From 99961bedab1518f592668727a4d692c4ddf3c336 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Mon, 19 Dec 2022 11:44:18 +0000 Subject: [PATCH 01/12] Generate new screengrabs with rich-codex --- docs/images/nf-core-bump-version.svg | 88 ++-- docs/images/nf-core-create.svg | 126 ++--- docs/images/nf-core-download.svg | 86 ++-- docs/images/nf-core-launch-rnaseq.svg | 82 ++-- docs/images/nf-core-licences.svg | 130 +++--- docs/images/nf-core-lint.svg | 182 +++----- docs/images/nf-core-list-rna.svg | 118 ++--- docs/images/nf-core-list-stars.svg | 104 ++--- docs/images/nf-core-list.svg | 108 ++--- docs/images/nf-core-modules-bump-version.svg | 106 ++--- docs/images/nf-core-modules-create-test.svg | 98 ++-- docs/images/nf-core-modules-create.svg | 84 ++-- docs/images/nf-core-modules-info.svg | 206 ++++----- docs/images/nf-core-modules-install.svg | 86 ++-- docs/images/nf-core-modules-lint.svg | 112 ++--- docs/images/nf-core-modules-list-local.svg | 130 +++--- docs/images/nf-core-modules-list-remote.svg | 132 +++--- docs/images/nf-core-modules-mulled.svg | 78 ++-- docs/images/nf-core-modules-patch.svg | 72 +-- docs/images/nf-core-modules-remove.svg | 70 +-- docs/images/nf-core-modules-test.svg | 74 +-- docs/images/nf-core-modules-update.svg | 86 ++-- docs/images/nf-core-schema-build.svg | 84 ++-- docs/images/nf-core-schema-lint.svg | 78 ++-- docs/images/nf-core-schema-validate.svg | 82 ++-- .../nf-core-subworkflows-create-test.svg | 128 ++--- docs/images/nf-core-subworkflows-create.svg | 108 ++--- docs/images/nf-core-subworkflows-info.svg | 436 +++++++++--------- docs/images/nf-core-subworkflows-install.svg | 128 ++--- .../nf-core-subworkflows-list-local.svg | 130 +++--- .../nf-core-subworkflows-list-remote.svg | 132 +++--- docs/images/nf-core-subworkflows-remove.svg | 128 ++--- docs/images/nf-core-subworkflows-test.svg | 128 ++--- docs/images/nf-core-subworkflows-update.svg | 128 ++--- docs/images/nf-core-sync.svg | 82 ++-- 35 files changed, 2048 insertions(+), 2082 deletions(-) diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg index d63cc442c5..89843856b2 100644 --- a/docs/images/nf-core-bump-version.svg +++ b/docs/images/nf-core-bump-version.svg @@ -19,77 +19,77 @@ font-weight: 700; } - .terminal-2897532537-matrix { + .terminal-2980173434-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2897532537-title { + .terminal-2980173434-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2897532537-r1 { fill: #c5c8c6 } -.terminal-2897532537-r2 { fill: #98a84b } -.terminal-2897532537-r3 { fill: #9a9b99 } -.terminal-2897532537-r4 { fill: #608ab1 } -.terminal-2897532537-r5 { fill: #d0b344 } -.terminal-2897532537-r6 { fill: #cc555a } + .terminal-2980173434-r1 { fill: #c5c8c6 } +.terminal-2980173434-r2 { fill: #98a84b } +.terminal-2980173434-r3 { fill: #9a9b99 } +.terminal-2980173434-r4 { fill: #608ab1 } +.terminal-2980173434-r5 { fill: #d0b344 } +.terminal-2980173434-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -101,26 +101,26 @@ - + - - $ nf-core bump-version 1.1 - - ,--./,-. - ___ __ __ __ ___ /,-._.--~\ - |\ | |__ __ / ` / \ |__) |__ } { - | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' - - nf-core/tools version 2.7.1 - https://nf-co.re - - -INFO Changing version number from '1.0dev' to '1.1' -INFO Updated version in 'nextflow.config' - - version = '1.0dev' - + version = '1.1' - - + + $ nf-core bump-version 1.1 + + ,--./,-. + ___ __ __ __ ___ /,-._.--~\ + |\ | |__ __ / ` / \ |__) |__ } { + | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' + + nf-core/tools version 2.7.2 - https://nf-co.re + + +INFO Changing version number from '1.0dev' to '1.1' +INFO Updated version in 'nextflow.config' + - version = '1.0dev' + + version = '1.1' + + diff --git a/docs/images/nf-core-create.svg b/docs/images/nf-core-create.svg index 78343c2d34..17b28b0b67 100644 --- a/docs/images/nf-core-create.svg +++ b/docs/images/nf-core-create.svg @@ -19,104 +19,104 @@ font-weight: 700; } - .terminal-3886862987-matrix { + .terminal-4135113356-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3886862987-title { + .terminal-4135113356-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3886862987-r1 { fill: #c5c8c6 } -.terminal-3886862987-r2 { fill: #98a84b } -.terminal-3886862987-r3 { fill: #9a9b99 } -.terminal-3886862987-r4 { fill: #608ab1 } -.terminal-3886862987-r5 { fill: #d0b344 } -.terminal-3886862987-r6 { fill: #98729f } -.terminal-3886862987-r7 { fill: #ff2c7a } -.terminal-3886862987-r8 { fill: #98a84b;font-weight: bold } -.terminal-3886862987-r9 { fill: #1984e9;text-decoration: underline; } + .terminal-4135113356-r1 { fill: #c5c8c6 } +.terminal-4135113356-r2 { fill: #98a84b } +.terminal-4135113356-r3 { fill: #9a9b99 } +.terminal-4135113356-r4 { fill: #608ab1 } +.terminal-4135113356-r5 { fill: #d0b344 } +.terminal-4135113356-r6 { fill: #98729f } +.terminal-4135113356-r7 { fill: #ff2c7a } +.terminal-4135113356-r8 { fill: #98a84b;font-weight: bold } +.terminal-4135113356-r9 { fill: #1984e9;text-decoration: underline; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -128,34 +128,34 @@ - + - - $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" --a "Big Steve" --plain - - ,--./,-. - ___ __ __ __ ___ /,-._.--~\ - |\ | |__ __ / ` / \ |__) |__ } { - | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' - - nf-core/tools version 2.7.1 - 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 + + $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" +-a "Big Steve" --plain + + ,--./,-. + ___ __ __ __ ___ /,-._.--~\ + |\ | |__ __ / ` / \ |__) |__ } { + | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' + + nf-core/tools version 2.7.2 - 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 4db5b62de9..d26c6011d5 100644 --- a/docs/images/nf-core-download.svg +++ b/docs/images/nf-core-download.svg @@ -19,76 +19,76 @@ font-weight: 700; } - .terminal-405352606-matrix { + .terminal-512307359-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-405352606-title { + .terminal-512307359-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-405352606-r1 { fill: #c5c8c6 } -.terminal-405352606-r2 { fill: #98a84b } -.terminal-405352606-r3 { fill: #9a9b99 } -.terminal-405352606-r4 { fill: #608ab1 } -.terminal-405352606-r5 { fill: #d0b344 } + .terminal-512307359-r1 { fill: #c5c8c6 } +.terminal-512307359-r2 { fill: #98a84b } +.terminal-512307359-r3 { fill: #9a9b99 } +.terminal-512307359-r4 { fill: #608ab1 } +.terminal-512307359-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -c none - - ,--./,-. - ___ __ __ __ ___ /,-._.--~\ - |\ | |__ __ / ` / \ |__) |__ } { - | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' - - nf-core/tools version 2.7.1 - https://nf-co.re - - -INFO Saving 'nf-core/rnaseq' - Pipeline revision: '3.8' - Pull containers: 'none' - Output directory: 'nf-core-rnaseq' -INFO Downloading workflow files from GitHub -INFO Downloading centralised configs from GitHub + + $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -c none + + ,--./,-. + ___ __ __ __ ___ /,-._.--~\ + |\ | |__ __ / ` / \ |__) |__ } { + | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' + + nf-core/tools version 2.7.2 - https://nf-co.re + + +INFO Saving 'nf-core/rnaseq' + Pipeline revision: '3.8' + Pull containers: 'none' + Output directory: 'nf-core-rnaseq' +INFO Downloading workflow files from GitHub +INFO Downloading centralised configs from GitHub diff --git a/docs/images/nf-core-launch-rnaseq.svg b/docs/images/nf-core-launch-rnaseq.svg index 52cfc344e2..c36c892e5a 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-3090263558-matrix { + .terminal-3166875143-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3090263558-title { + .terminal-3166875143-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3090263558-r1 { fill: #c5c8c6 } -.terminal-3090263558-r2 { fill: #98a84b } -.terminal-3090263558-r3 { fill: #9a9b99 } -.terminal-3090263558-r4 { fill: #608ab1 } -.terminal-3090263558-r5 { fill: #d0b344 } -.terminal-3090263558-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3090263558-r7 { fill: #68a0b3;font-weight: bold } + .terminal-3166875143-r1 { fill: #c5c8c6 } +.terminal-3166875143-r2 { fill: #98a84b } +.terminal-3166875143-r3 { fill: #9a9b99 } +.terminal-3166875143-r4 { fill: #608ab1 } +.terminal-3166875143-r5 { fill: #d0b344 } +.terminal-3166875143-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3166875143-r7 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,24 +96,24 @@ - + - - $ nf-core launch rnaseq -r 3.8.1 - - ,--./,-. - ___ __ __ __ ___ /,-._.--~\ - |\ | |__ __ / ` / \ |__) |__ } { - | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' - - nf-core/tools version 2.7.1 - https://nf-co.re - - -INFO NOTE: This tool ignores any pipeline parameter defaults overwritten by Nextflow config - files or profiles - -INFO Downloading workflow: nf-core/rnaseq (3.8.1) + + $ nf-core launch rnaseq -r 3.8.1 + + ,--./,-. + ___ __ __ __ ___ /,-._.--~\ + |\ | |__ __ / ` / \ |__) |__ } { + | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' + + nf-core/tools version 2.7.2 - 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 38d2266df9..f96e135487 100644 --- a/docs/images/nf-core-licences.svg +++ b/docs/images/nf-core-licences.svg @@ -19,108 +19,108 @@ font-weight: 700; } - .terminal-3614362229-matrix { + .terminal-3773418102-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3614362229-title { + .terminal-3773418102-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3614362229-r1 { fill: #c5c8c6 } -.terminal-3614362229-r2 { fill: #98a84b } -.terminal-3614362229-r3 { fill: #9a9b99 } -.terminal-3614362229-r4 { fill: #608ab1 } -.terminal-3614362229-r5 { fill: #d0b344 } -.terminal-3614362229-r6 { fill: #68a0b3;font-weight: bold } -.terminal-3614362229-r7 { fill: #c5c8c6;font-weight: bold } + .terminal-3773418102-r1 { fill: #c5c8c6 } +.terminal-3773418102-r2 { fill: #98a84b } +.terminal-3773418102-r3 { fill: #9a9b99 } +.terminal-3773418102-r4 { fill: #608ab1 } +.terminal-3773418102-r5 { fill: #d0b344 } +.terminal-3773418102-r6 { fill: #68a0b3;font-weight: bold } +.terminal-3773418102-r7 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,36 +132,36 @@ - + - - $ nf-core licences deepvariant - - ,--./,-. - ___ __ __ __ ___ /,-._.--~\ - |\ | |__ __ / ` / \ |__) |__ } { - | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' - - nf-core/tools version 2.7.1 - https://nf-co.re - - -INFO Fetching licence information for 8 tools -INFO Warning: This tool only prints licence information for the software tools packaged using - conda. -INFO The pipeline may use other software and dependencies not described here. -┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓ -┃Package Name┃Version┃Licence┃ -┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩ -│ lbzip2 │ 2.5 │ GPL v3 │ -│ deepvariant │ 0.7.0 │ MIT │ -│ htslib │ 1.9 │ MIT │ -│ picard │ 2.18.7 │ MIT │ -│ pip │ 10.0.1 │ MIT │ -│ samtools │ 1.9 │ MIT │ -│ python │ 2.7.15 │ PSF │ -│ bzip2 │ 1.0.6 │ bzip2 │ -└──────────────┴─────────┴─────────┘ + + $ nf-core licences deepvariant + + ,--./,-. + ___ __ __ __ ___ /,-._.--~\ + |\ | |__ __ / ` / \ |__) |__ } { + | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' + + nf-core/tools version 2.7.2 - https://nf-co.re + + +INFO Fetching licence information for 8 tools +INFO Warning: This tool only prints licence information for the software tools packaged using + conda. +INFO The pipeline may use other software and dependencies not described here. +┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓ +┃Package Name┃Version┃Licence┃ +┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩ +│ lbzip2 │ 2.5 │ GPL v3 │ +│ deepvariant │ 0.7.0 │ MIT │ +│ htslib │ 1.9 │ MIT │ +│ picard │ 2.18.7 │ MIT │ +│ pip │ 10.0.1 │ MIT │ +│ samtools │ 1.9 │ MIT │ +│ python │ 2.7.15 │ PSF │ +│ bzip2 │ 1.0.6 │ bzip2 │ +└──────────────┴─────────┴─────────┘ diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg index 6ba942292b..d375ae1f11 100644 --- a/docs/images/nf-core-lint.svg +++ b/docs/images/nf-core-lint.svg @@ -1,4 +1,4 @@ -