From 17b2b093cd8c2e5666f74873ef4f8eab89bd3dff Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 29 Feb 2024 15:43:07 +0000 Subject: [PATCH] Generate new screengrabs with rich-codex --- docs/images/nf-core-bump-version.svg | 148 ++++----- docs/images/nf-core-create-logo.svg | 68 ++-- docs/images/nf-core-create.svg | 126 +++---- docs/images/nf-core-download.svg | 100 +++--- docs/images/nf-core-launch-rnaseq.svg | 82 ++--- docs/images/nf-core-licences.svg | 68 ++-- docs/images/nf-core-lint.svg | 174 +++++----- docs/images/nf-core-list-rna.svg | 134 ++++---- 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.svg | 84 ++--- docs/images/nf-core-modules-info.svg | 206 ++++++------ docs/images/nf-core-modules-install.svg | 86 ++--- docs/images/nf-core-modules-lint.svg | 74 ++--- docs/images/nf-core-modules-list-local.svg | 116 +++---- docs/images/nf-core-modules-list-remote.svg | 132 ++++---- docs/images/nf-core-modules-patch.svg | 156 ++++----- docs/images/nf-core-modules-remove.svg | 70 ++-- docs/images/nf-core-modules-test.svg | 70 ++-- docs/images/nf-core-modules-update.svg | 82 ++--- 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-subworkflows-create.svg | 104 +++--- docs/images/nf-core-subworkflows-info.svg | 138 ++++---- docs/images/nf-core-subworkflows-install.svg | 92 +++--- docs/images/nf-core-subworkflows-lint.svg | 308 +++++++++--------- .../nf-core-subworkflows-list-local.svg | 130 ++++---- .../nf-core-subworkflows-list-remote.svg | 132 ++++---- docs/images/nf-core-subworkflows-remove.svg | 124 +++---- docs/images/nf-core-subworkflows-test.svg | 70 ++-- docs/images/nf-core-subworkflows-update.svg | 93 +++--- docs/images/nf-core-sync.svg | 108 +++--- 34 files changed, 1938 insertions(+), 1899 deletions(-) diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg index 838d1cfc7f..70171475d9 100644 --- a/docs/images/nf-core-bump-version.svg +++ b/docs/images/nf-core-bump-version.svg @@ -19,122 +19,122 @@ font-weight: 700; } - .terminal-978478039-matrix { + .terminal-3430704182-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-978478039-title { + .terminal-3430704182-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-978478039-r1 { fill: #c5c8c6 } -.terminal-978478039-r2 { fill: #98a84b } -.terminal-978478039-r3 { fill: #9a9b99 } -.terminal-978478039-r4 { fill: #608ab1 } -.terminal-978478039-r5 { fill: #d0b344 } -.terminal-978478039-r6 { fill: #cc555a } + .terminal-3430704182-r1 { fill: #c5c8c6 } +.terminal-3430704182-r2 { fill: #98a84b } +.terminal-3430704182-r3 { fill: #9a9b99 } +.terminal-3430704182-r4 { fill: #608ab1 } +.terminal-3430704182-r5 { fill: #d0b344 } +.terminal-3430704182-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -146,41 +146,41 @@ - + - - $ nf-core bump-version 1.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - -INFO     Changing version number from '1.0dev' to '1.1' -INFO     Updated version in 'nextflow.config' - - version         = '1.0dev' - + version         = '1.1' - - -INFO     Updated version in 'assets/multiqc_config.yml' - - This report has been generated by the <a  -href="https://github.com/nf-core/nextbigthing/tree/dev" target="_blank">nf-core/nextbigthing</a> - + This report has been generated by the <a  -href="https://github.com/nf-core/nextbigthing/releases/tag/1.1"  -target="_blank">nf-core/nextbigthing</a> - - -INFO     Updated version in 'assets/multiqc_config.yml' - - <a href="https://nf-co.re/nextbigthing/dev/docs/output"  -target="_blank">documentation</a>. - + <a href="https://nf-co.re/nextbigthing/1.1/docs/output"  -target="_blank">documentation</a>. - - + + $ nf-core bump-version 1.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + +INFO     Changing version number from '1.0dev' to '1.1' +INFO     Updated version in 'nextflow.config' + - version         = '1.0dev' + + version         = '1.1' + + +INFO     Updated version in 'assets/multiqc_config.yml' + - This report has been generated by the <a  +href="https://github.com/nf-core/nextbigthing/tree/dev" target="_blank">nf-core/nextbigthing</a> + + This report has been generated by the <a  +href="https://github.com/nf-core/nextbigthing/releases/tag/1.1"  +target="_blank">nf-core/nextbigthing</a> + + +INFO     Updated version in 'assets/multiqc_config.yml' + - <a href="https://nf-co.re/nextbigthing/dev/docs/output"  +target="_blank">documentation</a>. + + <a href="https://nf-co.re/nextbigthing/1.1/docs/output"  +target="_blank">documentation</a>. + + diff --git a/docs/images/nf-core-create-logo.svg b/docs/images/nf-core-create-logo.svg index ac5d872b94..c6e7269363 100644 --- a/docs/images/nf-core-create-logo.svg +++ b/docs/images/nf-core-create-logo.svg @@ -19,62 +19,62 @@ font-weight: 700; } - .terminal-189794694-matrix { + .terminal-2584676837-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-189794694-title { + .terminal-2584676837-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-189794694-r1 { fill: #c5c8c6 } -.terminal-189794694-r2 { fill: #98a84b } -.terminal-189794694-r3 { fill: #9a9b99 } -.terminal-189794694-r4 { fill: #608ab1 } -.terminal-189794694-r5 { fill: #d0b344 } -.terminal-189794694-r6 { fill: #98729f } + .terminal-2584676837-r1 { fill: #c5c8c6 } +.terminal-2584676837-r2 { fill: #98a84b } +.terminal-2584676837-r3 { fill: #9a9b99 } +.terminal-2584676837-r4 { fill: #608ab1 } +.terminal-2584676837-r5 { fill: #d0b344 } +.terminal-2584676837-r6 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + @@ -86,21 +86,21 @@ - + - - $ nf-core create-logo nextbigthing - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - -INFO     Created logo: nf-core-nextbigthing_logo_light.png + + $ nf-core create-logo nextbigthing + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + +INFO     Created logo: nf-core-nextbigthing_logo_light.png diff --git a/docs/images/nf-core-create.svg b/docs/images/nf-core-create.svg index 68cae552b3..422e6734ce 100644 --- a/docs/images/nf-core-create.svg +++ b/docs/images/nf-core-create.svg @@ -19,104 +19,104 @@ font-weight: 700; } - .terminal-2074661465-matrix { + .terminal-165925560-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2074661465-title { + .terminal-165925560-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2074661465-r1 { fill: #c5c8c6 } -.terminal-2074661465-r2 { fill: #98a84b } -.terminal-2074661465-r3 { fill: #9a9b99 } -.terminal-2074661465-r4 { fill: #608ab1 } -.terminal-2074661465-r5 { fill: #d0b344 } -.terminal-2074661465-r6 { fill: #98729f } -.terminal-2074661465-r7 { fill: #ff2c7a } -.terminal-2074661465-r8 { fill: #98a84b;font-weight: bold } -.terminal-2074661465-r9 { fill: #1984e9;text-decoration: underline; } + .terminal-165925560-r1 { fill: #c5c8c6 } +.terminal-165925560-r2 { fill: #98a84b } +.terminal-165925560-r3 { fill: #9a9b99 } +.terminal-165925560-r4 { fill: #608ab1 } +.terminal-165925560-r5 { fill: #d0b344 } +.terminal-165925560-r6 { fill: #98729f } +.terminal-165925560-r7 { fill: #ff2c7a } +.terminal-165925560-r8 { fill: #98a84b;font-weight: bold } +.terminal-165925560-r9 { fill: #1984e9;text-decoration: underline; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -128,34 +128,34 @@ - + - - $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique"  --a "Big Steve" --plain - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - -INFO     Creating new nf-core pipeline: 'nf-core/nextbigthing' -INFO     Initialising pipeline git repository                                                        -INFO     Done. Remember to add a remote and push to GitHub:                                          - cd /home/runner/work/tools/tools/tmp/nf-core-nextbigthing - git remote add origin git@github.com:USERNAME/REPO_NAME.git  - git push --all origin                                        -INFO     This will also push your newly created dev branch and the TEMPLATE branch for syncing.      -INFO    !!!!!! IMPORTANT !!!!!! - -If you are interested in adding your pipeline to the nf-core community, -PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE! - -Please read: https://nf-co.re/developers/adding_pipelines#join-the-community + + $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique"  +-a "Big Steve" --plain + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + +INFO     Creating new nf-core pipeline: 'nf-core/nextbigthing' +INFO     Initialising pipeline git repository                                                        +INFO     Done. Remember to add a remote and push to GitHub:                                          + cd /home/runner/work/tools/tools/tmp/nf-core-nextbigthing + git remote add origin git@github.com:USERNAME/REPO_NAME.git  + git push --all origin                                        +INFO     This will also push your newly created dev branch and the TEMPLATE branch for syncing.      +INFO    !!!!!! IMPORTANT !!!!!! + +If you are interested in adding your pipeline to the nf-core community, +PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE! + +Please read: https://nf-co.re/developers/adding_pipelines#join-the-community diff --git a/docs/images/nf-core-download.svg b/docs/images/nf-core-download.svg index e2ed5b22b4..5594930fa7 100644 --- a/docs/images/nf-core-download.svg +++ b/docs/images/nf-core-download.svg @@ -19,86 +19,86 @@ font-weight: 700; } - .terminal-2088037745-matrix { + .terminal-2899766736-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2088037745-title { + .terminal-2899766736-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2088037745-r1 { fill: #c5c8c6 } -.terminal-2088037745-r2 { fill: #98a84b } -.terminal-2088037745-r3 { fill: #9a9b99 } -.terminal-2088037745-r4 { fill: #608ab1 } -.terminal-2088037745-r5 { fill: #d0b344 } -.terminal-2088037745-r6 { fill: #cc555a } + .terminal-2899766736-r1 { fill: #c5c8c6 } +.terminal-2899766736-r2 { fill: #98a84b } +.terminal-2899766736-r3 { fill: #9a9b99 } +.terminal-2899766736-r4 { fill: #608ab1 } +.terminal-2899766736-r5 { fill: #d0b344 } +.terminal-2899766736-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -110,29 +110,29 @@ - + - - $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - -WARNING  Could not find GitHub authentication token. Some API requests may fail.                     -INFO     Saving 'nf-core/rnaseq' -          Pipeline revision: '3.8' -          Use containers: 'none' -          Container library: 'quay.io' -          Output directory: 'nf-core-rnaseq' -          Include default institutional configuration: 'True' -INFO     Downloading centralised configs from GitHub                                                 -INFO     Downloading workflow files from GitHub                                                      + + $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + +WARNING  Could not find GitHub authentication token. Some API requests may fail.                     +INFO     Saving 'nf-core/rnaseq' +          Pipeline revision: '3.8' +          Use containers: 'none' +          Container library: 'quay.io' +          Output directory: 'nf-core-rnaseq' +          Include default institutional configuration: 'True' +INFO     Downloading centralised configs from GitHub                                                 +INFO     Downloading workflow files from GitHub                                                      diff --git a/docs/images/nf-core-launch-rnaseq.svg b/docs/images/nf-core-launch-rnaseq.svg index 6bbbbaf099..f2608fe76f 100644 --- a/docs/images/nf-core-launch-rnaseq.svg +++ b/docs/images/nf-core-launch-rnaseq.svg @@ -19,72 +19,72 @@ font-weight: 700; } - .terminal-1939516884-matrix { + .terminal-3860049459-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1939516884-title { + .terminal-3860049459-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1939516884-r1 { fill: #c5c8c6 } -.terminal-1939516884-r2 { fill: #98a84b } -.terminal-1939516884-r3 { fill: #9a9b99 } -.terminal-1939516884-r4 { fill: #608ab1 } -.terminal-1939516884-r5 { fill: #d0b344 } -.terminal-1939516884-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1939516884-r7 { fill: #68a0b3;font-weight: bold } + .terminal-3860049459-r1 { fill: #c5c8c6 } +.terminal-3860049459-r2 { fill: #98a84b } +.terminal-3860049459-r3 { fill: #9a9b99 } +.terminal-3860049459-r4 { fill: #608ab1 } +.terminal-3860049459-r5 { fill: #d0b344 } +.terminal-3860049459-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3860049459-r7 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,24 +96,24 @@ - + - - $ nf-core launch rnaseq -r 3.8.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - -INFO     NOTE: This tool ignores any pipeline parameter defaults overwritten by Nextflow config      -         files or profiles                                                                           - -INFO     Downloading workflow: nf-core/rnaseq (3.8.1) + + $ nf-core launch rnaseq -r 3.8.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + +INFO     NOTE: This tool ignores any pipeline parameter defaults overwritten by Nextflow config      +         files or profiles                                                                           + +INFO     Downloading workflow: nf-core/rnaseq (3.8.1) diff --git a/docs/images/nf-core-licences.svg b/docs/images/nf-core-licences.svg index 35962d8e4f..8cc00c351b 100644 --- a/docs/images/nf-core-licences.svg +++ b/docs/images/nf-core-licences.svg @@ -19,62 +19,62 @@ font-weight: 700; } - .terminal-2800093472-matrix { + .terminal-918620543-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2800093472-title { + .terminal-918620543-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2800093472-r1 { fill: #c5c8c6 } -.terminal-2800093472-r2 { fill: #98a84b } -.terminal-2800093472-r3 { fill: #9a9b99 } -.terminal-2800093472-r4 { fill: #608ab1 } -.terminal-2800093472-r5 { fill: #d0b344 } -.terminal-2800093472-r6 { fill: #68a0b3;font-weight: bold } + .terminal-918620543-r1 { fill: #c5c8c6 } +.terminal-918620543-r2 { fill: #98a84b } +.terminal-918620543-r3 { fill: #9a9b99 } +.terminal-918620543-r4 { fill: #608ab1 } +.terminal-918620543-r5 { fill: #d0b344 } +.terminal-918620543-r6 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + @@ -86,21 +86,21 @@ - + - - $ nf-core licences deepvariant - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - -INFO     Fetching licence information for 8 tools                                                    + + $ nf-core licences deepvariant + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + +INFO     Fetching licence information for 8 tools                                                    diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg index 74e41870d3..2e55a7e11e 100644 --- a/docs/images/nf-core-lint.svg +++ b/docs/images/nf-core-lint.svg @@ -19,139 +19,139 @@ font-weight: 700; } - .terminal-3628718215-matrix { + .terminal-2900416932-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3628718215-title { + .terminal-2900416932-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3628718215-r1 { fill: #c5c8c6 } -.terminal-3628718215-r2 { fill: #98a84b } -.terminal-3628718215-r3 { fill: #9a9b99 } -.terminal-3628718215-r4 { fill: #608ab1 } -.terminal-3628718215-r5 { fill: #d0b344 } -.terminal-3628718215-r6 { fill: #98729f } -.terminal-3628718215-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-3628718215-r8 { fill: #608ab1;text-decoration: underline; } -.terminal-3628718215-r9 { fill: #d0b344;font-weight: bold } -.terminal-3628718215-r10 { fill: #68a0b3;font-weight: bold } -.terminal-3628718215-r11 { fill: #cc555a } + .terminal-2900416932-r1 { fill: #c5c8c6 } +.terminal-2900416932-r2 { fill: #98a84b } +.terminal-2900416932-r3 { fill: #9a9b99 } +.terminal-2900416932-r4 { fill: #608ab1 } +.terminal-2900416932-r5 { fill: #d0b344 } +.terminal-2900416932-r6 { fill: #98729f } +.terminal-2900416932-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2900416932-r8 { fill: #608ab1;text-decoration: underline; } +.terminal-2900416932-r9 { fill: #d0b344;font-weight: bold } +.terminal-2900416932-r10 { fill: #68a0b3;font-weight: bold } +.terminal-2900416932-r11 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -163,45 +163,45 @@ - + - - $ nf-core lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Testing pipeline: . - - -╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ -││ -│pipeline_todos: pipeline_todos                                                                  │ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─[!] 1 Pipeline Test Warning────────────────────────────────────────────────────────────────────╮ -││ -│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │ -│doi (after the first release).                                                                  │ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - - -╭──────────────────────╮ -│LINT RESULTS SUMMARY│ -├──────────────────────┤ -│[✔] 188 Tests Passed│ -│[?]   1 Test Ignored│ -│[!]   1 Test Warning│ -│[✗]   0 Tests Failed│ -╰──────────────────────╯ + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Testing pipeline: . + + +╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ +││ +│pipeline_todos: pipeline_todos                                                                  │ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─[!] 1 Pipeline Test Warning────────────────────────────────────────────────────────────────────╮ +││ +│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │ +│doi (after the first release).                                                                  │ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + + +╭──────────────────────╮ +│LINT RESULTS SUMMARY│ +├──────────────────────┤ +│[✔] 188 Tests Passed│ +│[?]   1 Test Ignored│ +│[!]   1 Test Warning│ +│[✗]   0 Tests Failed│ +╰──────────────────────╯ diff --git a/docs/images/nf-core-list-rna.svg b/docs/images/nf-core-list-rna.svg index ff51d523e4..643545c6fc 100644 --- a/docs/images/nf-core-list-rna.svg +++ b/docs/images/nf-core-list-rna.svg @@ -19,111 +19,111 @@ font-weight: 700; } - .terminal-822138325-matrix { + .terminal-1703728371-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-822138325-title { + .terminal-1703728371-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-822138325-r1 { fill: #c5c8c6 } -.terminal-822138325-r2 { fill: #98a84b } -.terminal-822138325-r3 { fill: #9a9b99 } -.terminal-822138325-r4 { fill: #608ab1 } -.terminal-822138325-r5 { fill: #d0b344 } -.terminal-822138325-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-822138325-r7 { fill: #868887 } + .terminal-1703728371-r1 { fill: #c5c8c6 } +.terminal-1703728371-r2 { fill: #98a84b } +.terminal-1703728371-r3 { fill: #9a9b99 } +.terminal-1703728371-r4 { fill: #608ab1 } +.terminal-1703728371-r5 { fill: #d0b344 } +.terminal-1703728371-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1703728371-r7 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -135,37 +135,37 @@ - + - - $ nf-core list rna rna-seq - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnasplice            │    22 │          1.0.2 │ 1 months ago │           - │ -                   │ -│ circrna              │    34 │            dev │    yesterday │           - │ -                   │ -│ rnaseq               │   735 │         3.14.0 │ 1 months ago │           - │ -                   │ -│ smrnaseq             │    64 │          2.2.4 │ 4 months ago │           - │ -                   │ -│ scrnaseq             │   124 │          2.5.1 │  4 weeks ago │           - │ -                   │ -│ differentialabundan… │    38 │          1.4.0 │ 3 months ago │           - │ -                   │ -│ rnafusion            │   126 │          3.0.1 │ 3 months ago │           - │ -                   │ -│ spatialtranscriptom… │    36 │            dev │  3 weeks ago │           - │ -                   │ -│ dualrnaseq           │    16 │          1.0.0 │  3 years ago │           - │ -                   │ -│ marsseq              │     5 │          1.0.3 │ 7 months ago │           - │ -                   │ -│ lncpipe              │    28 │            dev │  1 years ago │           - │ -                   │ -│ scflow               │    24 │            dev │  2 years ago │           - │ -                   │ -└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ + + $ nf-core list rna rna-seq + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq               │   742 │         3.14.0 │ 2 months ago │           - │ -                   │ +│ differentialabundan… │    38 │          1.4.0 │ 3 months ago │           - │ -                   │ +│ smrnaseq             │    64 │          2.3.0 │   6 days ago │           - │ -                   │ +│ rnasplice            │    25 │          1.0.3 │   6 days ago │           - │ -                   │ +│ circrna              │    34 │            dev │  1 weeks ago │           - │ -                   │ +│ scrnaseq             │   125 │          2.5.1 │ 1 months ago │           - │ -                   │ +│ rnafusion            │   126 │          3.0.1 │ 3 months ago │           - │ -                   │ +│ spatialtranscriptom… │    36 │            dev │  4 weeks ago │           - │ -                   │ +│ dualrnaseq           │    16 │          1.0.0 │  3 years ago │           - │ -                   │ +│ marsseq              │     5 │          1.0.3 │ 8 months ago │           - │ -                   │ +│ lncpipe              │    28 │            dev │  1 years ago │           - │ -                   │ +│ scflow               │    24 │            dev │  3 years ago │           - │ -                   │ +└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg index 4b020b0dc7..8ea120599f 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-2391931080-matrix { + .terminal-3700160896-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2391931080-title { + .terminal-3700160896-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2391931080-r1 { fill: #c5c8c6 } -.terminal-2391931080-r2 { fill: #98a84b } -.terminal-2391931080-r3 { fill: #9a9b99 } -.terminal-2391931080-r4 { fill: #608ab1 } -.terminal-2391931080-r5 { fill: #d0b344 } -.terminal-2391931080-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2391931080-r7 { fill: #868887 } -.terminal-2391931080-r8 { fill: #868887;font-style: italic; } + .terminal-3700160896-r1 { fill: #c5c8c6 } +.terminal-3700160896-r2 { fill: #98a84b } +.terminal-3700160896-r3 { fill: #9a9b99 } +.terminal-3700160896-r4 { fill: #608ab1 } +.terminal-3700160896-r5 { fill: #d0b344 } +.terminal-3700160896-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3700160896-r7 { fill: #868887 } +.terminal-3700160896-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -112,29 +112,29 @@ - + - - $ nf-core list -s stars - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq              │   735 │         3.14.0 │  1 months ago │           - │ -                   │ -│ sarek               │   312 │          3.4.0 │  3 months ago │           - │ -                   │ -│ mag                 │   170 │          2.5.4 │    1 week ago │           - │ -                   │ -│ chipseq             │   160 │          2.0.0 │   1 years ago │           - │ -                   │ -[..truncated..] + + $ nf-core list -s stars + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq              │   742 │         3.14.0 │  2 months ago │           - │ -                   │ +│ sarek               │   320 │          3.4.0 │  4 months ago │           - │ -                   │ +│ mag                 │   175 │          2.5.4 │   2 weeks ago │           - │ -                   │ +│ chipseq             │   161 │          2.0.0 │   1 years ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg index aa93f830ee..5e4939f746 100644 --- a/docs/images/nf-core-list.svg +++ b/docs/images/nf-core-list.svg @@ -19,91 +19,91 @@ font-weight: 700; } - .terminal-1155039927-matrix { + .terminal-3505815442-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1155039927-title { + .terminal-3505815442-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1155039927-r1 { fill: #c5c8c6 } -.terminal-1155039927-r2 { fill: #98a84b } -.terminal-1155039927-r3 { fill: #9a9b99 } -.terminal-1155039927-r4 { fill: #608ab1 } -.terminal-1155039927-r5 { fill: #d0b344 } -.terminal-1155039927-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1155039927-r7 { fill: #868887 } -.terminal-1155039927-r8 { fill: #868887;font-style: italic; } + .terminal-3505815442-r1 { fill: #c5c8c6 } +.terminal-3505815442-r2 { fill: #98a84b } +.terminal-3505815442-r3 { fill: #9a9b99 } +.terminal-3505815442-r4 { fill: #608ab1 } +.terminal-3505815442-r5 { fill: #d0b344 } +.terminal-3505815442-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3505815442-r7 { fill: #868887 } +.terminal-3505815442-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +115,30 @@ - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ fetchngs            │   100 │         1.11.0 │  4 months ago │           - │ -                   │ -│ phageannotator      │     7 │            dev │  20 hours ago │           - │ -                   │ -│ riboseq             │     2 │            dev │  22 hours ago │           - │ -                   │ -│ bacass              │    48 │          2.1.0 │  4 months ago │           - │ -                   │ -│ rnasplice           │    22 │          1.0.2 │  1 months ago │           - │ -                   │ -[..truncated..] + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ raredisease         │    65 │          1.1.1 │  7 months ago │           - │ -                   │ +│ fetchngs            │   101 │         1.11.0 │  4 months ago │           - │ -                   │ +│ sarek               │   320 │          3.4.0 │  4 months ago │           - │ -                   │ +│ methylseq           │   126 │          2.6.0 │  2 months ago │           - │ -                   │ +│ rnaseq              │   742 │         3.14.0 │  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 c886806891..093a0cebc6 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-692975589-matrix { + .terminal-1669068868-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-692975589-title { + .terminal-1669068868-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-692975589-r1 { fill: #c5c8c6 } -.terminal-692975589-r2 { fill: #98a84b } -.terminal-692975589-r3 { fill: #9a9b99 } -.terminal-692975589-r4 { fill: #608ab1 } -.terminal-692975589-r5 { fill: #d0b344 } -.terminal-692975589-r6 { fill: #98a84b;font-weight: bold } -.terminal-692975589-r7 { fill: #c5c8c6;font-weight: bold } + .terminal-1669068868-r1 { fill: #c5c8c6 } +.terminal-1669068868-r2 { fill: #98a84b } +.terminal-1669068868-r3 { fill: #9a9b99 } +.terminal-1669068868-r4 { fill: #608ab1 } +.terminal-1669068868-r5 { fill: #d0b344 } +.terminal-1669068868-r6 { fill: #98a84b;font-weight: bold } +.terminal-1669068868-r7 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -114,30 +114,30 @@ - + - - $ nf-core modules bump-versions fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - 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 2.13.1 - https://nf-co.re + + + + +╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ +│[!] 1 Module version up to date.│ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ +│Module name                             │Update Message                                       │ +├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ +│ fastqc                                   │ Module version up to date: fastqc                     │ +╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index 295289aaca..caa9c389f0 100644 --- a/docs/images/nf-core-modules-create.svg +++ b/docs/images/nf-core-modules-create.svg @@ -19,74 +19,74 @@ font-weight: 700; } - .terminal-2070228187-matrix { + .terminal-2912300346-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2070228187-title { + .terminal-2912300346-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2070228187-r1 { fill: #c5c8c6 } -.terminal-2070228187-r2 { fill: #98a84b } -.terminal-2070228187-r3 { fill: #9a9b99 } -.terminal-2070228187-r4 { fill: #608ab1 } -.terminal-2070228187-r5 { fill: #d0b344 } -.terminal-2070228187-r6 { fill: #68a0b3;font-weight: bold } + .terminal-2912300346-r1 { fill: #c5c8c6 } +.terminal-2912300346-r2 { fill: #98a84b } +.terminal-2912300346-r3 { fill: #9a9b99 } +.terminal-2912300346-r4 { fill: #608ab1 } +.terminal-2912300346-r5 { fill: #d0b344 } +.terminal-2912300346-r6 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -98,25 +98,25 @@ - + - - $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Repository type: modules -INFO    Press enter to use default values (shown in brackets)or type your own responses.  -ctrl+click underlined text to open links. -INFO     Using Bioconda package: 'bioconda::fastqc=0.12.1' + + $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Repository type: modules +INFO    Press enter to use default values (shown in brackets)or type your own responses.  +ctrl+click underlined text to open links. +INFO     Using Bioconda package: 'bioconda::fastqc=0.12.1' diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg index a35ecdec75..255c595e7c 100644 --- a/docs/images/nf-core-modules-info.svg +++ b/docs/images/nf-core-modules-info.svg @@ -19,163 +19,163 @@ font-weight: 700; } - .terminal-3092902354-matrix { + .terminal-1309602353-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3092902354-title { + .terminal-1309602353-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3092902354-r1 { fill: #c5c8c6 } -.terminal-3092902354-r2 { fill: #98a84b } -.terminal-3092902354-r3 { fill: #9a9b99 } -.terminal-3092902354-r4 { fill: #608ab1 } -.terminal-3092902354-r5 { fill: #d0b344 } -.terminal-3092902354-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3092902354-r7 { fill: #98a84b;font-weight: bold } -.terminal-3092902354-r8 { fill: #868887 } -.terminal-3092902354-r9 { fill: #d08442 } -.terminal-3092902354-r10 { fill: #868887;font-style: italic; } -.terminal-3092902354-r11 { fill: #98729f } + .terminal-1309602353-r1 { fill: #c5c8c6 } +.terminal-1309602353-r2 { fill: #98a84b } +.terminal-1309602353-r3 { fill: #9a9b99 } +.terminal-1309602353-r4 { fill: #608ab1 } +.terminal-1309602353-r5 { fill: #d0b344 } +.terminal-1309602353-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1309602353-r7 { fill: #98a84b;font-weight: bold } +.terminal-1309602353-r8 { fill: #868887 } +.terminal-1309602353-r9 { fill: #d08442 } +.terminal-1309602353-r10 { fill: #868887;font-style: italic; } +.terminal-1309602353-r11 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -187,53 +187,53 @@ - + - - $ nf-core modules info abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - 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  (file) │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 2.13.1 - https://nf-co.re + + + +╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ +│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ +│ 🔧 Tools: abacas                                                                                 │ +│ 📖 Description: contiguate draft genome assembly                                                 │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +                  ╷                                                                   ╷              +📥 Inputs        │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} +                  ╵                                                                   ╵              +                  ╷                                                                   ╷              +📤 Outputs       │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + results  (file) │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 d0ac5b2946..2b0331bcaa 100644 --- a/docs/images/nf-core-modules-install.svg +++ b/docs/images/nf-core-modules-install.svg @@ -19,76 +19,76 @@ font-weight: 700; } - .terminal-2787740720-matrix { + .terminal-310938767-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2787740720-title { + .terminal-310938767-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2787740720-r1 { fill: #c5c8c6 } -.terminal-2787740720-r2 { fill: #98a84b } -.terminal-2787740720-r3 { fill: #9a9b99 } -.terminal-2787740720-r4 { fill: #608ab1 } -.terminal-2787740720-r5 { fill: #d0b344 } + .terminal-310938767-r1 { fill: #c5c8c6 } +.terminal-310938767-r2 { fill: #98a84b } +.terminal-310938767-r3 { fill: #9a9b99 } +.terminal-310938767-r4 { fill: #608ab1 } +.terminal-310938767-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core modules install abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Installing 'abacas' -INFO     Use the following statement to include this module:                                         - - include { ABACAS } from '../modules/nf-core/abacas/main'                                            - + + $ nf-core modules install abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Installing 'abacas' +INFO     Use the following statement to include this module:                                         + + include { ABACAS } from '../modules/nf-core/abacas/main'                                            + diff --git a/docs/images/nf-core-modules-lint.svg b/docs/images/nf-core-modules-lint.svg index c53b1dfdbc..2809eeee22 100644 --- a/docs/images/nf-core-modules-lint.svg +++ b/docs/images/nf-core-modules-lint.svg @@ -19,67 +19,67 @@ font-weight: 700; } - .terminal-1620728557-matrix { + .terminal-1680431948-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1620728557-title { + .terminal-1680431948-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1620728557-r1 { fill: #c5c8c6 } -.terminal-1620728557-r2 { fill: #98a84b } -.terminal-1620728557-r3 { fill: #9a9b99 } -.terminal-1620728557-r4 { fill: #608ab1 } -.terminal-1620728557-r5 { fill: #d0b344 } + .terminal-1680431948-r1 { fill: #c5c8c6 } +.terminal-1680431948-r2 { fill: #98a84b } +.terminal-1680431948-r3 { fill: #9a9b99 } +.terminal-1680431948-r4 { fill: #608ab1 } +.terminal-1680431948-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -91,23 +91,23 @@ - + - - $ nf-core modules lint multiqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Linting modules repo: '.' -INFO     Linting module: 'multiqc' + + $ nf-core modules lint multiqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Linting modules repo: '.' +INFO     Linting module: 'multiqc' diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index 4b06362a82..ecb9ed499a 100644 --- a/docs/images/nf-core-modules-list-local.svg +++ b/docs/images/nf-core-modules-list-local.svg @@ -19,98 +19,98 @@ font-weight: 700; } - .terminal-4225841500-matrix { + .terminal-2419669372-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4225841500-title { + .terminal-2419669372-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4225841500-r1 { fill: #c5c8c6 } -.terminal-4225841500-r2 { fill: #98a84b } -.terminal-4225841500-r3 { fill: #9a9b99 } -.terminal-4225841500-r4 { fill: #608ab1 } -.terminal-4225841500-r5 { fill: #d0b344 } -.terminal-4225841500-r6 { fill: #c5c8c6;font-weight: bold } + .terminal-2419669372-r1 { fill: #c5c8c6 } +.terminal-2419669372-r2 { fill: #98a84b } +.terminal-2419669372-r3 { fill: #9a9b99 } +.terminal-2419669372-r4 { fill: #608ab1 } +.terminal-2419669372-r5 { fill: #d0b344 } +.terminal-2419669372-r6 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -122,33 +122,33 @@ - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Modules installed in '.':                                                                   - -self.repo_type='pipeline' -┏━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -┃Module Name┃Repository           ┃Version SHA          ┃Message              ┃Date      ┃ -┡━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ fastqc      │ https://github.com/n… │ f4ae1d942bd50c5c0b9b… │ Update FASTQC to use  │ 2024-01-31 │ -│             │                       │                       │ unique names for      │            │ -│             │                       │                       │ snapshots (#4825)     │            │ -│ multiqc     │ https://github.com/n… │ ccacf6f5de6df3bc6d73… │ Bump Multiqc to 1.20  │ 2024-02-14 │ -│             │                       │                       │ (#4910)               │            │ -└─────────────┴───────────────────────┴───────────────────────┴───────────────────────┴────────────┘ + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Modules installed in '.':                                                                   + +self.repo_type='pipeline' +┏━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +┃Module Name┃Repository           ┃Version SHA          ┃Message              ┃Date      ┃ +┡━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ fastqc      │ https://github.com/n… │ f4ae1d942bd50c5c0b9b… │ Update FASTQC to use  │ 2024-01-31 │ +│             │                       │                       │ unique names for      │            │ +│             │                       │                       │ snapshots (#4825)     │            │ +│ multiqc     │ https://github.com/n… │ b7ebe95761cd389603f9… │ Update MQC container  │ 2024-02-29 │ +│             │                       │                       │ (#5006)               │            │ +└─────────────┴───────────────────────┴───────────────────────┴───────────────────────┴────────────┘ diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index aca2dc7d9b..138be73068 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-2422626649-matrix { + .terminal-2384550328-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2422626649-title { + .terminal-2384550328-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2422626649-r1 { fill: #c5c8c6 } -.terminal-2422626649-r2 { fill: #98a84b } -.terminal-2422626649-r3 { fill: #9a9b99 } -.terminal-2422626649-r4 { fill: #608ab1 } -.terminal-2422626649-r5 { fill: #d0b344 } -.terminal-2422626649-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-2422626649-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-2422626649-r8 { fill: #868887;font-style: italic; } + .terminal-2384550328-r1 { fill: #c5c8c6 } +.terminal-2384550328-r2 { fill: #98a84b } +.terminal-2384550328-r3 { fill: #9a9b99 } +.terminal-2384550328-r4 { fill: #608ab1 } +.terminal-2384550328-r5 { fill: #d0b344 } +.terminal-2384550328-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-2384550328-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2384550328-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core modules list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Modules available from https://github.com/nf-core/modules.git(master):                     - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Module Name                                          ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ abacas                                                │ -│ abricate/run                                          │ -│ abricate/summary                                      │ -│ abritamr/run                                          │ -│ adapterremoval                                        │ -│ adapterremovalfixprefix                               │ -│ admixture                                             │ -│ affy/justrma                                          │ -│ agat/convertspgff2gtf                                 │ -[..truncated..] + + $ nf-core modules list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Modules available from https://github.com/nf-core/modules.git(master):                     + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Module Name                                          ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ abacas                                                │ +│ abricate/run                                          │ +│ abricate/summary                                      │ +│ abritamr/run                                          │ +│ adapterremoval                                        │ +│ adapterremovalfixprefix                               │ +│ admixture                                             │ +│ affy/justrma                                          │ +│ agat/convertspgff2gtf                                 │ +[..truncated..] diff --git a/docs/images/nf-core-modules-patch.svg b/docs/images/nf-core-modules-patch.svg index 84ad24867e..5ed5e2f4d1 100644 --- a/docs/images/nf-core-modules-patch.svg +++ b/docs/images/nf-core-modules-patch.svg @@ -19,127 +19,127 @@ font-weight: 700; } - .terminal-3587976170-matrix { + .terminal-1838296137-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3587976170-title { + .terminal-1838296137-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3587976170-r1 { fill: #c5c8c6 } -.terminal-3587976170-r2 { fill: #98a84b } -.terminal-3587976170-r3 { fill: #9a9b99 } -.terminal-3587976170-r4 { fill: #608ab1 } -.terminal-3587976170-r5 { fill: #d0b344 } -.terminal-3587976170-r6 { fill: #ff2627 } -.terminal-3587976170-r7 { fill: #00823d } -.terminal-3587976170-r8 { fill: #ff2c7a;font-weight: bold } + .terminal-1838296137-r1 { fill: #c5c8c6 } +.terminal-1838296137-r2 { fill: #98a84b } +.terminal-1838296137-r3 { fill: #9a9b99 } +.terminal-1838296137-r4 { fill: #608ab1 } +.terminal-1838296137-r5 { fill: #d0b344 } +.terminal-1838296137-r6 { fill: #ff2627 } +.terminal-1838296137-r7 { fill: #00823d } +.terminal-1838296137-r8 { fill: #ff2c7a;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -151,42 +151,42 @@ - + - - $ nf-core modules patch fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Changes in module 'nf-core/fastqc' -INFO    'modules/nf-core/fastqc/environment.yml' is unchanged                                       -INFO    'modules/nf-core/fastqc/meta.yml' is unchanged                                              -INFO     Changes in 'fastqc/main.nf':                                                                - ---- modules/nf-core/fastqc/main.nf -+++ modules/nf-core/fastqc/main.nf -@@ -1,6 +1,6 @@ -process FASTQC {                                                                                   -    tag "$meta.id"                                                                                 --    label 'process_medium' -+    label 'process_low' - -    conda "${moduleDir}/environment.yml"                                                           -    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_  - - -INFO    'modules/nf-core/fastqc/tests/tags.yml' is unchanged                                        -INFO    'modules/nf-core/fastqc/tests/main.nf.test' is unchanged                                    -INFO    'modules/nf-core/fastqc/tests/main.nf.test.snap' is unchanged                               -INFO     Patch file of 'modules/nf-core/fastqc' written to 'modules/nf-core/fastqc/fastqc.diff' + + $ nf-core modules patch fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Changes in module 'nf-core/fastqc' +INFO    'modules/nf-core/fastqc/environment.yml' is unchanged                                       +INFO    'modules/nf-core/fastqc/meta.yml' is unchanged                                              +INFO     Changes in 'fastqc/main.nf':                                                                + +--- modules/nf-core/fastqc/main.nf ++++ modules/nf-core/fastqc/main.nf +@@ -1,6 +1,6 @@ +process FASTQC {                                                                                   +    tag "$meta.id"                                                                                 +-    label 'process_medium' ++    label 'process_low' + +    conda "${moduleDir}/environment.yml"                                                           +    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_  + + +INFO    'modules/nf-core/fastqc/tests/tags.yml' is unchanged                                        +INFO    'modules/nf-core/fastqc/tests/main.nf.test' is unchanged                                    +INFO    'modules/nf-core/fastqc/tests/main.nf.test.snap' is unchanged                               +INFO     Patch file of 'modules/nf-core/fastqc' written to 'modules/nf-core/fastqc/fastqc.diff' diff --git a/docs/images/nf-core-modules-remove.svg b/docs/images/nf-core-modules-remove.svg index c78034e35c..91f7020043 100644 --- a/docs/images/nf-core-modules-remove.svg +++ b/docs/images/nf-core-modules-remove.svg @@ -19,64 +19,64 @@ font-weight: 700; } - .terminal-3332058498-matrix { + .terminal-2115907041-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3332058498-title { + .terminal-2115907041-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3332058498-r1 { fill: #c5c8c6 } -.terminal-3332058498-r2 { fill: #98a84b } -.terminal-3332058498-r3 { fill: #9a9b99 } -.terminal-3332058498-r4 { fill: #608ab1 } -.terminal-3332058498-r5 { fill: #d0b344 } + .terminal-2115907041-r1 { fill: #c5c8c6 } +.terminal-2115907041-r2 { fill: #98a84b } +.terminal-2115907041-r3 { fill: #9a9b99 } +.terminal-2115907041-r4 { fill: #608ab1 } +.terminal-2115907041-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -88,22 +88,22 @@ - + - - $ nf-core modules remove abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Removed files for 'abacas' and its dependencies 'abacas'.                                   + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Removed files for 'abacas' and its dependencies 'abacas'.                                   diff --git a/docs/images/nf-core-modules-test.svg b/docs/images/nf-core-modules-test.svg index daff523354..52e86ba826 100644 --- a/docs/images/nf-core-modules-test.svg +++ b/docs/images/nf-core-modules-test.svg @@ -19,64 +19,64 @@ font-weight: 700; } - .terminal-2250961056-matrix { + .terminal-9171199-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2250961056-title { + .terminal-9171199-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2250961056-r1 { fill: #c5c8c6 } -.terminal-2250961056-r2 { fill: #98a84b } -.terminal-2250961056-r3 { fill: #9a9b99 } -.terminal-2250961056-r4 { fill: #608ab1 } -.terminal-2250961056-r5 { fill: #d0b344 } + .terminal-9171199-r1 { fill: #c5c8c6 } +.terminal-9171199-r2 { fill: #98a84b } +.terminal-9171199-r3 { fill: #9a9b99 } +.terminal-9171199-r4 { fill: #608ab1 } +.terminal-9171199-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -88,22 +88,22 @@ - + - - $ nf-core modules test fastqc --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Generating nf-test snapshot                                                                 + + $ nf-core modules test fastqc --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Generating nf-test snapshot                                                                 diff --git a/docs/images/nf-core-modules-update.svg b/docs/images/nf-core-modules-update.svg index ddc5facf65..23d9931ce2 100644 --- a/docs/images/nf-core-modules-update.svg +++ b/docs/images/nf-core-modules-update.svg @@ -19,73 +19,73 @@ font-weight: 700; } - .terminal-3937334707-matrix { + .terminal-2984179218-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3937334707-title { + .terminal-2984179218-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3937334707-r1 { fill: #c5c8c6 } -.terminal-3937334707-r2 { fill: #98a84b } -.terminal-3937334707-r3 { fill: #9a9b99 } -.terminal-3937334707-r4 { fill: #608ab1 } -.terminal-3937334707-r5 { fill: #d0b344 } + .terminal-2984179218-r1 { fill: #c5c8c6 } +.terminal-2984179218-r2 { fill: #98a84b } +.terminal-2984179218-r3 { fill: #9a9b99 } +.terminal-2984179218-r4 { fill: #608ab1 } +.terminal-2984179218-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -97,25 +97,25 @@ - + - - $ nf-core modules update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO    'modules/nf-core/abacas' is already up to date                                              -INFO    'modules/nf-core/fastqc' is already up to date                                              -INFO    'modules/nf-core/multiqc' is already up to date                                             -INFO     Updates complete ✨                                                                         + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO    'modules/nf-core/abacas' is already up to date                                              +INFO    'modules/nf-core/fastqc' is already up to date                                              +INFO    'modules/nf-core/multiqc' is already up to date                                             +INFO     Updates complete ✨                                                                         diff --git a/docs/images/nf-core-schema-build.svg b/docs/images/nf-core-schema-build.svg index cf0ab90005..7236440a0d 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-2534001313-matrix { + .terminal-978569984-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2534001313-title { + .terminal-978569984-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2534001313-r1 { fill: #c5c8c6 } -.terminal-2534001313-r2 { fill: #98a84b } -.terminal-2534001313-r3 { fill: #9a9b99 } -.terminal-2534001313-r4 { fill: #608ab1 } -.terminal-2534001313-r5 { fill: #d0b344 } -.terminal-2534001313-r6 { fill: #98a84b;font-weight: bold } -.terminal-2534001313-r7 { fill: #868887;font-weight: bold } -.terminal-2534001313-r8 { fill: #868887 } -.terminal-2534001313-r9 { fill: #4e707b;font-weight: bold } -.terminal-2534001313-r10 { fill: #68a0b3;font-weight: bold } + .terminal-978569984-r1 { fill: #c5c8c6 } +.terminal-978569984-r2 { fill: #98a84b } +.terminal-978569984-r3 { fill: #9a9b99 } +.terminal-978569984-r4 { fill: #608ab1 } +.terminal-978569984-r5 { fill: #d0b344 } +.terminal-978569984-r6 { fill: #98a84b;font-weight: bold } +.terminal-978569984-r7 { fill: #868887;font-weight: bold } +.terminal-978569984-r8 { fill: #868887 } +.terminal-978569984-r9 { fill: #4e707b;font-weight: bold } +.terminal-978569984-r10 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,23 +96,23 @@ - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 30 params) -INFO     Writing schema with 31 params: 'nextflow_schema.json' + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 30 params) +INFO     Writing schema with 31 params: 'nextflow_schema.json' diff --git a/docs/images/nf-core-schema-lint.svg b/docs/images/nf-core-schema-lint.svg index fc3b8f5f31..d08a01144b 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-3503377192-matrix { + .terminal-3566947207-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3503377192-title { + .terminal-3566947207-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3503377192-r1 { fill: #c5c8c6 } -.terminal-3503377192-r2 { fill: #98a84b } -.terminal-3503377192-r3 { fill: #9a9b99 } -.terminal-3503377192-r4 { fill: #608ab1 } -.terminal-3503377192-r5 { fill: #d0b344 } -.terminal-3503377192-r6 { fill: #98a84b;font-weight: bold } -.terminal-3503377192-r7 { fill: #868887;font-weight: bold } -.terminal-3503377192-r8 { fill: #868887 } -.terminal-3503377192-r9 { fill: #4e707b;font-weight: bold } + .terminal-3566947207-r1 { fill: #c5c8c6 } +.terminal-3566947207-r2 { fill: #98a84b } +.terminal-3566947207-r3 { fill: #9a9b99 } +.terminal-3566947207-r4 { fill: #608ab1 } +.terminal-3566947207-r5 { fill: #d0b344 } +.terminal-3566947207-r6 { fill: #98a84b;font-weight: bold } +.terminal-3566947207-r7 { fill: #868887;font-weight: bold } +.terminal-3566947207-r8 { fill: #868887 } +.terminal-3566947207-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -92,22 +92,22 @@ - + - - $ nf-core schema lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 31 params) + + $ nf-core schema lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 31 params) diff --git a/docs/images/nf-core-schema-validate.svg b/docs/images/nf-core-schema-validate.svg index c5bbd59a37..33984ccbeb 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-2855795864-matrix { + .terminal-2456222967-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2855795864-title { + .terminal-2456222967-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2855795864-r1 { fill: #c5c8c6 } -.terminal-2855795864-r2 { fill: #98a84b } -.terminal-2855795864-r3 { fill: #9a9b99 } -.terminal-2855795864-r4 { fill: #608ab1 } -.terminal-2855795864-r5 { fill: #d0b344 } -.terminal-2855795864-r6 { fill: #98a84b;font-weight: bold } -.terminal-2855795864-r7 { fill: #868887;font-weight: bold } -.terminal-2855795864-r8 { fill: #868887 } -.terminal-2855795864-r9 { fill: #4e707b;font-weight: bold } + .terminal-2456222967-r1 { fill: #c5c8c6 } +.terminal-2456222967-r2 { fill: #98a84b } +.terminal-2456222967-r3 { fill: #9a9b99 } +.terminal-2456222967-r4 { fill: #608ab1 } +.terminal-2456222967-r5 { fill: #d0b344 } +.terminal-2456222967-r6 { fill: #98a84b;font-weight: bold } +.terminal-2456222967-r7 { fill: #868887;font-weight: bold } +.terminal-2456222967-r8 { fill: #868887 } +.terminal-2456222967-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -95,23 +95,23 @@ - + - - $ nf-core schema validate nf-core-rnaseq/3_8 nf-params.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 93 params) -INFO    [✓] Input parameters look valid + + $ nf-core schema validate nf-core-rnaseq/3_8 nf-params.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 93 params) +INFO    [✓] Input parameters look valid diff --git a/docs/images/nf-core-subworkflows-create.svg b/docs/images/nf-core-subworkflows-create.svg index e39d489764..fd20914cfe 100644 --- a/docs/images/nf-core-subworkflows-create.svg +++ b/docs/images/nf-core-subworkflows-create.svg @@ -19,89 +19,89 @@ font-weight: 700; } - .terminal-1669631293-matrix { + .terminal-694979996-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1669631293-title { + .terminal-694979996-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1669631293-r1 { fill: #c5c8c6 } -.terminal-1669631293-r2 { fill: #98a84b } -.terminal-1669631293-r3 { fill: #9a9b99 } -.terminal-1669631293-r4 { fill: #608ab1 } -.terminal-1669631293-r5 { fill: #d0b344 } -.terminal-1669631293-r6 { fill: #68a0b3;font-weight: bold } + .terminal-694979996-r1 { fill: #c5c8c6 } +.terminal-694979996-r2 { fill: #98a84b } +.terminal-694979996-r3 { fill: #9a9b99 } +.terminal-694979996-r4 { fill: #608ab1 } +.terminal-694979996-r5 { fill: #d0b344 } +.terminal-694979996-r6 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -113,30 +113,30 @@ - + - - $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Repository type: modules -INFO    Press enter to use default values (shown in brackets)or type your own responses.  -ctrl+click underlined text to open links. -INFO     Created component template: 'bam_stats_samtools' -INFO     Created following files:                                                                    -           subworkflows/nf-core/bam_stats_samtools/main.nf                                           -           subworkflows/nf-core/bam_stats_samtools/meta.yml                                          -           subworkflows/nf-core/bam_stats_samtools/tests/tags.yml                                    -           subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test                                + + $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Repository type: modules +INFO    Press enter to use default values (shown in brackets)or type your own responses.  +ctrl+click underlined text to open links. +INFO     Created component template: 'bam_stats_samtools' +INFO     Created following files:                                                                    +           subworkflows/nf-core/bam_stats_samtools/main.nf                                           +           subworkflows/nf-core/bam_stats_samtools/meta.yml                                          +           subworkflows/nf-core/bam_stats_samtools/tests/tags.yml                                    +           subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test                                diff --git a/docs/images/nf-core-subworkflows-info.svg b/docs/images/nf-core-subworkflows-info.svg index 5e792aaf27..b3f4f38ed3 100644 --- a/docs/images/nf-core-subworkflows-info.svg +++ b/docs/images/nf-core-subworkflows-info.svg @@ -19,112 +19,112 @@ font-weight: 700; } - .terminal-3309876258-matrix { + .terminal-1309193345-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3309876258-title { + .terminal-1309193345-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3309876258-r1 { fill: #c5c8c6 } -.terminal-3309876258-r2 { fill: #98a84b } -.terminal-3309876258-r3 { fill: #9a9b99 } -.terminal-3309876258-r4 { fill: #608ab1 } -.terminal-3309876258-r5 { fill: #d0b344 } -.terminal-3309876258-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3309876258-r7 { fill: #98a84b;font-weight: bold } -.terminal-3309876258-r8 { fill: #868887 } -.terminal-3309876258-r9 { fill: #868887;font-style: italic; } -.terminal-3309876258-r10 { fill: #d08442 } -.terminal-3309876258-r11 { fill: #98729f } + .terminal-1309193345-r1 { fill: #c5c8c6 } +.terminal-1309193345-r2 { fill: #98a84b } +.terminal-1309193345-r3 { fill: #9a9b99 } +.terminal-1309193345-r4 { fill: #608ab1 } +.terminal-1309193345-r5 { fill: #d0b344 } +.terminal-1309193345-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1309193345-r7 { fill: #98a84b;font-weight: bold } +.terminal-1309193345-r8 { fill: #868887 } +.terminal-1309193345-r9 { fill: #868887;font-style: italic; } +.terminal-1309193345-r10 { fill: #d08442 } +.terminal-1309193345-r11 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -136,36 +136,36 @@ - + - - $ nf-core subworkflows info bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -╭─ Subworkflow: bam_rseqc  ────────────────────────────────────────────────────────────────────────╮ -│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ -│ 📖 Description: Subworkflow to run multiple commands in the RSeqC package                        │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -[..truncated..] - readduplication_rscript  (file)    │script to reproduce the plot       │                      *.R -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - tin_txt  (file)                    │TXT file containing tin.py results │                    *.txt -                                     │summary                            │ -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - versions  (file)                   │File containing software versions  │             versions.yml -                                     ╵                                   ╵                           - - 💻  Installation command: nf-core subworkflows install bam_rseqc - + + $ nf-core subworkflows info bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +╭─ Subworkflow: bam_rseqc  ────────────────────────────────────────────────────────────────────────╮ +│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ +│ 📖 Description: Subworkflow to run multiple commands in the RSeqC package                        │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +[..truncated..] + readduplication_rscript  (file)    │script to reproduce the plot       │                      *.R +╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ + tin_txt  (file)                    │TXT file containing tin.py results │                    *.txt +                                     │summary                            │ +╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ + versions  (file)                   │File containing software versions  │             versions.yml +                                     ╵                                   ╵                           + + 💻  Installation command: nf-core subworkflows install bam_rseqc + diff --git a/docs/images/nf-core-subworkflows-install.svg b/docs/images/nf-core-subworkflows-install.svg index 84c9fe6ac9..8c86c3a7e4 100644 --- a/docs/images/nf-core-subworkflows-install.svg +++ b/docs/images/nf-core-subworkflows-install.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + - + - + - - $ nf-core subworkflows install bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Installing 'bam_rseqc' + + $ nf-core subworkflows install bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Installing 'bam_rseqc' +INFO     Use the following statement to include this subworkflow:                                    + + include { BAM_RSEQC } from '../subworkflows/nf-core/bam_rseqc/main'                                 + diff --git a/docs/images/nf-core-subworkflows-lint.svg b/docs/images/nf-core-subworkflows-lint.svg index 3199189c16..7e827661ac 100644 --- a/docs/images/nf-core-subworkflows-lint.svg +++ b/docs/images/nf-core-subworkflows-lint.svg @@ -19,239 +19,239 @@ font-weight: 700; } - .terminal-785643940-matrix { + .terminal-3511810563-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-785643940-title { + .terminal-3511810563-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-785643940-r1 { fill: #c5c8c6 } -.terminal-785643940-r2 { fill: #98a84b } -.terminal-785643940-r3 { fill: #9a9b99 } -.terminal-785643940-r4 { fill: #608ab1 } -.terminal-785643940-r5 { fill: #d0b344 } -.terminal-785643940-r6 { fill: #d0b344;font-weight: bold } -.terminal-785643940-r7 { fill: #8d7b39 } -.terminal-785643940-r8 { fill: #68a0b3;font-weight: bold } -.terminal-785643940-r9 { fill: #d0b344;font-style: italic; } -.terminal-785643940-r10 { fill: #c5c8c6;font-weight: bold } -.terminal-785643940-r11 { fill: #98a84b;font-weight: bold } -.terminal-785643940-r12 { fill: #cc555a } + .terminal-3511810563-r1 { fill: #c5c8c6 } +.terminal-3511810563-r2 { fill: #98a84b } +.terminal-3511810563-r3 { fill: #9a9b99 } +.terminal-3511810563-r4 { fill: #608ab1 } +.terminal-3511810563-r5 { fill: #d0b344 } +.terminal-3511810563-r6 { fill: #d0b344;font-weight: bold } +.terminal-3511810563-r7 { fill: #8d7b39 } +.terminal-3511810563-r8 { fill: #68a0b3;font-weight: bold } +.terminal-3511810563-r9 { fill: #d0b344;font-style: italic; } +.terminal-3511810563-r10 { fill: #c5c8c6;font-weight: bold } +.terminal-3511810563-r11 { fill: #98a84b;font-weight: bold } +.terminal-3511810563-r12 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -263,78 +263,78 @@ - + - - $ nf-core subworkflows lint bam_stats_samtools - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Linting modules repo: '.' -INFO     Linting subworkflow: 'bam_stats_samtools' - -╭─[!] 14 Subworkflow Test Warnings───────────────────────────────────────────────────────────────╮ -│                     ╷                                     ╷                                      │ -│Subworkflow name   │File path                          │Test message                        │ -│╶────────────────────┼─────────────────────────────────────┼─────────────────────────────────────╴│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: //Add │ -│││all required assertions to verify │ -│││the test output.│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Add │ -│││tags for all modules used within │ -│││this subworkflow. Example:│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Change │ -│││the test name preferably indicating │ -│││the test-data and file-format used│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Once │ -│││you have added the required tests, │ -│││please run the following command to │ -│││build this file:│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: define │ -│││inputs of the workflow here. │ -│││Example:│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: A │ -│││subworkflow SHOULD import at least │ -│││two modules│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: If in doubt │ -│││look at other nf-core/subworkflows │ -│││to see how we are doing things! :)│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit emitted│ -│││channels│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit input │ -│││(take) channels│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: substitute │ -│││modules here for the modules of your│ -│││subworkflow│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a │ -│││description of the subworkflow and │ -│││list keywords│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a list│ -│││of the modules and/or subworkflows │ -│││used in the subworkflow│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ -│││of the channels used as input with a│ -│││description and their structure│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ -│││of the channels used as output with │ -│││a descriptions and their structure│ -│                     ╵                                     ╵                                      │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────╮ -│LINT RESULTS SUMMARY│ -├───────────────────────┤ -│[✔]  42 Tests Passed │ -│[!]  14 Test Warnings│ -│[✗]   0 Tests Failed │ -╰───────────────────────╯ + + $ nf-core subworkflows lint bam_stats_samtools + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Linting modules repo: '.' +INFO     Linting subworkflow: 'bam_stats_samtools' + +╭─[!] 14 Subworkflow Test Warnings───────────────────────────────────────────────────────────────╮ +│                     ╷                                     ╷                                      │ +│Subworkflow name   │File path                          │Test message                        │ +│╶────────────────────┼─────────────────────────────────────┼─────────────────────────────────────╴│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: //Add │ +│││all required assertions to verify │ +│││the test output.│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Add │ +│││tags for all modules used within │ +│││this subworkflow. Example:│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Change │ +│││the test name preferably indicating │ +│││the test-data and file-format used│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Once │ +│││you have added the required tests, │ +│││please run the following command to │ +│││build this file:│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: define │ +│││inputs of the workflow here. │ +│││Example:│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: A │ +│││subworkflow SHOULD import at least │ +│││two modules│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: If in doubt │ +│││look at other nf-core/subworkflows │ +│││to see how we are doing things! :)│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit emitted│ +│││channels│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit input │ +│││(take) channels│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: substitute │ +│││modules here for the modules of your│ +│││subworkflow│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a │ +│││description of the subworkflow and │ +│││list keywords│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a list│ +│││of the modules and/or subworkflows │ +│││used in the subworkflow│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ +│││of the channels used as input with a│ +│││description and their structure│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ +│││of the channels used as output with │ +│││a descriptions and their structure│ +│                     ╵                                     ╵                                      │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭───────────────────────╮ +│LINT RESULTS SUMMARY│ +├───────────────────────┤ +│[✔]  42 Tests Passed │ +│[!]  14 Test Warnings│ +│[✗]   0 Tests Failed │ +╰───────────────────────╯ diff --git a/docs/images/nf-core-subworkflows-list-local.svg b/docs/images/nf-core-subworkflows-list-local.svg index 04a21b7708..6bec883e1f 100644 --- a/docs/images/nf-core-subworkflows-list-local.svg +++ b/docs/images/nf-core-subworkflows-list-local.svg @@ -19,108 +19,108 @@ font-weight: 700; } - .terminal-2970876245-matrix { + .terminal-2930702375-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2970876245-title { + .terminal-2930702375-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2970876245-r1 { fill: #c5c8c6 } -.terminal-2970876245-r2 { fill: #98a84b } -.terminal-2970876245-r3 { fill: #9a9b99 } -.terminal-2970876245-r4 { fill: #608ab1 } -.terminal-2970876245-r5 { fill: #d0b344 } -.terminal-2970876245-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2970876245-r7 { fill: #868887;font-style: italic; } + .terminal-2930702375-r1 { fill: #c5c8c6 } +.terminal-2930702375-r2 { fill: #98a84b } +.terminal-2930702375-r3 { fill: #9a9b99 } +.terminal-2930702375-r4 { fill: #608ab1 } +.terminal-2930702375-r5 { fill: #d0b344 } +.terminal-2930702375-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-2930702375-r7 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,36 +132,36 @@ - + - - $ nf-core subworkflows list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Subworkflows installed in '.':                                                              - -self.repo_type='pipeline' -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -┃Subworkflow Name   ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ utils_nextflow_pip… │ https://github.co… │ cd08c91373cd00a732… │ nicer assertions   │ 2024-01-19 │ -│                     │                    │                     │ in utils           │            │ -│                     │                    │                     │ subworkflows       │            │ -│                     │                    │                     │ (#4779)            │            │ -│ utils_nfcore_pipel… │ https://github.co… │ 262b17ed2aad591039… │ Update             │ 2024-02-12 │ -│                     │                    │                     │ utils-nfcore-pipe… │            │ -│                     │                    │                     │ add multiqc report │            │ -│                     │                    │                     │ to completion      │            │ -[..truncated..] + + $ nf-core subworkflows list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Subworkflows installed in '.':                                                              + +self.repo_type='pipeline' +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +┃Subworkflow Name   ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ utils_nextflow_pip… │ https://github.co… │ 5caf7640a9ef1d18d7… │ remove             │ 2024-02-28 │ +│                     │                    │                     │ params.outdir from │            │ +│                     │                    │                     │ modules and        │            │ +│                     │                    │                     │ subworfklows tests │            │ +│                     │                    │                     │ (#5007)            │            │ +│ utils_nfcore_pipel… │ https://github.co… │ 5caf7640a9ef1d18d7… │ remove             │ 2024-02-28 │ +│                     │                    │                     │ params.outdir from │            │ +│                     │                    │                     │ modules and        │            │ +[..truncated..] diff --git a/docs/images/nf-core-subworkflows-list-remote.svg b/docs/images/nf-core-subworkflows-list-remote.svg index 28754bea25..704c2e9a45 100644 --- a/docs/images/nf-core-subworkflows-list-remote.svg +++ b/docs/images/nf-core-subworkflows-list-remote.svg @@ -19,109 +19,109 @@ font-weight: 700; } - .terminal-3053865645-matrix { + .terminal-2294237964-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3053865645-title { + .terminal-2294237964-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3053865645-r1 { fill: #c5c8c6 } -.terminal-3053865645-r2 { fill: #98a84b } -.terminal-3053865645-r3 { fill: #9a9b99 } -.terminal-3053865645-r4 { fill: #608ab1 } -.terminal-3053865645-r5 { fill: #d0b344 } -.terminal-3053865645-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-3053865645-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-3053865645-r8 { fill: #868887;font-style: italic; } + .terminal-2294237964-r1 { fill: #c5c8c6 } +.terminal-2294237964-r2 { fill: #98a84b } +.terminal-2294237964-r3 { fill: #9a9b99 } +.terminal-2294237964-r4 { fill: #608ab1 } +.terminal-2294237964-r5 { fill: #d0b344 } +.terminal-2294237964-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-2294237964-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2294237964-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core subworkflows list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Subworkflow Name                             ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ bam_cnv_wisecondorx                           │ -│ bam_create_som_pon_gatk                       │ -│ bam_dedup_stats_samtools_umitools             │ -│ bam_docounts_contamination_angsd              │ -│ bam_markduplicates_picard                     │ -│ bam_markduplicates_samtools                   │ -│ bam_ngscheckmate                              │ -│ bam_qc_picard                                 │ -│ bam_rseqc                                     │ -[..truncated..] + + $ nf-core subworkflows list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Subworkflow Name                             ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ bam_cnv_wisecondorx                           │ +│ bam_create_som_pon_gatk                       │ +│ bam_dedup_stats_samtools_umitools             │ +│ bam_docounts_contamination_angsd              │ +│ bam_markduplicates_picard                     │ +│ bam_markduplicates_samtools                   │ +│ bam_ngscheckmate                              │ +│ bam_qc_picard                                 │ +│ bam_rseqc                                     │ +[..truncated..] diff --git a/docs/images/nf-core-subworkflows-remove.svg b/docs/images/nf-core-subworkflows-remove.svg index 91bce3c2ef..42c576f4c5 100644 --- a/docs/images/nf-core-subworkflows-remove.svg +++ b/docs/images/nf-core-subworkflows-remove.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + - + - + - - $ nf-core subworkflows remove bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Removed files for 'rseqc/bamstat' and its dependencies 'rseqc/bamstat'.                     -INFO     Removed files for 'rseqc/inferexperiment' and its dependencies 'rseqc/inferexperiment'.     -INFO     Removed files for 'rseqc/innerdistance' and its dependencies 'rseqc/innerdistance'.         -INFO     Removed files for 'rseqc/junctionannotation' and its dependencies                           -'rseqc/junctionannotation'.                                                                 -INFO     Removed files for 'rseqc/junctionsaturation' and its dependencies                           -'rseqc/junctionsaturation'.                                                                 -INFO     Removed files for 'rseqc/readdistribution' and its dependencies 'rseqc/readdistribution'.   -INFO     Removed files for 'bam_rseqc' and its dependencies 'bam_rseqc, rseqc_bamstat,  -rseqc_inferexperiment, rseqc_innerdistance, rseqc_junctionannotation,  -rseqc_junctionsaturation, rseqc_readdistribution'.                                          + + $ nf-core subworkflows remove bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Removed files for 'rseqc/bamstat' and its dependencies 'rseqc/bamstat'.                     +INFO     Removed files for 'rseqc/inferexperiment' and its dependencies 'rseqc/inferexperiment'.     +INFO     Removed files for 'rseqc/innerdistance' and its dependencies 'rseqc/innerdistance'.         +INFO     Removed files for 'rseqc/junctionannotation' and its dependencies                           +'rseqc/junctionannotation'.                                                                 +INFO     Removed files for 'rseqc/junctionsaturation' and its dependencies                           +'rseqc/junctionsaturation'.                                                                 +INFO     Removed files for 'rseqc/readdistribution' and its dependencies 'rseqc/readdistribution'.   +INFO     Removed files for 'rseqc/readduplication' and its dependencies 'rseqc/readduplication'.     +INFO     Removed files for 'rseqc/tin' and its dependencies 'rseqc/tin'.                             +INFO     Removed files for 'bam_rseqc' and its dependencies 'bam_rseqc, rseqc_bamstat,  +rseqc_inferexperiment, rseqc_innerdistance, rseqc_junctionannotation,  +rseqc_junctionsaturation, rseqc_readdistribution, rseqc_readduplication, rseqc_tin'.        diff --git a/docs/images/nf-core-subworkflows-test.svg b/docs/images/nf-core-subworkflows-test.svg index f4261d37f5..9cda6beda6 100644 --- a/docs/images/nf-core-subworkflows-test.svg +++ b/docs/images/nf-core-subworkflows-test.svg @@ -19,64 +19,64 @@ font-weight: 700; } - .terminal-3894408202-matrix { + .terminal-1767175273-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3894408202-title { + .terminal-1767175273-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3894408202-r1 { fill: #c5c8c6 } -.terminal-3894408202-r2 { fill: #98a84b } -.terminal-3894408202-r3 { fill: #9a9b99 } -.terminal-3894408202-r4 { fill: #608ab1 } -.terminal-3894408202-r5 { fill: #d0b344 } + .terminal-1767175273-r1 { fill: #c5c8c6 } +.terminal-1767175273-r2 { fill: #98a84b } +.terminal-1767175273-r3 { fill: #9a9b99 } +.terminal-1767175273-r4 { fill: #608ab1 } +.terminal-1767175273-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -88,22 +88,22 @@ - + - - $ nf-core subworkflows test bam_rseqc --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -INFO     Generating nf-test snapshot                                                                 + + $ nf-core subworkflows test bam_rseqc --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO     Generating nf-test snapshot                                                                 diff --git a/docs/images/nf-core-subworkflows-update.svg b/docs/images/nf-core-subworkflows-update.svg index 64919a7e3d..3398899b7e 100644 --- a/docs/images/nf-core-subworkflows-update.svg +++ b/docs/images/nf-core-subworkflows-update.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + - + - + - - $ nf-core subworkflows update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - - -ERROR   'rseqc/readduplication' + + $ nf-core subworkflows update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + + +INFO    'subworkflows/nf-core/bam_rseqc' is already up to date                                      +INFO    'subworkflows/nf-core/utils_nextflow_pipeline' is already up to date                        +INFO    'subworkflows/nf-core/utils_nfcore_pipeline' is already up to date                          +INFO    'subworkflows/nf-core/utils_nfvalidation_plugin' is already up to date                      +INFO     Updates complete ✨                                                                         diff --git a/docs/images/nf-core-sync.svg b/docs/images/nf-core-sync.svg index 1b2917e5db..b2c6d734fc 100644 --- a/docs/images/nf-core-sync.svg +++ b/docs/images/nf-core-sync.svg @@ -19,91 +19,91 @@ font-weight: 700; } - .terminal-1194172937-matrix { + .terminal-559850088-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1194172937-title { + .terminal-559850088-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1194172937-r1 { fill: #c5c8c6 } -.terminal-1194172937-r2 { fill: #98a84b } -.terminal-1194172937-r3 { fill: #9a9b99 } -.terminal-1194172937-r4 { fill: #608ab1 } -.terminal-1194172937-r5 { fill: #d0b344 } -.terminal-1194172937-r6 { fill: #cc555a } -.terminal-1194172937-r7 { fill: #98729f } -.terminal-1194172937-r8 { fill: #ff2c7a } + .terminal-559850088-r1 { fill: #c5c8c6 } +.terminal-559850088-r2 { fill: #98a84b } +.terminal-559850088-r3 { fill: #9a9b99 } +.terminal-559850088-r4 { fill: #608ab1 } +.terminal-559850088-r5 { fill: #d0b344 } +.terminal-559850088-r6 { fill: #cc555a } +.terminal-559850088-r7 { fill: #98729f } +.terminal-559850088-r8 { fill: #ff2c7a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +115,30 @@ - + - - $ nf-core sync - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.13 - https://nf-co.re - - -WARNING  Could not find GitHub authentication token. Some API requests may fail.                     -INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthing -INFO     Original pipeline repository branch is 'master' -INFO     Deleting all files in 'TEMPLATE' branch                                                     -INFO     Making a new template pipeline using pipeline variables                                     -INFO     Committed changes to 'TEMPLATE' branch                                                      -INFO     Checking out original branch: 'master' -INFO     Now try to merge the updates in to your pipeline:                                           -           cd /home/runner/work/tools/tools/tmp/nf-core-nextbigthing -           git merge TEMPLATE                                                                        + + $ nf-core sync + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.13.1 - https://nf-co.re + + +WARNING  Could not find GitHub authentication token. Some API requests may fail.                     +INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthing +INFO     Original pipeline repository branch is 'master' +INFO     Deleting all files in 'TEMPLATE' branch                                                     +INFO     Making a new template pipeline using pipeline variables                                     +INFO     Committed changes to 'TEMPLATE' branch                                                      +INFO     Checking out original branch: 'master' +INFO     Now try to merge the updates in to your pipeline:                                           +           cd /home/runner/work/tools/tools/tmp/nf-core-nextbigthing +           git merge TEMPLATE