #868887 } +.terminal-1258795901-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +115,30 @@ - + - - $ 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 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ mag                  │    99 │          2.2.1 │   5 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           │    75 │            2.5 │ 2 months ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index e76e7a0a12..946da37712 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-1308324414-matrix { + .terminal-1004368033-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1308324414-title { + .terminal-1004368033-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1308324414-r1 { fill: #c5c8c6 } -.terminal-1308324414-r2 { fill: #98a84b } -.terminal-1308324414-r3 { fill: #9a9b99 } -.terminal-1308324414-r4 { fill: #608ab1 } -.terminal-1308324414-r5 { fill: #d0b344 } -.terminal-1308324414-r6 { fill: #98a84b;font-weight: bold } -.terminal-1308324414-r7 { fill: #c5c8c6;font-weight: bold } + .terminal-1004368033-r1 { fill: #c5c8c6 } +.terminal-1004368033-r2 { fill: #98a84b } +.terminal-1004368033-r3 { fill: #9a9b99 } +.terminal-1004368033-r4 { fill: #608ab1 } +.terminal-1004368033-r5 { fill: #d0b344 } +.terminal-1004368033-r6 { fill: #98a84b;font-weight: bold } +.terminal-1004368033-r7 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -114,30 +114,30 @@ - + - - $ 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 - 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 5711bd8431..f8ced5520b 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 - 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     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/tmpe2lt4618 +-work-dir /tmp/tmpimxa97gt diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index 47be3b89c3..741c98771e 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' + + $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5 - https://nf-co.re + + +INFO     Repository type: modulescreate.py:93 +INFO    Press enter to use default values (shown in brackets)or type your own create.py:97 +responses. ctrl+click underlined text to open links. +INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9'create.py:165 +INFO     Using Docker container: 'quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1'create.py:191 +INFO     Using Singularity container:                                                  create.py:192 +'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--hdfd78af_1' +INFO     Created / edited following files:                                             create.py:270 +           ./modules/fastqc/main.nf +           ./modules/fastqc/meta.yml +           ./tests/modules/fastqc/main.nf +           ./tests/modules/fastqc/test.yml +           ./tests/modules/fastqc/nextflow.config +           ./tests/config/pytest_modules.yml diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg index 9659c49c45..ba471c1863 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 - - - -INFO     Reinstalling modules found in 'modules.json' but missing from           modules_json.py:452 -         directory: 'nf-core/modules/custom/dumpsoftwareversions',                -'nf-core/modules/fastqc', 'nf-core/modules/multiqc' -╭─ 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 - 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 3b8fc97194..d3527d270a 100644 --- a/docs/images/nf-core-modules-install.svg +++ b/docs/images/nf-core-modules-install.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + - + - + - - $ nf-core modules install abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -ERROR    Could not find a 'main.nf' or 'nextflow.config' file in '.'__main__.py:483 + + $ nf-core modules install abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5 - https://nf-co.re + + + +INFO     Installing 'abacas'install.py:116 +INFO     Include statement: include { ABACAS } from                                   install.py:125 +'../modules/nf-core/modules/abacas/main' diff --git a/docs/images/nf-core-modules-lint.svg b/docs/images/nf-core-modules-lint.svg index 24ea8054b9..e16d844a01 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:200 -INFO     Linting module: 'multiqc'__init__.py:204 - -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━0 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc - - -╭─[!] 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 - https://nf-co.re + + + +INFO     Linting modules repo: '.'__init__.py:200 +INFO     Linting module: 'multiqc'__init__.py:204 + +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━0 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc + + +╭─[!] 1 Module Test Warning ──────────────────────────────────────────────────────────────────────╮ +│                                           ╷                         ╷                            │ +│Module name                              │File path              │Test message              │ +│╶──────────────────────────────────────────┼─────────────────────────┼───────────────────────────╴│ +│multiqc│modules/multiqc/main.nf│Conda update: │ +│││bioconda::multiqc 1.10 -> │ +│││1.13a│ +│                                           ╵                         ╵                            │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────╮ +│LINT RESULTS SUMMARY│ +├──────────────────────┤ +│[✔]  22 Tests Passed│ +│[!]   1 Test Warning│ +│[✗]   0 Tests Failed│ +╰──────────────────────╯ diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index a8957f7e99..0344143c2b 100644 --- a/docs/images/nf-core-modules-list-local.svg +++ b/docs/images/nf-core-modules-list-local.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -ERROR    Could not find a 'main.nf' or 'nextflow.config' file in '.'list.py:64 - + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5 - https://nf-co.re + + + +INFO     Modules installed in '.':                                                       list.py:124 + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +┃Module Name         ┃Repository     ┃Version SHA        ┃Message             ┃Date      ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ custom/dumpsoftware… │ nf-core/modules │ e745e167c1020928ef… │ Fix formatting in    │ 2022-02-15 │ +│                      │                 │                     │ yaml files, add      │            │ +│                      │                 │                     │ yamllint config      │            │ +│                      │                 │                     │ (#1279)              │            │ +│ fastqc               │ nf-core/modules │ e745e167c1020928ef… │ Fix formatting in    │ 2022-02-15 │ +│                      │                 │                     │ yaml files, add      │            │ +│                      │                 │                     │ yamllint config      │            │ +│                      │                 │                     │ (#1279)              │            │ +│ multiqc              │ nf-core/modules │ e745e167c1020928ef… │ Fix formatting in    │ 2022-02-15 │ +[..truncated..] diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index 96b91a83f9..dfbe22e11a 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-277652753-matrix { + .terminal-1837409140-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-277652753-title { + .terminal-1837409140-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-1837409140-r1 { fill: #c5c8c6 } +.terminal-1837409140-r2 { fill: #98a84b } +.terminal-1837409140-r3 { fill: #9a9b99 } +.terminal-1837409140-r4 { fill: #608ab1 } +.terminal-1837409140-r5 { fill: #d0b344 } +.terminal-1837409140-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1837409140-r7 { fill: #868887 } +.terminal-1837409140-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ 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 - https://nf-co.re + + + +INFO     Modules available from nf-core/modules (master):                                list.py:119 + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Module Name                             ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ abacas                                   │ +│ abricate/run                             │ +│ abricate/summary                         │ +│ adapterremoval                           │ +│ adapterremovalfixprefix                  │ +│ agrvate                                  │ +│ allelecounter                            │ +│ ampir                                    │ +│ amplify/predict                          │ +[..truncated..] diff --git a/docs/images/nf-core-modules-mulled.svg b/docs/images/nf-core-modules-mulled.svg index 4e13039d6b..163f41a53d 100644 --- a/docs/images/nf-core-modules-mulled.svg +++ b/docs/images/nf-core-modules-mulled.svg @@ -19,70 +19,70 @@ font-weight: 700; } - .terminal-3387661225-matrix { + .terminal-1187224076-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3387661225-title { + .terminal-1187224076-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3387661225-r1 { fill: #c5c8c6 } -.terminal-3387661225-r2 { fill: #98a84b } -.terminal-3387661225-r3 { fill: #9a9b99 } -.terminal-3387661225-r4 { fill: #608ab1 } -.terminal-3387661225-r5 { fill: #d0b344 } -.terminal-3387661225-r6 { fill: #868887 } -.terminal-3387661225-r7 { fill: #00823d;font-weight: bold } -.terminal-3387661225-r8 { fill: #68a0b3;font-weight: bold } + .terminal-1187224076-r1 { fill: #c5c8c6 } +.terminal-1187224076-r2 { fill: #98a84b } +.terminal-1187224076-r3 { fill: #9a9b99 } +.terminal-1187224076-r4 { fill: #608ab1 } +.terminal-1187224076-r5 { fill: #d0b344 } +.terminal-1187224076-r6 { fill: #868887 } +.terminal-1187224076-r7 { fill: #00823d;font-weight: bold } +.terminal-1187224076-r8 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -94,23 +94,23 @@ - + - - $ 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:828 -mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 + + $ nf-core modules mulled pysam==0.16.0.1 biopython==1.78 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5 - https://nf-co.re + + +INFO     Found docker image on quay.io! ✨                                              mulled.py:68 +INFO     Mulled container hash:                                                      __main__.py:828 +mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 diff --git a/docs/images/nf-core-modules-patch.svg b/docs/images/nf-core-modules-patch.svg index 757ef4abf9..0c7a4dd9f8 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 - - - -ERROR    Could not find a 'main.nf' or 'nextflow.config' file in '.'__main__.py:571 + + $ nf-core modules patch fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5 - https://nf-co.re + + + +INFO     Changes in module 'nf-core/modules/fastqc'modules_differ.py:252 +INFO    'modules/nf-core/modules/fastqc/meta.yml' is unchanged                modules_differ.py:257 +INFO     Changes in 'fastqc/main.nf':                                          modules_differ.py:266 + +--- modules/nf-core/modules/fastqc/main.nf ++++ modules/nf-core/modules/fastqc/main.nf +@@ -1,6 +1,6 @@ +process FASTQC {                                                                                   +    tag "$meta.id"                                                                                 +-    label 'process_medium' ++    label 'process_low' + +    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)                                 +    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_  + + +INFO     Patch file of 'nf-core/modules/fastqc' written to                              patch.py:115 +'modules/nf-core/modules/fastqc/fastqc.diff' diff --git a/docs/images/nf-core-modules-remove.svg b/docs/images/nf-core-modules-remove.svg index 20726d93e6..bc67a96483 100644 --- a/docs/images/nf-core-modules-remove.svg +++ b/docs/images/nf-core-modules-remove.svg @@ -19,66 +19,65 @@ font-weight: 700; } - .terminal-1917479430-matrix { + .terminal-1051680509-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1917479430-title { + .terminal-1051680509-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1917479430-r1 { fill: #c5c8c6 } -.terminal-1917479430-r2 { fill: #98a84b } -.terminal-1917479430-r3 { fill: #9a9b99 } -.terminal-1917479430-r4 { fill: #608ab1 } -.terminal-1917479430-r5 { fill: #d0b344 } -.terminal-1917479430-r6 { fill: #292929;font-weight: bold } -.terminal-1917479430-r7 { fill: #868887 } + .terminal-1051680509-r1 { fill: #c5c8c6 } +.terminal-1051680509-r2 { fill: #98a84b } +.terminal-1051680509-r3 { fill: #9a9b99 } +.terminal-1051680509-r4 { fill: #608ab1 } +.terminal-1051680509-r5 { fill: #d0b344 } +.terminal-1051680509-r6 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -90,22 +89,22 @@ - - - - $ nf-core modules remove abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -CRITICAL Could not find a 'main.nf' or 'nextflow.config' file in '.'__main__.py:599 + + + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5 - https://nf-co.re + + + +INFO     Removing abacas                                                                remove.py:52 diff --git a/docs/images/nf-core-modules-test.svg b/docs/images/nf-core-modules-test.svg index 20b7f7bb7f..b65ae7a6ad 100644 --- a/docs/images/nf-core-modules-test.svg +++ b/docs/images/nf-core-modules-test.svg @@ -19,68 +19,68 @@ font-weight: 700; } - .terminal-2872056789-matrix { + .terminal-2926910008-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2872056789-title { + .terminal-2926910008-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2872056789-r1 { fill: #c5c8c6 } -.terminal-2872056789-r2 { fill: #98a84b } -.terminal-2872056789-r3 { fill: #9a9b99 } -.terminal-2872056789-r4 { fill: #608ab1 } -.terminal-2872056789-r5 { fill: #d0b344 } -.terminal-2872056789-r6 { fill: #868887 } + .terminal-2926910008-r1 { fill: #c5c8c6 } +.terminal-2926910008-r2 { fill: #98a84b } +.terminal-2926910008-r3 { fill: #9a9b99 } +.terminal-2926910008-r4 { fill: #608ab1 } +.terminal-2926910008-r5 { fill: #d0b344 } +.terminal-2926910008-r6 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -92,23 +92,23 @@ - + - - $ 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 - https://nf-co.re + + + +────────────────────────────────────────── samtools/view ─────────────────────────────────────────── +INFO     Running pytest for module 'samtools/view'module_test.py:184 diff --git a/docs/images/nf-core-modules-update.svg b/docs/images/nf-core-modules-update.svg index 2acd0bdba6..080277cff0 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 - - - -ERROR    Could not find a 'main.nf' or 'nextflow.config' file in '.'__main__.py:540 + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5 - https://nf-co.re + + + +INFO    'nf-core/modules/abacas' is already up to date                                update.py:160 +INFO     Updating 'nf-core/modules/custom/dumpsoftwareversions'update.py:516 +INFO     Updating 'nf-core/modules/fastqc'update.py:516 +INFO     Updating 'nf-core/modules/multiqc'update.py:516 +INFO     Updates complete ✨                                                           update.py:242 diff --git a/docs/images/nf-core-schema-build.svg b/docs/images/nf-core-schema-build.svg index 3c5f4b3370..87f27862ac 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-1219208311-matrix { + .terminal-3538854618-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1219208311-title { + .terminal-3538854618-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1219208311-r1 { fill: #c5c8c6 } -.terminal-1219208311-r2 { fill: #98a84b } -.terminal-1219208311-r3 { fill: #9a9b99 } -.terminal-1219208311-r4 { fill: #608ab1 } -.terminal-1219208311-r5 { fill: #d0b344 } -.terminal-1219208311-r6 { fill: #98a84b;font-weight: bold } -.terminal-1219208311-r7 { fill: #868887 } -.terminal-1219208311-r8 { fill: #868887;font-weight: bold } -.terminal-1219208311-r9 { fill: #4e707b;font-weight: bold } -.terminal-1219208311-r10 { fill: #68a0b3;font-weight: bold } + .terminal-3538854618-r1 { fill: #c5c8c6 } +.terminal-3538854618-r2 { fill: #98a84b } +.terminal-3538854618-r3 { fill: #9a9b99 } +.terminal-3538854618-r4 { fill: #608ab1 } +.terminal-3538854618-r5 { fill: #d0b344 } +.terminal-3538854618-r6 { fill: #98a84b;font-weight: bold } +.terminal-3538854618-r7 { fill: #868887 } +.terminal-3538854618-r8 { fill: #868887;font-weight: bold } +.terminal-3538854618-r9 { fill: #4e707b;font-weight: bold } +.terminal-3538854618-r10 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,23 +96,23 @@ - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validationschema.py:237 -INFO    [✓] Pipeline schema looks valid(found 27 params)schema.py:95 -INFO     Writing schema with 28 params: './nextflow_schema.json'schema.py:173 + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validationschema.py:237 +INFO    [✓] Pipeline schema looks valid(found 27 params)schema.py:95 +INFO     Writing schema with 28 params: './nextflow_schema.json'schema.py:173 diff --git a/docs/images/nf-core-schema-lint.svg b/docs/images/nf-core-schema-lint.svg index aa28d99e0e..0083a44941 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-3729820431-matrix { + .terminal-4207053170-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3729820431-title { + .terminal-4207053170-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3729820431-r1 { fill: #c5c8c6 } -.terminal-3729820431-r2 { fill: #98a84b } -.terminal-3729820431-r3 { fill: #9a9b99 } -.terminal-3729820431-r4 { fill: #608ab1 } -.terminal-3729820431-r5 { fill: #d0b344 } -.terminal-3729820431-r6 { fill: #98a84b;font-weight: bold } -.terminal-3729820431-r7 { fill: #868887 } -.terminal-3729820431-r8 { fill: #868887;font-weight: bold } -.terminal-3729820431-r9 { fill: #4e707b;font-weight: bold } + .terminal-4207053170-r1 { fill: #c5c8c6 } +.terminal-4207053170-r2 { fill: #98a84b } +.terminal-4207053170-r3 { fill: #9a9b99 } +.terminal-4207053170-r4 { fill: #608ab1 } +.terminal-4207053170-r5 { fill: #d0b344 } +.terminal-4207053170-r6 { fill: #98a84b;font-weight: bold } +.terminal-4207053170-r7 { fill: #868887 } +.terminal-4207053170-r8 { fill: #868887;font-weight: bold } +.terminal-4207053170-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -92,22 +92,22 @@ - + - - $ nf-core schema lint nextflow_schema.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validationschema.py:237 -INFO    [✓] Pipeline schema looks valid(found 28 params)schema.py:95 + + $ nf-core schema lint nextflow_schema.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validationschema.py:237 +INFO    [✓] Pipeline schema looks valid(found 28 params)schema.py:95 diff --git a/docs/images/nf-core-schema-validate.svg b/docs/images/nf-core-schema-validate.svg index 41376f5bdb..2e089460a0 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-3209931885-matrix { + .terminal-229550800-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3209931885-title { + .terminal-229550800-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3209931885-r1 { fill: #c5c8c6 } -.terminal-3209931885-r2 { fill: #98a84b } -.terminal-3209931885-r3 { fill: #9a9b99 } -.terminal-3209931885-r4 { fill: #608ab1 } -.terminal-3209931885-r5 { fill: #d0b344 } -.terminal-3209931885-r6 { fill: #98a84b;font-weight: bold } -.terminal-3209931885-r7 { fill: #868887 } -.terminal-3209931885-r8 { fill: #868887;font-weight: bold } -.terminal-3209931885-r9 { fill: #4e707b;font-weight: bold } + .terminal-229550800-r1 { fill: #c5c8c6 } +.terminal-229550800-r2 { fill: #98a84b } +.terminal-229550800-r3 { fill: #9a9b99 } +.terminal-229550800-r4 { fill: #608ab1 } +.terminal-229550800-r5 { fill: #d0b344 } +.terminal-229550800-r6 { fill: #98a84b;font-weight: bold } +.terminal-229550800-r7 { fill: #868887 } +.terminal-229550800-r8 { fill: #868887;font-weight: bold } +.terminal-229550800-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 2.5.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 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validationschema.py:237 +INFO    [✓] Pipeline schema looks valid(found 93 params)schema.py:95 +INFO    [✓] Input parameters look validschema.py:213 diff --git a/docs/images/nf-core-sync.svg b/docs/images/nf-core-sync.svg index 1b6f3a9e83..ec1ac051e8 100644 --- a/docs/images/nf-core-sync.svg +++ b/docs/images/nf-core-sync.svg @@ -19,73 +19,73 @@ font-weight: 700; } - .terminal-2822682943-matrix { + .terminal-3145054114-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2822682943-title { + .terminal-3145054114-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2822682943-r1 { fill: #c5c8c6 } -.terminal-2822682943-r2 { fill: #98a84b } -.terminal-2822682943-r3 { fill: #9a9b99 } -.terminal-2822682943-r4 { fill: #608ab1 } -.terminal-2822682943-r5 { fill: #d0b344 } -.terminal-2822682943-r6 { fill: #98729f } -.terminal-2822682943-r7 { fill: #ff2c7a } -.terminal-2822682943-r8 { fill: #868887 } + .terminal-3145054114-r1 { fill: #c5c8c6 } +.terminal-3145054114-r2 { fill: #98a84b } +.terminal-3145054114-r3 { fill: #9a9b99 } +.terminal-3145054114-r4 { fill: #608ab1 } +.terminal-3145054114-r5 { fill: #d0b344 } +.terminal-3145054114-r6 { fill: #98729f } +.terminal-3145054114-r7 { fill: #ff2c7a } +.terminal-3145054114-r8 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -97,24 +97,24 @@ - + - - $ 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 - 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