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 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - + - + - - $ nf-core lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -INFO     Testing pipeline: . - - -╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ -││ -│pipeline_todos: pipeline_todos│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - -╭─[!] 2 Module Test Warnings─────────────────────────────────────────────────────────────────────╮ -│                                           ╷                          ╷                           │ -│Module name                              │File path               │Test message             │ -│╶──────────────────────────────────────────┼──────────────────────────┼──────────────────────────╴│ -│custom/dumpsoftwareversions│modules/nf-core/custom/…│New version available│ -│fastqc│modules/nf-core/fastqc  │New version available│ -│                                           ╵                          ╵                           │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────╮ -│LINT RESULTS SUMMARY │ -├───────────────────────┤ -│[✔] 178 Tests Passed│ -│[?]   1 Test Ignored│ -│[!]   2 Test Warnings│ -│[✗]   0 Tests Failed│ -╰───────────────────────╯ + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +INFO     Testing pipeline: . + + +╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ +││ +│pipeline_todos: pipeline_todos│ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + +╭───────────────────────╮ +│LINT RESULTS SUMMARY │ +├───────────────────────┤ +│[✔] 181 Tests Passed│ +│[?]   1 Test Ignored│ +│[!]   0 Test Warnings│ +│[✗]   0 Tests Failed│ +╰───────────────────────╯ diff --git a/docs/images/nf-core-list-rna.svg b/docs/images/nf-core-list-rna.svg index 40830b3176..e8346c16ca 100644 --- a/docs/images/nf-core-list-rna.svg +++ b/docs/images/nf-core-list-rna.svg @@ -19,99 +19,99 @@ font-weight: 700; } - .terminal-3770022571-matrix { + .terminal-3844799147-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3770022571-title { + .terminal-3844799147-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3770022571-r1 { fill: #c5c8c6 } -.terminal-3770022571-r2 { fill: #98a84b } -.terminal-3770022571-r3 { fill: #9a9b99 } -.terminal-3770022571-r4 { fill: #608ab1 } -.terminal-3770022571-r5 { fill: #d0b344 } -.terminal-3770022571-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3770022571-r7 { fill: #868887 } + .terminal-3844799147-r1 { fill: #c5c8c6 } +.terminal-3844799147-r2 { fill: #98a84b } +.terminal-3844799147-r3 { fill: #9a9b99 } +.terminal-3844799147-r4 { fill: #608ab1 } +.terminal-3844799147-r5 { fill: #d0b344 } +.terminal-3844799147-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3844799147-r7 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -123,33 +123,33 @@ - + - - $ nf-core list rna rna-seq - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ smrnaseq             │    44 │          2.1.0 │ 1 months ago │           - │ -                   │ -│ rnaseq               │   538 │            3.9 │ 2 months ago │           - │ -                   │ -│ rnafusion            │    83 │          2.1.0 │ 5 months ago │           - │ -                   │ -│ dualrnaseq           │     8 │          1.0.0 │  2 years ago │           - │ -                   │ -│ circrna              │    24 │            dev │            - │           - │ -                   │ -│ lncpipe              │    23 │            dev │            - │           - │ -                   │ -│ scflow               │    14 │            dev │            - │           - │ -                   │ -│ spatialtranscriptom… │    12 │            dev │            - │           - │ -                   │ -└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ + + $ nf-core list rna rna-seq + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ smrnaseq             │    44 │          2.1.0 │ 2 months ago │           - │ -                   │ +│ rnaseq               │   542 │            3.9 │ 3 months ago │           - │ -                   │ +│ rnafusion            │    85 │          2.1.0 │ 5 months ago │           - │ -                   │ +│ dualrnaseq           │     8 │          1.0.0 │  2 years ago │           - │ -                   │ +│ circrna              │    23 │            dev │            - │           - │ -                   │ +│ lncpipe              │    23 │            dev │            - │           - │ -                   │ +│ scflow               │    15 │            dev │            - │           - │ -                   │ +│ spatialtranscriptom… │    12 │            dev │            - │           - │ -                   │ +└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg index af68101512..57c4f1dba1 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-4159699833-matrix { + .terminal-1326709712-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4159699833-title { + .terminal-1326709712-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4159699833-r1 { fill: #c5c8c6 } -.terminal-4159699833-r2 { fill: #98a84b } -.terminal-4159699833-r3 { fill: #9a9b99 } -.terminal-4159699833-r4 { fill: #608ab1 } -.terminal-4159699833-r5 { fill: #d0b344 } -.terminal-4159699833-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-4159699833-r7 { fill: #868887 } -.terminal-4159699833-r8 { fill: #868887;font-style: italic; } + .terminal-1326709712-r1 { fill: #c5c8c6 } +.terminal-1326709712-r2 { fill: #98a84b } +.terminal-1326709712-r3 { fill: #9a9b99 } +.terminal-1326709712-r4 { fill: #608ab1 } +.terminal-1326709712-r5 { fill: #d0b344 } +.terminal-1326709712-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1326709712-r7 { fill: #868887 } +.terminal-1326709712-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -112,29 +112,29 @@ - + - - $ nf-core list -s stars - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq               │   538 │            3.9 │ 2 months ago │           - │ -                   │ -│ sarek                │   210 │          3.1.1 │  2 weeks ago │           - │ -                   │ -│ chipseq              │   133 │          2.0.0 │ 2 months ago │           - │ -                   │ -│ atacseq              │   123 │            2.0 │   1 week ago │           - │ -                   │ -[..truncated..] + + $ nf-core list -s stars + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq               │   542 │            3.9 │ 3 months ago │           - │ -                   │ +│ sarek                │   211 │          3.1.1 │  4 weeks ago │           - │ -                   │ +│ chipseq              │   133 │          2.0.0 │ 3 months ago │           - │ -                   │ +│ atacseq              │   124 │            2.0 │  3 weeks ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg index 24bc71baf4..cf4bc6f125 100644 --- a/docs/images/nf-core-list.svg +++ b/docs/images/nf-core-list.svg @@ -19,91 +19,91 @@ font-weight: 700; } - .terminal-3135274331-matrix { + .terminal-4187913691-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3135274331-title { + .terminal-4187913691-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3135274331-r1 { fill: #c5c8c6 } -.terminal-3135274331-r2 { fill: #98a84b } -.terminal-3135274331-r3 { fill: #9a9b99 } -.terminal-3135274331-r4 { fill: #608ab1 } -.terminal-3135274331-r5 { fill: #d0b344 } -.terminal-3135274331-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3135274331-r7 { fill: #868887 } -.terminal-3135274331-r8 { fill: #868887;font-style: italic; } + .terminal-4187913691-r1 { fill: #c5c8c6 } +.terminal-4187913691-r2 { fill: #98a84b } +.terminal-4187913691-r3 { fill: #9a9b99 } +.terminal-4187913691-r4 { fill: #608ab1 } +.terminal-4187913691-r5 { fill: #d0b344 } +.terminal-4187913691-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-4187913691-r7 { fill: #868887 } +.terminal-4187913691-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +115,30 @@ - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ ampliseq             │   101 │          2.4.1 │ 21 hours ago │           - │ -                   │ -│ airrflow             │    24 │          2.4.0 │   2 days ago │           - │ -                   │ -│ mhcquant             │    21 │          2.4.0 │   6 days ago │           - │ -                   │ -│ atacseq              │   123 │            2.0 │   1 week ago │           - │ -                   │ -│ methylseq            │    95 │          2.2.0 │  1 weeks ago │           - │ -                   │ -[..truncated..] + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ methylseq            │    95 │          2.3.0 │   2 days ago │           - │ -                   │ +│ ampliseq             │   102 │          2.4.1 │  2 weeks ago │           - │ -                   │ +│ airrflow             │    23 │          2.4.0 │  2 weeks ago │           - │ -                   │ +│ mhcquant             │    21 │          2.4.0 │  2 weeks ago │           - │ -                   │ +│ atacseq              │   124 │            2.0 │  3 weeks ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index bdd738ba03..227de6bb26 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-1795029015-matrix { + .terminal-2041051160-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1795029015-title { + .terminal-2041051160-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1795029015-r1 { fill: #c5c8c6 } -.terminal-1795029015-r2 { fill: #98a84b } -.terminal-1795029015-r3 { fill: #9a9b99 } -.terminal-1795029015-r4 { fill: #608ab1 } -.terminal-1795029015-r5 { fill: #d0b344 } -.terminal-1795029015-r6 { fill: #98a84b;font-weight: bold } -.terminal-1795029015-r7 { fill: #c5c8c6;font-weight: bold } + .terminal-2041051160-r1 { fill: #c5c8c6 } +.terminal-2041051160-r2 { fill: #98a84b } +.terminal-2041051160-r3 { fill: #9a9b99 } +.terminal-2041051160-r4 { fill: #608ab1 } +.terminal-2041051160-r5 { fill: #d0b344 } +.terminal-2041051160-r6 { fill: #98a84b;font-weight: bold } +.terminal-2041051160-r7 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -114,30 +114,30 @@ - + - - $ nf-core modules bump-versions fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - - -╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ -│[!] 1 Module version up to date.│ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ -│Module name                             │Update Message                                       │ -├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ -│ fastqc                                   │ Module version up to date: fastqc                     │ -╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ + + $ nf-core modules bump-versions fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + + +╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ +│[!] 1 Module version up to date.│ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ +│Module name                             │Update Message                                       │ +├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ +│ fastqc                                   │ Module version up to date: fastqc                     │ +╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ diff --git a/docs/images/nf-core-modules-create-test.svg b/docs/images/nf-core-modules-create-test.svg index ab9e254f37..57e29b961f 100644 --- a/docs/images/nf-core-modules-create-test.svg +++ b/docs/images/nf-core-modules-create-test.svg @@ -19,84 +19,84 @@ font-weight: 700; } - .terminal-1810277116-matrix { + .terminal-474522378-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1810277116-title { + .terminal-474522378-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1810277116-r1 { fill: #c5c8c6 } -.terminal-1810277116-r2 { fill: #98a84b } -.terminal-1810277116-r3 { fill: #9a9b99 } -.terminal-1810277116-r4 { fill: #608ab1 } -.terminal-1810277116-r5 { fill: #d0b344 } -.terminal-1810277116-r6 { fill: #ff2c7a } -.terminal-1810277116-r7 { fill: #98729f } + .terminal-474522378-r1 { fill: #c5c8c6 } +.terminal-474522378-r2 { fill: #98a84b } +.terminal-474522378-r3 { fill: #9a9b99 } +.terminal-474522378-r4 { fill: #608ab1 } +.terminal-474522378-r5 { fill: #d0b344 } +.terminal-474522378-r6 { fill: #ff2c7a } +.terminal-474522378-r7 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -108,28 +108,28 @@ - + - - $ nf-core modules create-test-yml fastqc --no-prompts --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -INFO     Looking for test workflow entry points: 'tests/modules/nf-core/fastqc/main.nf' -──────────────────────────────────────────────────────────────────────────────────────────────────── -INFO     Building test meta for entry point 'test_fastqc_single_end' -INFO     Running 'fastqc' test with command:                                                         -nextflow run ./tests/modules/nf-core/fastqc -entry test_fastqc_single_end -c  -./tests/config/nextflow.config -c ./tests/modules/nf-core/fastqc/nextflow.config --outdir  -/tmp/tmplzj5q_cr -work-dir /tmp/tmpwkq3pr51 + + $ nf-core modules create-test-yml fastqc --no-prompts --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +INFO     Looking for test workflow entry points: 'tests/modules/nf-core/fastqc/main.nf' +──────────────────────────────────────────────────────────────────────────────────────────────────── +INFO     Building test meta for entry point 'test_fastqc_single_end' +INFO     Running 'fastqc' test with command:                                                         +nextflow run ./tests/modules/nf-core/fastqc -entry test_fastqc_single_end -c  +./tests/config/nextflow.config -c ./tests/modules/nf-core/fastqc/nextflow.config --outdir  +/tmp/tmp17isquh4 -work-dir /tmp/tmpseaglcoa diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index 82c008269b..6b3ce27a41 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-2925538580-matrix { + .terminal-3073846549-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2925538580-title { + .terminal-3073846549-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2925538580-r1 { fill: #c5c8c6 } -.terminal-2925538580-r2 { fill: #98a84b } -.terminal-2925538580-r3 { fill: #9a9b99 } -.terminal-2925538580-r4 { fill: #608ab1 } -.terminal-2925538580-r5 { fill: #d0b344 } -.terminal-2925538580-r6 { fill: #68a0b3;font-weight: bold } + .terminal-3073846549-r1 { fill: #c5c8c6 } +.terminal-3073846549-r2 { fill: #98a84b } +.terminal-3073846549-r3 { fill: #9a9b99 } +.terminal-3073846549-r4 { fill: #608ab1 } +.terminal-3073846549-r5 { fill: #d0b344 } +.terminal-3073846549-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 2.7.1 - https://nf-co.re - - - -INFO     Repository type: modules -INFO    Press enter to use default values (shown in brackets)or type your own responses.  -ctrl+click underlined text to open links. -INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9' + + $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +INFO     Repository type: modules +INFO    Press enter to use default values (shown in brackets)or type your own responses.  +ctrl+click underlined text to open links. +INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9' diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg index b3f667942c..320672f91a 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-2882269783-matrix { + .terminal-3462197848-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2882269783-title { + .terminal-3462197848-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2882269783-r1 { fill: #c5c8c6 } -.terminal-2882269783-r2 { fill: #98a84b } -.terminal-2882269783-r3 { fill: #9a9b99 } -.terminal-2882269783-r4 { fill: #608ab1 } -.terminal-2882269783-r5 { fill: #d0b344 } -.terminal-2882269783-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2882269783-r7 { fill: #98a84b;font-weight: bold } -.terminal-2882269783-r8 { fill: #868887 } -.terminal-2882269783-r9 { fill: #d08442 } -.terminal-2882269783-r10 { fill: #868887;font-style: italic; } -.terminal-2882269783-r11 { fill: #98729f } + .terminal-3462197848-r1 { fill: #c5c8c6 } +.terminal-3462197848-r2 { fill: #98a84b } +.terminal-3462197848-r3 { fill: #9a9b99 } +.terminal-3462197848-r4 { fill: #608ab1 } +.terminal-3462197848-r5 { fill: #d0b344 } +.terminal-3462197848-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3462197848-r7 { fill: #98a84b;font-weight: bold } +.terminal-3462197848-r8 { fill: #868887 } +.terminal-3462197848-r9 { fill: #d08442 } +.terminal-3462197848-r10 { fill: #868887;font-style: italic; } +.terminal-3462197848-r11 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -187,53 +187,53 @@ - + - - $ nf-core modules info abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ -│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ -│ 🔧 Tools: abacas                                                                                 │ -│ 📖 Description: contiguate draft genome assembly                                                 │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -                  ╷                                                                   ╷              -📥 Inputs        │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} -                  ╵                                                                   ╵              -                  ╷                                                                   ╷              -📤 Outputs       │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - results  (files)│List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* -                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ -                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ -                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ -                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - versions  (file)│File containing software versions                                  │versions.yml -                  ╵                                                                   ╵              - - 💻  Installation command: nf-core modules install abacas - + + $ nf-core modules info abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ +│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ +│ 🔧 Tools: abacas                                                                                 │ +│ 📖 Description: contiguate draft genome assembly                                                 │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +                  ╷                                                                   ╷              +📥 Inputs        │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} +                  ╵                                                                   ╵              +                  ╷                                                                   ╷              +📤 Outputs       │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + results  (files)│List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* +                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ +                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ +                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ +                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + versions  (file)│File containing software versions                                  │versions.yml +                  ╵                                                                   ╵              + + 💻  Installation command: nf-core modules install abacas + diff --git a/docs/images/nf-core-modules-install.svg b/docs/images/nf-core-modules-install.svg index fa6c7b941c..6fb029df0a 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-3882716258-matrix { + .terminal-3957689443-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3882716258-title { + .terminal-3957689443-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3882716258-r1 { fill: #c5c8c6 } -.terminal-3882716258-r2 { fill: #98a84b } -.terminal-3882716258-r3 { fill: #9a9b99 } -.terminal-3882716258-r4 { fill: #608ab1 } -.terminal-3882716258-r5 { fill: #d0b344 } + .terminal-3957689443-r1 { fill: #c5c8c6 } +.terminal-3957689443-r2 { fill: #98a84b } +.terminal-3957689443-r3 { fill: #9a9b99 } +.terminal-3957689443-r4 { fill: #608ab1 } +.terminal-3957689443-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core modules install abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -INFO     Installing 'abacas' -INFO     Use the following statement to include this module:                                         - - include { ABACAS } from '../modules/nf-core/abacas/main'                                            - + + $ nf-core modules install abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - 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 f63cf77d39..b39f7aa4fd 100644 --- a/docs/images/nf-core-modules-lint.svg +++ b/docs/images/nf-core-modules-lint.svg @@ -19,94 +19,94 @@ font-weight: 700; } - .terminal-3569125489-matrix { + .terminal-3722872946-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3569125489-title { + .terminal-3722872946-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3569125489-r1 { fill: #c5c8c6 } -.terminal-3569125489-r2 { fill: #98a84b } -.terminal-3569125489-r3 { fill: #9a9b99 } -.terminal-3569125489-r4 { fill: #608ab1 } -.terminal-3569125489-r5 { fill: #d0b344 } -.terminal-3569125489-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3569125489-r7 { fill: #98a84b;font-weight: bold } -.terminal-3569125489-r8 { fill: #cc555a } + .terminal-3722872946-r1 { fill: #c5c8c6 } +.terminal-3722872946-r2 { fill: #98a84b } +.terminal-3722872946-r3 { fill: #9a9b99 } +.terminal-3722872946-r4 { fill: #608ab1 } +.terminal-3722872946-r5 { fill: #d0b344 } +.terminal-3722872946-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3722872946-r7 { fill: #98a84b;font-weight: bold } +.terminal-3722872946-r8 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -118,31 +118,31 @@ - + - - $ nf-core modules lint multiqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -INFO     Linting modules repo: '.' -INFO     Linting module: 'multiqc' - -╭───────────────────────╮ -│LINT RESULTS SUMMARY│ -├───────────────────────┤ -│[✔]  23 Tests Passed │ -│[!]   0 Test Warnings│ -│[✗]   0 Tests Failed │ -╰───────────────────────╯ + + $ nf-core modules lint multiqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +INFO     Linting modules repo: '.' +INFO     Linting module: 'multiqc' + +╭───────────────────────╮ +│LINT RESULTS SUMMARY│ +├───────────────────────┤ +│[✔]  23 Tests Passed │ +│[!]   0 Test Warnings│ +│[✗]   0 Tests Failed │ +╰───────────────────────╯ diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index c2cbe2b236..fab2cecf7e 100644 --- a/docs/images/nf-core-modules-list-local.svg +++ b/docs/images/nf-core-modules-list-local.svg @@ -19,108 +19,108 @@ font-weight: 700; } - .terminal-801966325-matrix { + .terminal-2617511112-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-801966325-title { + .terminal-2617511112-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-801966325-r1 { fill: #c5c8c6 } -.terminal-801966325-r2 { fill: #98a84b } -.terminal-801966325-r3 { fill: #9a9b99 } -.terminal-801966325-r4 { fill: #608ab1 } -.terminal-801966325-r5 { fill: #d0b344 } -.terminal-801966325-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-801966325-r7 { fill: #868887;font-style: italic; } + .terminal-2617511112-r1 { fill: #c5c8c6 } +.terminal-2617511112-r2 { fill: #98a84b } +.terminal-2617511112-r3 { fill: #9a9b99 } +.terminal-2617511112-r4 { fill: #608ab1 } +.terminal-2617511112-r5 { fill: #d0b344 } +.terminal-2617511112-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-2617511112-r7 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,36 +132,36 @@ - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -INFO     Modules installed in '.':                                                                   - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -┃Module Name        ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ custom/dumpsoftwar… │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ -│                     │                    │                     │ nf-core/modules    │            │ -│                     │                    │                     │ repo (#2141)       │            │ -│ fastqc              │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ -│                     │                    │                     │ nf-core/modules    │            │ -│                     │                    │                     │ repo (#2141)       │            │ -│ multiqc             │ https://github.co… │ 5e34754d42cd2d5d24… │ Restructure        │ 2022-10-04 │ -│                     │                    │                     │ nf-core/modules    │            │ -│                     │                    │                     │ repo (#2141)       │            │ -[..truncated..] + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +INFO     Modules installed in '.':                                                                   + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +┃Module Name        ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ custom/dumpsoftwar… │ https://github.co… │ c8e35eb2055c099720… │ Bulk change conda  │ 2022-12-13 │ +│                     │                    │                     │ syntax for all     │            │ +│                     │                    │                     │ modules (#2654)    │            │ +│ fastqc              │ https://github.co… │ c8e35eb2055c099720… │ Bulk change conda  │ 2022-12-13 │ +│                     │                    │                     │ syntax for all     │            │ +│                     │                    │                     │ modules (#2654)    │            │ +│ multiqc             │ https://github.co… │ c8e35eb2055c099720… │ Bulk change conda  │ 2022-12-13 │ +│                     │                    │                     │ syntax for all     │            │ +│                     │                    │                     │ modules (#2654)    │            │ +[..truncated..] diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index 701b00db57..cd2d1df6e5 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-3298778939-matrix { + .terminal-3444989756-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3298778939-title { + .terminal-3444989756-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3298778939-r1 { fill: #c5c8c6 } -.terminal-3298778939-r2 { fill: #98a84b } -.terminal-3298778939-r3 { fill: #9a9b99 } -.terminal-3298778939-r4 { fill: #608ab1 } -.terminal-3298778939-r5 { fill: #d0b344 } -.terminal-3298778939-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-3298778939-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-3298778939-r8 { fill: #868887;font-style: italic; } + .terminal-3444989756-r1 { fill: #c5c8c6 } +.terminal-3444989756-r2 { fill: #98a84b } +.terminal-3444989756-r3 { fill: #9a9b99 } +.terminal-3444989756-r4 { fill: #608ab1 } +.terminal-3444989756-r5 { fill: #d0b344 } +.terminal-3444989756-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-3444989756-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-3444989756-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core modules list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -INFO     Modules available from https://github.com/nf-core/modules.git(master):                     - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Module Name                                          ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ abacas                                                │ -│ abricate/run                                          │ -│ abricate/summary                                      │ -│ adapterremoval                                        │ -│ adapterremovalfixprefix                               │ -│ agat/convertspgff2gtf                                 │ -│ agat/convertspgxf2gxf                                 │ -│ agat/spstatistics                                     │ -│ agat/sqstatbasic                                      │ -[..truncated..] + + $ nf-core modules list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +INFO     Modules available from https://github.com/nf-core/modules.git(master):                     + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Module Name                                          ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ abacas                                                │ +│ abricate/run                                          │ +│ abricate/summary                                      │ +│ adapterremoval                                        │ +│ adapterremovalfixprefix                               │ +│ agat/convertspgff2gtf                                 │ +│ agat/convertspgxf2gxf                                 │ +│ agat/spstatistics                                     │ +│ agat/sqstatbasic                                      │ +[..truncated..] diff --git a/docs/images/nf-core-modules-mulled.svg b/docs/images/nf-core-modules-mulled.svg index b6ead66b4b..2ac4b28f23 100644 --- a/docs/images/nf-core-modules-mulled.svg +++ b/docs/images/nf-core-modules-mulled.svg @@ -19,69 +19,69 @@ font-weight: 700; } - .terminal-1123202598-matrix { + .terminal-1198110247-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1123202598-title { + .terminal-1198110247-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1123202598-r1 { fill: #c5c8c6 } -.terminal-1123202598-r2 { fill: #98a84b } -.terminal-1123202598-r3 { fill: #9a9b99 } -.terminal-1123202598-r4 { fill: #608ab1 } -.terminal-1123202598-r5 { fill: #d0b344 } -.terminal-1123202598-r6 { fill: #00823d;font-weight: bold } -.terminal-1123202598-r7 { fill: #68a0b3;font-weight: bold } + .terminal-1198110247-r1 { fill: #c5c8c6 } +.terminal-1198110247-r2 { fill: #98a84b } +.terminal-1198110247-r3 { fill: #9a9b99 } +.terminal-1198110247-r4 { fill: #608ab1 } +.terminal-1198110247-r5 { fill: #d0b344 } +.terminal-1198110247-r6 { fill: #00823d;font-weight: bold } +.terminal-1198110247-r7 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -93,23 +93,23 @@ - + - - $ nf-core modules mulled pysam==0.16.0.1 biopython==1.78 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - -INFO     Found docker image on quay.io! ✨                                                           -INFO     Mulled container hash:                                                                      -mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 + + $ nf-core modules mulled pysam==0.16.0.1 biopython==1.78 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + +INFO     Found docker image on quay.io! ✨                                                           +INFO     Mulled container hash:                                                                      +mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 diff --git a/docs/images/nf-core-modules-patch.svg b/docs/images/nf-core-modules-patch.svg index f54bff1e97..729bb1d519 100644 --- a/docs/images/nf-core-modules-patch.svg +++ b/docs/images/nf-core-modules-patch.svg @@ -19,65 +19,65 @@ font-weight: 700; } - .terminal-2789283426-matrix { + .terminal-2827097699-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2789283426-title { + .terminal-2827097699-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2789283426-r1 { fill: #c5c8c6 } -.terminal-2789283426-r2 { fill: #98a84b } -.terminal-2789283426-r3 { fill: #9a9b99 } -.terminal-2789283426-r4 { fill: #608ab1 } -.terminal-2789283426-r5 { fill: #d0b344 } -.terminal-2789283426-r6 { fill: #cc555a;font-weight: bold } + .terminal-2827097699-r1 { fill: #c5c8c6 } +.terminal-2827097699-r2 { fill: #98a84b } +.terminal-2827097699-r3 { fill: #9a9b99 } +.terminal-2827097699-r4 { fill: #608ab1 } +.terminal-2827097699-r5 { fill: #d0b344 } +.terminal-2827097699-r6 { fill: #cc555a;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -89,22 +89,22 @@ - + - - $ nf-core modules patch fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -ERROR    Module 'modules/nf-core/fastqc' is unchanged. No patch to compute                           + + $ nf-core modules patch fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +ERROR    Module 'modules/nf-core/fastqc' is unchanged. No patch to compute                           diff --git a/docs/images/nf-core-modules-remove.svg b/docs/images/nf-core-modules-remove.svg index e495def404..ce72c00e13 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-2407804337-matrix { + .terminal-2450992562-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2407804337-title { + .terminal-2450992562-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2407804337-r1 { fill: #c5c8c6 } -.terminal-2407804337-r2 { fill: #98a84b } -.terminal-2407804337-r3 { fill: #9a9b99 } -.terminal-2407804337-r4 { fill: #608ab1 } -.terminal-2407804337-r5 { fill: #d0b344 } + .terminal-2450992562-r1 { fill: #c5c8c6 } +.terminal-2450992562-r2 { fill: #98a84b } +.terminal-2450992562-r3 { fill: #9a9b99 } +.terminal-2450992562-r4 { fill: #608ab1 } +.terminal-2450992562-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -88,22 +88,22 @@ - + - - $ nf-core modules remove abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -INFO     Removed files for 'abacas' and it's dependencies 'abacas'.                                  + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +INFO     Removed files for 'abacas' and it's dependencies 'abacas'.                                  diff --git a/docs/images/nf-core-modules-test.svg b/docs/images/nf-core-modules-test.svg index 1ff788e24b..c11314a7d1 100644 --- a/docs/images/nf-core-modules-test.svg +++ b/docs/images/nf-core-modules-test.svg @@ -19,67 +19,67 @@ font-weight: 700; } - .terminal-367250223-matrix { + .terminal-424201008-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-367250223-title { + .terminal-424201008-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-367250223-r1 { fill: #c5c8c6 } -.terminal-367250223-r2 { fill: #98a84b } -.terminal-367250223-r3 { fill: #9a9b99 } -.terminal-367250223-r4 { fill: #608ab1 } -.terminal-367250223-r5 { fill: #d0b344 } + .terminal-424201008-r1 { fill: #c5c8c6 } +.terminal-424201008-r2 { fill: #98a84b } +.terminal-424201008-r3 { fill: #9a9b99 } +.terminal-424201008-r4 { fill: #608ab1 } +.terminal-424201008-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -91,23 +91,23 @@ - + - - $ nf-core modules test samtools/view --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -────────────────────────────────────────── samtools/view ─────────────────────────────────────────── -INFO     Running pytest for module 'samtools/view' + + $ nf-core modules test samtools/view --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +────────────────────────────────────────── samtools/view ─────────────────────────────────────────── +INFO     Running pytest for module 'samtools/view' diff --git a/docs/images/nf-core-modules-update.svg b/docs/images/nf-core-modules-update.svg index 34ee63f06e..161c6b2a56 100644 --- a/docs/images/nf-core-modules-update.svg +++ b/docs/images/nf-core-modules-update.svg @@ -19,76 +19,76 @@ font-weight: 700; } - .terminal-586434981-matrix { + .terminal-555766662-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-586434981-title { + .terminal-555766662-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-586434981-r1 { fill: #c5c8c6 } -.terminal-586434981-r2 { fill: #98a84b } -.terminal-586434981-r3 { fill: #9a9b99 } -.terminal-586434981-r4 { fill: #608ab1 } -.terminal-586434981-r5 { fill: #d0b344 } + .terminal-555766662-r1 { fill: #c5c8c6 } +.terminal-555766662-r2 { fill: #98a84b } +.terminal-555766662-r3 { fill: #9a9b99 } +.terminal-555766662-r4 { fill: #608ab1 } +.terminal-555766662-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core modules update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -INFO    'modules/nf-core/abacas' is already up to date                                              -INFO     Updating 'nf-core/custom/dumpsoftwareversions' -INFO     Updating 'nf-core/fastqc' -INFO    'modules/nf-core/multiqc' is already up to date                                             -INFO     Updates complete ✨                                                                         + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +INFO    'modules/nf-core/abacas' is already up to date                                              +INFO    'modules/nf-core/custom/dumpsoftwareversions' 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 91b1c4482f..ac95ebba84 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-1763756786-matrix { + .terminal-1833749233-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1763756786-title { + .terminal-1833749233-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1763756786-r1 { fill: #c5c8c6 } -.terminal-1763756786-r2 { fill: #98a84b } -.terminal-1763756786-r3 { fill: #9a9b99 } -.terminal-1763756786-r4 { fill: #608ab1 } -.terminal-1763756786-r5 { fill: #d0b344 } -.terminal-1763756786-r6 { fill: #98a84b;font-weight: bold } -.terminal-1763756786-r7 { fill: #868887;font-weight: bold } -.terminal-1763756786-r8 { fill: #868887 } -.terminal-1763756786-r9 { fill: #4e707b;font-weight: bold } -.terminal-1763756786-r10 { fill: #68a0b3;font-weight: bold } + .terminal-1833749233-r1 { fill: #c5c8c6 } +.terminal-1833749233-r2 { fill: #98a84b } +.terminal-1833749233-r3 { fill: #9a9b99 } +.terminal-1833749233-r4 { fill: #608ab1 } +.terminal-1833749233-r5 { fill: #d0b344 } +.terminal-1833749233-r6 { fill: #98a84b;font-weight: bold } +.terminal-1833749233-r7 { fill: #868887;font-weight: bold } +.terminal-1833749233-r8 { fill: #868887 } +.terminal-1833749233-r9 { fill: #4e707b;font-weight: bold } +.terminal-1833749233-r10 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,23 +96,23 @@ - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 31 params) -INFO     Writing schema with 32 params: './nextflow_schema.json' + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - 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 9bb3f251e6..79113e70ec 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-953635754-matrix { + .terminal-1041388458-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-953635754-title { + .terminal-1041388458-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-953635754-r1 { fill: #c5c8c6 } -.terminal-953635754-r2 { fill: #98a84b } -.terminal-953635754-r3 { fill: #9a9b99 } -.terminal-953635754-r4 { fill: #608ab1 } -.terminal-953635754-r5 { fill: #d0b344 } -.terminal-953635754-r6 { fill: #98a84b;font-weight: bold } -.terminal-953635754-r7 { fill: #868887;font-weight: bold } -.terminal-953635754-r8 { fill: #868887 } -.terminal-953635754-r9 { fill: #4e707b;font-weight: bold } + .terminal-1041388458-r1 { fill: #c5c8c6 } +.terminal-1041388458-r2 { fill: #98a84b } +.terminal-1041388458-r3 { fill: #9a9b99 } +.terminal-1041388458-r4 { fill: #608ab1 } +.terminal-1041388458-r5 { fill: #d0b344 } +.terminal-1041388458-r6 { fill: #98a84b;font-weight: bold } +.terminal-1041388458-r7 { fill: #868887;font-weight: bold } +.terminal-1041388458-r8 { fill: #868887 } +.terminal-1041388458-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -92,22 +92,22 @@ - + - - $ nf-core schema lint nextflow_schema.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 32 params) + + $ nf-core schema lint nextflow_schema.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - 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 8cc98e50b9..3133ec66b8 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-2859597691-matrix { + .terminal-2998337404-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2859597691-title { + .terminal-2998337404-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2859597691-r1 { fill: #c5c8c6 } -.terminal-2859597691-r2 { fill: #98a84b } -.terminal-2859597691-r3 { fill: #9a9b99 } -.terminal-2859597691-r4 { fill: #608ab1 } -.terminal-2859597691-r5 { fill: #d0b344 } -.terminal-2859597691-r6 { fill: #98a84b;font-weight: bold } -.terminal-2859597691-r7 { fill: #868887;font-weight: bold } -.terminal-2859597691-r8 { fill: #868887 } -.terminal-2859597691-r9 { fill: #4e707b;font-weight: bold } + .terminal-2998337404-r1 { fill: #c5c8c6 } +.terminal-2998337404-r2 { fill: #98a84b } +.terminal-2998337404-r3 { fill: #9a9b99 } +.terminal-2998337404-r4 { fill: #608ab1 } +.terminal-2998337404-r5 { fill: #d0b344 } +.terminal-2998337404-r6 { fill: #98a84b;font-weight: bold } +.terminal-2998337404-r7 { fill: #868887;font-weight: bold } +.terminal-2998337404-r8 { fill: #868887 } +.terminal-2998337404-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -95,23 +95,23 @@ - + - - $ nf-core schema validate nf-core-rnaseq/workflow nf-params.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 93 params) -INFO    [✓] Input parameters look valid + + $ nf-core schema validate nf-core-rnaseq/workflow nf-params.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 93 params) +INFO    [✓] Input parameters look valid diff --git a/docs/images/nf-core-subworkflows-create-test.svg b/docs/images/nf-core-subworkflows-create-test.svg index efe5f5bd5e..5e8841a50e 100644 --- a/docs/images/nf-core-subworkflows-create-test.svg +++ b/docs/images/nf-core-subworkflows-create-test.svg @@ -19,107 +19,107 @@ font-weight: 700; } - .terminal-374083174-matrix { + .terminal-464653927-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-374083174-title { + .terminal-464653927-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-374083174-r1 { fill: #c5c8c6 } -.terminal-374083174-r2 { fill: #98a84b } -.terminal-374083174-r3 { fill: #9a9b99 } -.terminal-374083174-r4 { fill: #608ab1 } -.terminal-374083174-r5 { fill: #d0b344 } -.terminal-374083174-r6 { fill: #cc555a } + .terminal-464653927-r1 { fill: #c5c8c6 } +.terminal-464653927-r2 { fill: #98a84b } +.terminal-464653927-r3 { fill: #9a9b99 } +.terminal-464653927-r4 { fill: #608ab1 } +.terminal-464653927-r5 { fill: #d0b344 } +.terminal-464653927-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -131,36 +131,36 @@ - + - - $ nf-core subworkflows create-test-yml bam_stats_samtools --no-prompts --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -WARNING 'repository_type' not defined in .nf-core.yml                                               -Warning: Input is not a terminal (fd=0). -? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - » Pipeline -   nf-core/modules - - - -        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - -Aborted. + + $ nf-core subworkflows create-test-yml bam_stats_samtools --no-prompts --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. diff --git a/docs/images/nf-core-subworkflows-create.svg b/docs/images/nf-core-subworkflows-create.svg index 9542f9758d..763a5a5d94 100644 --- a/docs/images/nf-core-subworkflows-create.svg +++ b/docs/images/nf-core-subworkflows-create.svg @@ -19,90 +19,90 @@ font-weight: 700; } - .terminal-2185943670-matrix { + .terminal-2389301879-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2185943670-title { + .terminal-2389301879-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2185943670-r1 { fill: #c5c8c6 } -.terminal-2185943670-r2 { fill: #98a84b } -.terminal-2185943670-r3 { fill: #9a9b99 } -.terminal-2185943670-r4 { fill: #608ab1 } -.terminal-2185943670-r5 { fill: #d0b344 } -.terminal-2185943670-r6 { fill: #68a0b3;font-weight: bold } -.terminal-2185943670-r7 { fill: #868887 } -.terminal-2185943670-r8 { fill: #4a637a } -.terminal-2185943670-r9 { fill: #4a637a;font-weight: bold } -.terminal-2185943670-r10 { fill: #cc555a } + .terminal-2389301879-r1 { fill: #c5c8c6 } +.terminal-2389301879-r2 { fill: #98a84b } +.terminal-2389301879-r3 { fill: #9a9b99 } +.terminal-2389301879-r4 { fill: #608ab1 } +.terminal-2389301879-r5 { fill: #d0b344 } +.terminal-2389301879-r6 { fill: #68a0b3;font-weight: bold } +.terminal-2389301879-r7 { fill: #868887 } +.terminal-2389301879-r8 { fill: #4a637a } +.terminal-2389301879-r9 { fill: #4a637a;font-weight: bold } +.terminal-2389301879-r10 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -114,29 +114,29 @@ - + - - $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot  --label process_low --meta  ---force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -Usage: nf-core subworkflows create [OPTIONS] subworkflow name                                       - -Try 'nf-core subworkflows create -h' for help. -╭─ Error ──────────────────────────────────────────────────────────────────────────────────────────╮ -│ No such option: --label Did you mean --help?                                                     │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - + + $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot  --label process_low --meta  +--force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +Usage: nf-core subworkflows create [OPTIONS] subworkflow name                                       + +Try 'nf-core subworkflows create -h' for help. +╭─ Error ──────────────────────────────────────────────────────────────────────────────────────────╮ +│ No such option: --label Did you mean --help?                                                     │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + diff --git a/docs/images/nf-core-subworkflows-info.svg b/docs/images/nf-core-subworkflows-info.svg index 680dbfc817..b00f918056 100644 --- a/docs/images/nf-core-subworkflows-info.svg +++ b/docs/images/nf-core-subworkflows-info.svg @@ -19,333 +19,333 @@ font-weight: 700; } - .terminal-1096786593-matrix { + .terminal-884777647-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1096786593-title { + .terminal-884777647-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1096786593-r1 { fill: #c5c8c6 } -.terminal-1096786593-r2 { fill: #98a84b } -.terminal-1096786593-r3 { fill: #9a9b99 } -.terminal-1096786593-r4 { fill: #608ab1 } -.terminal-1096786593-r5 { fill: #d0b344 } -.terminal-1096786593-r6 { fill: #cc555a } -.terminal-1096786593-r7 { fill: #cc555a;font-weight: bold } -.terminal-1096786593-r8 { fill: #8a4346;font-weight: bold } -.terminal-1096786593-r9 { fill: #8d7b39 } -.terminal-1096786593-r10 { fill: #d0b344;font-weight: bold } -.terminal-1096786593-r11 { fill: #1984e9 } -.terminal-1096786593-r12 { fill: #00823d } -.terminal-1096786593-r13 { fill: #868887 } -.terminal-1096786593-r14 { fill: #398280 } -.terminal-1096786593-r15 { fill: #ff2c7a } -.terminal-1096786593-r16 { fill: #ff2627;font-weight: bold } + .terminal-884777647-r1 { fill: #c5c8c6 } +.terminal-884777647-r2 { fill: #98a84b } +.terminal-884777647-r3 { fill: #9a9b99 } +.terminal-884777647-r4 { fill: #608ab1 } +.terminal-884777647-r5 { fill: #d0b344 } +.terminal-884777647-r6 { fill: #cc555a } +.terminal-884777647-r7 { fill: #cc555a;font-weight: bold } +.terminal-884777647-r8 { fill: #8a4346;font-weight: bold } +.terminal-884777647-r9 { fill: #8d7b39 } +.terminal-884777647-r10 { fill: #d0b344;font-weight: bold } +.terminal-884777647-r11 { fill: #1984e9 } +.terminal-884777647-r12 { fill: #00823d } +.terminal-884777647-r13 { fill: #868887 } +.terminal-884777647-r14 { fill: #398280 } +.terminal-884777647-r15 { fill: #ff2c7a } +.terminal-884777647-r16 { fill: #ff2627;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -357,108 +357,108 @@ - + - - $ nf-core subworkflows info bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ -│/opt/hostedtoolcache/Python/3.11.0/x64/bin/nf-core:8 in <module>│ -││ -│7 │   sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])                         │ -│❱ 8 │   sys.exit(run_nf_core())                                                                  │ -│9 │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/nf_core/__main__.py:105 in   │ -│run_nf_core│ -││ -│ 104 │   # Launch the click cli│ -│❱  105 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │ -│ 106 │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/click/core.py:1130 in        │ -│__call__│ -││ -│1129 │   │   """Alias for :meth:`main`."""│ -│❱ 1130 │   │   returnself.main(*args, **kwargs)                                                 │ -│1131 │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/rich_click/rich_group.py:21│ -│ in main│ -││ -│20 │   │   try:                                                                                │ -│❱ 21 │   │   │   rv = super().main(*args, standalone_mode=False, **kwargs)                       │ -│22 │   │   │   ifnot standalone_mode:                                                         │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/click/core.py:1055 in main│ -││ -│1054 │   │   │   │   withself.make_context(prog_name, args, **extra) as ctx:                  │ -│❱ 1055 │   │   │   │   │   rv = self.invoke(ctx)                                                 │ -│1056 │   │   │   │   │   ifnot standalone_mode:                                               │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/click/core.py:1657 in invoke│ -││ -│1656 │   │   │   │   with sub_ctx:                                                             │ -│❱ 1657 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │ -│1658 │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/click/core.py:1657 in invoke│ -││ -│1656 │   │   │   │   with sub_ctx:                                                             │ -│❱ 1657 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │ -│1658 │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/click/core.py:1404 in invoke│ -││ -│1403 │   │   ifself.callback isnotNone:                                                     │ -│❱ 1404 │   │   │   return ctx.invoke(self.callback, **ctx.params)                                │ -│1405 │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/click/core.py:760 in invoke│ -││ -│ 759 │   │   │   with ctx:                                                                     │ -│❱  760 │   │   │   │   return __callback(*args, **kwargs)                                        │ -│ 761 │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/click/decorators.py:26 in    │ -│new_func│ -││ -│ 25 │   defnew_func(*args, **kwargs):  # type: ignore│ -│❱  26 │   │   return f(get_current_context(), *args, **kwargs)                                   │ -│ 27 │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/nf_core/__main__.py:1087 in  │ -│info│ -││ -│1086 │   │   )                                                                                 │ -│❱ 1087 │   │   stdout.print(subworkflow_info.get_component_info())                               │ -│1088 │   except (UserWarning, LookupError) as e:                                               │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/nf_core/components/info.py:1│ -│49 in get_component_info│ -││ -│148 │   │   │ -│❱ 149 │   │   returnself.generate_component_info_help()                                         │ -│150 │ -││ -│/opt/hostedtoolcache/Python/3.11.0/x64/lib/python3.11/site-packages/nf_core/components/info.py:2│ -│62 in generate_component_info_help│ -││ -│261 │   │   │   │   │   inputs_table.add_row(                                                  │ -│❱ 262 │   │   │   │   │   │   f"[orange1 on black] {key} [/][dim i] ({info['type']})",           │ -│263 │   │   │   │   │   │   Markdown(info["description"] if info["description"] else""),      │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -TypeError: 'NoneType' object is not subscriptable + + $ nf-core subworkflows info bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ +│/opt/hostedtoolcache/Python/3.11.1/x64/bin/nf-core:8 in <module>│ +││ +│7 │   sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])                         │ +│❱ 8 │   sys.exit(run_nf_core())                                                                  │ +│9 │ +││ +│/opt/hostedtoolcache/Python/3.11.1/x64/lib/python3.11/site-packages/nf_core/__main__.py:105 in   │ +│run_nf_core│ +││ +│ 104 │   # Launch the click cli│ +│❱  105 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │ +│ 106 │ +││ +│/opt/hostedtoolcache/Python/3.11.1/x64/lib/python3.11/site-packages/click/core.py:1130 in        │ +│__call__│ +││ +│1129 │   │   """Alias for :meth:`main`."""│ +│❱ 1130 │   │   returnself.main(*args, **kwargs)                                                 │ +│1131 │ +││ +│/opt/hostedtoolcache/Python/3.11.1/x64/lib/python3.11/site-packages/rich_click/rich_group.py:21│ +│ in main│ +││ +│20 │   │   try:                                                                                │ +│❱ 21 │   │   │   rv = super().main(*args, standalone_mode=False, **kwargs)                       │ +│22 │   │   │   ifnot standalone_mode:                                                         │ +││ +│/opt/hostedtoolcache/Python/3.11.1/x64/lib/python3.11/site-packages/click/core.py:1055 in main│ +││ +│1054 │   │   │   │   withself.make_context(prog_name, args, **extra) as ctx:                  │ +│❱ 1055 │   │   │   │   │   rv = self.invoke(ctx)                                                 │ +│1056 │   │   │   │   │   ifnot standalone_mode:                                               │ +││ +│/opt/hostedtoolcache/Python/3.11.1/x64/lib/python3.11/site-packages/click/core.py:1657 in invoke│ +││ +│1656 │   │   │   │   with sub_ctx:                                                             │ +│❱ 1657 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │ +│1658 │ +││ +│/opt/hostedtoolcache/Python/3.11.1/x64/lib/python3.11/site-packages/click/core.py:1657 in invoke│ +││ +│1656 │   │   │   │   with sub_ctx:                                                             │ +│❱ 1657 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │ +│1658 │ +││ +│/opt/hostedtoolcache/Python/3.11.1/x64/lib/python3.11/site-packages/click/core.py:1404 in invoke│ +││ +│1403 │   │   ifself.callback isnotNone:                                                     │ +│❱ 1404 │   │   │   return ctx.invoke(self.callback, **ctx.params)                                │ +│1405 │ +││ +│/opt/hostedtoolcache/Python/3.11.1/x64/lib/python3.11/site-packages/click/core.py:760 in invoke│ +││ +│ 759 │   │   │   with ctx:                                                                     │ +│❱  760 │   │   │   │   return __callback(*args, **kwargs)                                        │ +│ 761 │ +││ +│/opt/hostedtoolcache/Python/3.11.1/x64/lib/python3.11/site-packages/click/decorators.py:26 in    │ +│new_func│ +││ +│ 25 │   defnew_func(*args, **kwargs):  # type: ignore│ +│❱  26 │   │   return f(get_current_context(), *args, **kwargs)                                   │ +│ 27 │ +││ +│/opt/hostedtoolcache/Python/3.11.1/x64/lib/python3.11/site-packages/nf_core/__main__.py:1087 in  │ +│info│ +││ +│1086 │   │   )                                                                                 │ +│❱ 1087 │   │   stdout.print(subworkflow_info.get_component_info())                               │ +│1088 │   except (UserWarning, LookupError) as e:                                               │ +││ +│/opt/hostedtoolcache/Python/3.11.1/x64/lib/python3.11/site-packages/nf_core/components/info.py:1│ +│49 in get_component_info│ +││ +│148 │   │   │ +│❱ 149 │   │   returnself.generate_component_info_help()                                         │ +│150 │ +││ +│/opt/hostedtoolcache/Python/3.11.1/x64/lib/python3.11/site-packages/nf_core/components/info.py:2│ +│62 in generate_component_info_help│ +││ +│261 │   │   │   │   │   inputs_table.add_row(                                                  │ +│❱ 262 │   │   │   │   │   │   f"[orange1 on black] {key} [/][dim i] ({info['type']})",           │ +│263 │   │   │   │   │   │   Markdown(info["description"] if info["description"] else""),      │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +TypeError: 'NoneType' object is not subscriptable diff --git a/docs/images/nf-core-subworkflows-install.svg b/docs/images/nf-core-subworkflows-install.svg index 4ad2943f2d..a440ce839e 100644 --- a/docs/images/nf-core-subworkflows-install.svg +++ b/docs/images/nf-core-subworkflows-install.svg @@ -19,107 +19,107 @@ font-weight: 700; } - .terminal-1152843897-matrix { + .terminal-1243414650-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1152843897-title { + .terminal-1243414650-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1152843897-r1 { fill: #c5c8c6 } -.terminal-1152843897-r2 { fill: #98a84b } -.terminal-1152843897-r3 { fill: #9a9b99 } -.terminal-1152843897-r4 { fill: #608ab1 } -.terminal-1152843897-r5 { fill: #d0b344 } -.terminal-1152843897-r6 { fill: #cc555a } + .terminal-1243414650-r1 { fill: #c5c8c6 } +.terminal-1243414650-r2 { fill: #98a84b } +.terminal-1243414650-r3 { fill: #9a9b99 } +.terminal-1243414650-r4 { fill: #608ab1 } +.terminal-1243414650-r5 { fill: #d0b344 } +.terminal-1243414650-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -131,36 +131,36 @@ - + - - $ nf-core subworkflows install bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -WARNING 'repository_type' not defined in .nf-core.yml                                               -Warning: Input is not a terminal (fd=0). -? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - » Pipeline -   nf-core/modules - - - -        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - -Aborted. + + $ nf-core subworkflows install bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. diff --git a/docs/images/nf-core-subworkflows-list-local.svg b/docs/images/nf-core-subworkflows-list-local.svg index 3338be6182..208e28e40e 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-85784132-matrix { + .terminal-174716485-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-85784132-title { + .terminal-174716485-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-85784132-r1 { fill: #c5c8c6 } -.terminal-85784132-r2 { fill: #98a84b } -.terminal-85784132-r3 { fill: #9a9b99 } -.terminal-85784132-r4 { fill: #608ab1 } -.terminal-85784132-r5 { fill: #d0b344 } -.terminal-85784132-r6 { fill: #cc555a } -.terminal-85784132-r7 { fill: #868887;font-style: italic; } + .terminal-174716485-r1 { fill: #c5c8c6 } +.terminal-174716485-r2 { fill: #98a84b } +.terminal-174716485-r3 { fill: #9a9b99 } +.terminal-174716485-r4 { fill: #608ab1 } +.terminal-174716485-r5 { fill: #d0b344 } +.terminal-174716485-r6 { fill: #cc555a } +.terminal-174716485-r7 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,36 +132,36 @@ - + - - $ nf-core subworkflows list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -WARNING 'repository_type' not defined in .nf-core.yml                                               -Warning: Input is not a terminal (fd=0). -? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - » Pipeline -   nf-core/modules - - - -        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - -[..truncated..] + + $ nf-core subworkflows list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +[..truncated..] diff --git a/docs/images/nf-core-subworkflows-list-remote.svg b/docs/images/nf-core-subworkflows-list-remote.svg index 9c60556afe..4e2ff9f8a5 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-4078322582-matrix { + .terminal-4215096215-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4078322582-title { + .terminal-4215096215-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4078322582-r1 { fill: #c5c8c6 } -.terminal-4078322582-r2 { fill: #98a84b } -.terminal-4078322582-r3 { fill: #9a9b99 } -.terminal-4078322582-r4 { fill: #608ab1 } -.terminal-4078322582-r5 { fill: #d0b344 } -.terminal-4078322582-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-4078322582-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-4078322582-r8 { fill: #868887;font-style: italic; } + .terminal-4215096215-r1 { fill: #c5c8c6 } +.terminal-4215096215-r2 { fill: #98a84b } +.terminal-4215096215-r3 { fill: #9a9b99 } +.terminal-4215096215-r4 { fill: #608ab1 } +.terminal-4215096215-r5 { fill: #d0b344 } +.terminal-4215096215-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-4215096215-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-4215096215-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core subworkflows list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Subworkflow Name                            ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ bam_dedup_stats_samtools_umitools            │ -│ bam_markduplicates_picard                    │ -│ bam_qc_picard                                │ -│ bam_rseqc                                    │ -│ bam_sort_stats_samtools                      │ -│ bam_stats_samtools                           │ -│ bcl_demultiplex                              │ -│ bed_scatter_bedtools                         │ -│ bedgraph_bedclip_bedgraphtobigwig            │ -[..truncated..] + + $ nf-core subworkflows list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Subworkflow Name                            ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ bam_dedup_stats_samtools_umitools            │ +│ bam_markduplicates_picard                    │ +│ bam_qc_picard                                │ +│ bam_rseqc                                    │ +│ bam_sort_stats_samtools                      │ +│ bam_stats_samtools                           │ +│ bcl_demultiplex                              │ +│ bed_scatter_bedtools                         │ +│ bedgraph_bedclip_bedgraphtobigwig            │ +[..truncated..] diff --git a/docs/images/nf-core-subworkflows-remove.svg b/docs/images/nf-core-subworkflows-remove.svg index d6a95b7b77..33b93f5c19 100644 --- a/docs/images/nf-core-subworkflows-remove.svg +++ b/docs/images/nf-core-subworkflows-remove.svg @@ -19,107 +19,107 @@ font-weight: 700; } - .terminal-559218704-matrix { + .terminal-649789457-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-559218704-title { + .terminal-649789457-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-559218704-r1 { fill: #c5c8c6 } -.terminal-559218704-r2 { fill: #98a84b } -.terminal-559218704-r3 { fill: #9a9b99 } -.terminal-559218704-r4 { fill: #608ab1 } -.terminal-559218704-r5 { fill: #d0b344 } -.terminal-559218704-r6 { fill: #cc555a } + .terminal-649789457-r1 { fill: #c5c8c6 } +.terminal-649789457-r2 { fill: #98a84b } +.terminal-649789457-r3 { fill: #9a9b99 } +.terminal-649789457-r4 { fill: #608ab1 } +.terminal-649789457-r5 { fill: #d0b344 } +.terminal-649789457-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -131,36 +131,36 @@ - + - - $ nf-core subworkflows remove bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -WARNING 'repository_type' not defined in .nf-core.yml                                               -Warning: Input is not a terminal (fd=0). -? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - » Pipeline -   nf-core/modules - - - -        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - -Aborted. + + $ nf-core subworkflows remove bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. diff --git a/docs/images/nf-core-subworkflows-test.svg b/docs/images/nf-core-subworkflows-test.svg index 0e3904fc3c..44d0a5fc48 100644 --- a/docs/images/nf-core-subworkflows-test.svg +++ b/docs/images/nf-core-subworkflows-test.svg @@ -19,107 +19,107 @@ font-weight: 700; } - .terminal-2420114395-matrix { + .terminal-2510685148-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2420114395-title { + .terminal-2510685148-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2420114395-r1 { fill: #c5c8c6 } -.terminal-2420114395-r2 { fill: #98a84b } -.terminal-2420114395-r3 { fill: #9a9b99 } -.terminal-2420114395-r4 { fill: #608ab1 } -.terminal-2420114395-r5 { fill: #d0b344 } -.terminal-2420114395-r6 { fill: #cc555a } + .terminal-2510685148-r1 { fill: #c5c8c6 } +.terminal-2510685148-r2 { fill: #98a84b } +.terminal-2510685148-r3 { fill: #9a9b99 } +.terminal-2510685148-r4 { fill: #608ab1 } +.terminal-2510685148-r5 { fill: #d0b344 } +.terminal-2510685148-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -131,36 +131,36 @@ - + - - $ nf-core subworkflows test bam_rseqc --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -WARNING 'repository_type' not defined in .nf-core.yml                                               -Warning: Input is not a terminal (fd=0). -? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - » Pipeline -   nf-core/modules - - - -        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - -Aborted. + + $ nf-core subworkflows test bam_rseqc --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. diff --git a/docs/images/nf-core-subworkflows-update.svg b/docs/images/nf-core-subworkflows-update.svg index cee91fa471..4769128e73 100644 --- a/docs/images/nf-core-subworkflows-update.svg +++ b/docs/images/nf-core-subworkflows-update.svg @@ -19,107 +19,107 @@ font-weight: 700; } - .terminal-1454637681-matrix { + .terminal-1545208434-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1454637681-title { + .terminal-1545208434-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1454637681-r1 { fill: #c5c8c6 } -.terminal-1454637681-r2 { fill: #98a84b } -.terminal-1454637681-r3 { fill: #9a9b99 } -.terminal-1454637681-r4 { fill: #608ab1 } -.terminal-1454637681-r5 { fill: #d0b344 } -.terminal-1454637681-r6 { fill: #cc555a } + .terminal-1545208434-r1 { fill: #c5c8c6 } +.terminal-1545208434-r2 { fill: #98a84b } +.terminal-1545208434-r3 { fill: #9a9b99 } +.terminal-1545208434-r4 { fill: #608ab1 } +.terminal-1545208434-r5 { fill: #d0b344 } +.terminal-1545208434-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -131,36 +131,36 @@ - + - - $ nf-core subworkflows update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - - -WARNING 'repository_type' not defined in .nf-core.yml                                               -Warning: Input is not a terminal (fd=0). -? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - » Pipeline -   nf-core/modules - - - -        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr -                                                                               o -w keys) - -Aborted. + + $ nf-core subworkflows update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + + +WARNING 'repository_type' not defined in .nf-core.yml                                               +Warning: Input is not a terminal (fd=0). +? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + » Pipeline +   nf-core/modules + + + +        ? Is this repository an nf-core pipeline or a fork of nf-core/modules? (Use arr +                                                                               o +w keys) + +Aborted. diff --git a/docs/images/nf-core-sync.svg b/docs/images/nf-core-sync.svg index 2f22643569..99c164c146 100644 --- a/docs/images/nf-core-sync.svg +++ b/docs/images/nf-core-sync.svg @@ -19,72 +19,72 @@ font-weight: 700; } - .terminal-739183148-matrix { + .terminal-832309805-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-739183148-title { + .terminal-832309805-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-739183148-r1 { fill: #c5c8c6 } -.terminal-739183148-r2 { fill: #98a84b } -.terminal-739183148-r3 { fill: #9a9b99 } -.terminal-739183148-r4 { fill: #608ab1 } -.terminal-739183148-r5 { fill: #d0b344 } -.terminal-739183148-r6 { fill: #98729f } -.terminal-739183148-r7 { fill: #ff2c7a } + .terminal-832309805-r1 { fill: #c5c8c6 } +.terminal-832309805-r2 { fill: #98a84b } +.terminal-832309805-r3 { fill: #9a9b99 } +.terminal-832309805-r4 { fill: #608ab1 } +.terminal-832309805-r5 { fill: #d0b344 } +.terminal-832309805-r6 { fill: #98729f } +.terminal-832309805-r7 { fill: #ff2c7a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,24 +96,24 @@ - + - - $ nf-core sync - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.7.1 - https://nf-co.re - - -INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthing -INFO     Original pipeline repository branch is 'master' -INFO     Deleting all files in 'TEMPLATE' branch                                                     -INFO     Making a new template pipeline using pipeline variables                                     + + $ nf-core sync + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.7.2 - https://nf-co.re + + +INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthing +INFO     Original pipeline repository branch is 'master' +INFO     Deleting all files in 'TEMPLATE' branch                                                     +INFO     Making a new template pipeline using pipeline variables