diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg index c57af953e3..602b18304d 100644 --- a/docs/images/nf-core-bump-version.svg +++ b/docs/images/nf-core-bump-version.svg @@ -19,122 +19,122 @@ font-weight: 700; } - .terminal-2993841204-matrix { + .terminal-760177622-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2993841204-title { + .terminal-760177622-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2993841204-r1 { fill: #c5c8c6 } -.terminal-2993841204-r2 { fill: #98a84b } -.terminal-2993841204-r3 { fill: #9a9b99 } -.terminal-2993841204-r4 { fill: #608ab1 } -.terminal-2993841204-r5 { fill: #d0b344 } -.terminal-2993841204-r6 { fill: #cc555a } + .terminal-760177622-r1 { fill: #c5c8c6 } +.terminal-760177622-r2 { fill: #98a84b } +.terminal-760177622-r3 { fill: #9a9b99 } +.terminal-760177622-r4 { fill: #608ab1 } +.terminal-760177622-r5 { fill: #d0b344 } +.terminal-760177622-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -146,41 +146,41 @@ - + - - $ nf-core bump-version 1.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - -INFO     Changing version number from '1.0dev' to '1.1' -INFO     Updated version in 'nextflow.config' - - version         = '1.0dev' - + version         = '1.1' - - -INFO     Updated version in 'assets/multiqc_config.yml' - - This report has been generated by the <a  -href="https://github.com/nf-core/nextbigthing/tree/dev" target="_blank">nf-core/nextbigthing</a> - + This report has been generated by the <a  -href="https://github.com/nf-core/nextbigthing/releases/tag/1.1"  -target="_blank">nf-core/nextbigthing</a> - - -INFO     Updated version in 'assets/multiqc_config.yml' - - <a href="https://nf-co.re/nextbigthing/dev/docs/output"  -target="_blank">documentation</a>. - + <a href="https://nf-co.re/nextbigthing/1.1/docs/output"  -target="_blank">documentation</a>. - - + + $ nf-core bump-version 1.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + +INFO     Changing version number from '1.0dev' to '1.1' +INFO     Updated version in 'nextflow.config' + - version         = '1.0dev' + + version         = '1.1' + + +INFO     Updated version in 'assets/multiqc_config.yml' + - This report has been generated by the <a  +href="https://github.com/nf-core/nextbigthing/tree/dev" target="_blank">nf-core/nextbigthing</a> + + This report has been generated by the <a  +href="https://github.com/nf-core/nextbigthing/releases/tag/1.1"  +target="_blank">nf-core/nextbigthing</a> + + +INFO     Updated version in 'assets/multiqc_config.yml' + - <a href="https://nf-co.re/nextbigthing/dev/docs/output"  +target="_blank">documentation</a>. + + <a href="https://nf-co.re/nextbigthing/1.1/docs/output"  +target="_blank">documentation</a>. + + diff --git a/docs/images/nf-core-create-logo.svg b/docs/images/nf-core-create-logo.svg new file mode 100644 index 0000000000..b4d88480d9 --- /dev/null +++ b/docs/images/nf-core-create-logo.svg @@ -0,0 +1,108 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $ nf-core create-logo nextbigthing + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + +INFO     Created logo: /home/runner/work/tools/tools/tmp/nf-core-nextbigthing_logo_light.png + + + + diff --git a/docs/images/nf-core-create.svg b/docs/images/nf-core-create.svg index 99a7112fb4..79e349f4fc 100644 --- a/docs/images/nf-core-create.svg +++ b/docs/images/nf-core-create.svg @@ -19,104 +19,104 @@ font-weight: 700; } - .terminal-3963146934-matrix { + .terminal-1826411096-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3963146934-title { + .terminal-1826411096-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3963146934-r1 { fill: #c5c8c6 } -.terminal-3963146934-r2 { fill: #98a84b } -.terminal-3963146934-r3 { fill: #9a9b99 } -.terminal-3963146934-r4 { fill: #608ab1 } -.terminal-3963146934-r5 { fill: #d0b344 } -.terminal-3963146934-r6 { fill: #98729f } -.terminal-3963146934-r7 { fill: #ff2c7a } -.terminal-3963146934-r8 { fill: #98a84b;font-weight: bold } -.terminal-3963146934-r9 { fill: #1984e9;text-decoration: underline; } + .terminal-1826411096-r1 { fill: #c5c8c6 } +.terminal-1826411096-r2 { fill: #98a84b } +.terminal-1826411096-r3 { fill: #9a9b99 } +.terminal-1826411096-r4 { fill: #608ab1 } +.terminal-1826411096-r5 { fill: #d0b344 } +.terminal-1826411096-r6 { fill: #98729f } +.terminal-1826411096-r7 { fill: #ff2c7a } +.terminal-1826411096-r8 { fill: #98a84b;font-weight: bold } +.terminal-1826411096-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 2.11.1 - 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 2.12 - 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 cc6b17ebfd..05b7456fbd 100644 --- a/docs/images/nf-core-download.svg +++ b/docs/images/nf-core-download.svg @@ -19,86 +19,86 @@ font-weight: 700; } - .terminal-2599349710-matrix { + .terminal-1937960304-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2599349710-title { + .terminal-1937960304-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2599349710-r1 { fill: #c5c8c6 } -.terminal-2599349710-r2 { fill: #98a84b } -.terminal-2599349710-r3 { fill: #9a9b99 } -.terminal-2599349710-r4 { fill: #608ab1 } -.terminal-2599349710-r5 { fill: #d0b344 } -.terminal-2599349710-r6 { fill: #cc555a } + .terminal-1937960304-r1 { fill: #c5c8c6 } +.terminal-1937960304-r2 { fill: #98a84b } +.terminal-1937960304-r3 { fill: #9a9b99 } +.terminal-1937960304-r4 { fill: #608ab1 } +.terminal-1937960304-r5 { fill: #d0b344 } +.terminal-1937960304-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -110,29 +110,29 @@ - + - - $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - -WARNING  Could not find GitHub authentication token. Some API requests may fail.                     -INFO     Saving 'nf-core/rnaseq' -          Pipeline revision: '3.8' -          Use containers: 'none' -          Container library: 'quay.io' -          Output directory: 'nf-core-rnaseq' -          Include default institutional configuration: 'True' -INFO     Downloading centralised configs from GitHub                                                 -INFO     Downloading workflow files from GitHub                                                      + + $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + +WARNING  Could not find GitHub authentication token. Some API requests may fail.                     +INFO     Saving 'nf-core/rnaseq' +          Pipeline revision: '3.8' +          Use containers: 'none' +          Container library: 'quay.io' +          Output directory: 'nf-core-rnaseq' +          Include default institutional configuration: 'True' +INFO     Downloading centralised configs from GitHub                                                 +INFO     Downloading workflow files from GitHub                                                      diff --git a/docs/images/nf-core-launch-rnaseq.svg b/docs/images/nf-core-launch-rnaseq.svg index b76e4893c5..8956e15703 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-3706564145-matrix { + .terminal-1862905299-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3706564145-title { + .terminal-1862905299-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3706564145-r1 { fill: #c5c8c6 } -.terminal-3706564145-r2 { fill: #98a84b } -.terminal-3706564145-r3 { fill: #9a9b99 } -.terminal-3706564145-r4 { fill: #608ab1 } -.terminal-3706564145-r5 { fill: #d0b344 } -.terminal-3706564145-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3706564145-r7 { fill: #68a0b3;font-weight: bold } + .terminal-1862905299-r1 { fill: #c5c8c6 } +.terminal-1862905299-r2 { fill: #98a84b } +.terminal-1862905299-r3 { fill: #9a9b99 } +.terminal-1862905299-r4 { fill: #608ab1 } +.terminal-1862905299-r5 { fill: #d0b344 } +.terminal-1862905299-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1862905299-r7 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,24 +96,24 @@ - + - - $ nf-core launch rnaseq -r 3.8.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - 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 2.12 - 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 934458cf62..0512d5c954 100644 --- a/docs/images/nf-core-licences.svg +++ b/docs/images/nf-core-licences.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + - - $ nf-core licences deepvariant - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - 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 2.12 - https://nf-co.re + + +INFO     Fetching licence information for 8 tools                                                    diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg index 1c6f1dd1b0..140f02d3f2 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 2.11.1 - https://nf-co.re - - - -INFO     Testing pipeline: . - - -╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ -││ -│pipeline_todos: pipeline_todos│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─[!] 1 Pipeline Test Warning────────────────────────────────────────────────────────────────────╮ -││ -│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │ -│doi (after the first release).│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - -╭──────────────────────╮ -│LINT RESULTS SUMMARY│ -├──────────────────────┤ -│[✔] 192 Tests Passed│ -│[?]   1 Test Ignored│ -│[!]   1 Test Warning│ -│[✗]   0 Tests Failed│ -╰──────────────────────╯ + + + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Testing pipeline: . +INFO     Files to ignore: [] + + +╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ +││ +│pipeline_todos: pipeline_todos                                                                  │ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─[!] 1 Pipeline Test Warning────────────────────────────────────────────────────────────────────╮ +││ +│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │ +│doi (after the first release).                                                                  │ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + +╭──────────────────────╮ +│LINT RESULTS SUMMARY│ +├──────────────────────┤ +│[✔] 199 Tests Passed│ +│[?]   1 Test Ignored│ +│[!]   1 Test Warning│ +│[✗]   0 Tests Failed│ +╰──────────────────────╯ diff --git a/docs/images/nf-core-list-rna.svg b/docs/images/nf-core-list-rna.svg index ed22bfbc6f..deb9d390e2 100644 --- a/docs/images/nf-core-list-rna.svg +++ b/docs/images/nf-core-list-rna.svg @@ -19,111 +19,111 @@ font-weight: 700; } - .terminal-1199297796-matrix { + .terminal-1343542234-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1199297796-title { + .terminal-1343542234-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1199297796-r1 { fill: #c5c8c6 } -.terminal-1199297796-r2 { fill: #98a84b } -.terminal-1199297796-r3 { fill: #9a9b99 } -.terminal-1199297796-r4 { fill: #608ab1 } -.terminal-1199297796-r5 { fill: #d0b344 } -.terminal-1199297796-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1199297796-r7 { fill: #868887 } + .terminal-1343542234-r1 { fill: #c5c8c6 } +.terminal-1343542234-r2 { fill: #98a84b } +.terminal-1343542234-r3 { fill: #9a9b99 } +.terminal-1343542234-r4 { fill: #608ab1 } +.terminal-1343542234-r5 { fill: #d0b344 } +.terminal-1343542234-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1343542234-r7 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -135,37 +135,37 @@ - + - - $ nf-core list rna rna-seq - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnafusion            │   120 │          3.0.1 │  3 weeks ago │           - │ -                   │ -│ rnaseq               │   704 │         3.13.2 │  4 weeks ago │           - │ -                   │ -│ differentialabundan… │    32 │          1.4.0 │  3 weeks ago │           - │ -                   │ -│ spatialtranscriptom… │    31 │            dev │  3 weeks ago │           - │ -                   │ -│ circrna              │    33 │            dev │  3 weeks ago │           - │ -                   │ -│ rnasplice            │    14 │          1.0.1 │ 1 months ago │           - │ -                   │ -│ smrnaseq             │    60 │          2.2.4 │ 2 months ago │           - │ -                   │ -│ scrnaseq             │   110 │          2.4.1 │ 3 months ago │           - │ -                   │ -│ dualrnaseq           │    13 │          1.0.0 │  3 years ago │           - │ -                   │ -│ marsseq              │     4 │          1.0.3 │ 5 months ago │           - │ -                   │ -│ lncpipe              │    26 │            dev │  1 years ago │           - │ -                   │ -│ scflow               │    22 │            dev │  2 years ago │           - │ -                   │ -└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ + + $ nf-core list rna rna-seq + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnafusion            │   125 │          3.0.1 │ 2 months ago │           - │ -                   │ +│ differentialabundan… │    35 │          1.4.0 │ 2 months ago │           - │ -                   │ +│ circrna              │    33 │            dev │   2 days ago │           - │ -                   │ +│ smrnaseq             │    63 │          2.2.4 │ 3 months ago │           - │ -                   │ +│ spatialtranscriptom… │    35 │            dev │   3 days ago │           - │ -                   │ +│ scrnaseq             │   119 │          2.5.1 │   6 days ago │           - │ -                   │ +│ rnaseq               │   722 │         3.14.0 │  3 weeks ago │           - │ -                   │ +│ rnasplice            │    20 │          1.0.2 │  3 weeks ago │           - │ -                   │ +│ dualrnaseq           │    15 │          1.0.0 │  3 years ago │           - │ -                   │ +│ marsseq              │     5 │          1.0.3 │ 6 months ago │           - │ -                   │ +│ lncpipe              │    27 │            dev │  1 years ago │           - │ -                   │ +│ scflow               │    23 │            dev │  2 years ago │           - │ -                   │ +└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg index 01431bf102..f9a9d3d042 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-11073929-matrix { + .terminal-926284067-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-11073929-title { + .terminal-926284067-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-11073929-r1 { fill: #c5c8c6 } -.terminal-11073929-r2 { fill: #98a84b } -.terminal-11073929-r3 { fill: #9a9b99 } -.terminal-11073929-r4 { fill: #608ab1 } -.terminal-11073929-r5 { fill: #d0b344 } -.terminal-11073929-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-11073929-r7 { fill: #868887 } -.terminal-11073929-r8 { fill: #868887;font-style: italic; } + .terminal-926284067-r1 { fill: #c5c8c6 } +.terminal-926284067-r2 { fill: #98a84b } +.terminal-926284067-r3 { fill: #9a9b99 } +.terminal-926284067-r4 { fill: #608ab1 } +.terminal-926284067-r5 { fill: #d0b344 } +.terminal-926284067-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-926284067-r7 { fill: #868887 } +.terminal-926284067-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -112,29 +112,29 @@ - + - - $ nf-core list -s stars - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq              │   704 │         3.13.2 │   4 weeks ago │           - │ -                   │ -│ sarek               │   288 │          3.4.0 │  1 months ago │           - │ -                   │ -│ chipseq             │   157 │          2.0.0 │   1 years ago │           - │ -                   │ -│ mag                 │   156 │          2.5.1 │  1 months ago │           - │ -                   │ -[..truncated..] + + $ nf-core list -s stars + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq              │   722 │         3.14.0 │   3 weeks ago │           - │ -                   │ +│ sarek               │   303 │          3.4.0 │  2 months ago │           - │ -                   │ +│ mag                 │   167 │          2.5.1 │  2 months ago │           - │ -                   │ +│ chipseq             │   159 │          2.0.0 │   1 years ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg index d0b37306a3..e42799f98a 100644 --- a/docs/images/nf-core-list.svg +++ b/docs/images/nf-core-list.svg @@ -19,91 +19,91 @@ font-weight: 700; } - .terminal-691768826-matrix { + .terminal-1472038847-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-691768826-title { + .terminal-1472038847-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-691768826-r1 { fill: #c5c8c6 } -.terminal-691768826-r2 { fill: #98a84b } -.terminal-691768826-r3 { fill: #9a9b99 } -.terminal-691768826-r4 { fill: #608ab1 } -.terminal-691768826-r5 { fill: #d0b344 } -.terminal-691768826-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-691768826-r7 { fill: #868887 } -.terminal-691768826-r8 { fill: #868887;font-style: italic; } + .terminal-1472038847-r1 { fill: #c5c8c6 } +.terminal-1472038847-r2 { fill: #98a84b } +.terminal-1472038847-r3 { fill: #9a9b99 } +.terminal-1472038847-r4 { fill: #608ab1 } +.terminal-1472038847-r5 { fill: #d0b344 } +.terminal-1472038847-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1472038847-r7 { fill: #868887 } +.terminal-1472038847-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +115,30 @@ - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ callingcards        │     2 │            dev │  18 hours ago │           - │ -                   │ -│ ampliseq            │   140 │          2.7.1 │  1 months ago │           - │ -                   │ -│ raredisease         │    63 │          1.1.1 │  5 months ago │           - │ -                   │ -│ epitopeprediction   │    27 │          2.2.1 │  9 months ago │           - │ -                   │ -│ metatdenovo         │     3 │            dev │     yesterday │           - │ -                   │ -[..truncated..] + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnafusion           │   125 │          3.0.1 │  2 months ago │           - │ -                   │ +│ differentialabunda… │    35 │          1.4.0 │  2 months ago │           - │ -                   │ +│ raredisease         │    64 │          1.1.1 │  6 months ago │           - │ -                   │ +│ circrna             │    33 │            dev │    2 days ago │           - │ -                   │ +│ mag                 │   167 │          2.5.1 │  2 months ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index 13be58189e..657b1ffbc5 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-1176762434-matrix { + .terminal-446953444-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1176762434-title { + .terminal-446953444-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1176762434-r1 { fill: #c5c8c6 } -.terminal-1176762434-r2 { fill: #98a84b } -.terminal-1176762434-r3 { fill: #9a9b99 } -.terminal-1176762434-r4 { fill: #608ab1 } -.terminal-1176762434-r5 { fill: #d0b344 } -.terminal-1176762434-r6 { fill: #98a84b;font-weight: bold } -.terminal-1176762434-r7 { fill: #c5c8c6;font-weight: bold } + .terminal-446953444-r1 { fill: #c5c8c6 } +.terminal-446953444-r2 { fill: #98a84b } +.terminal-446953444-r3 { fill: #9a9b99 } +.terminal-446953444-r4 { fill: #608ab1 } +.terminal-446953444-r5 { fill: #d0b344 } +.terminal-446953444-r6 { fill: #98a84b;font-weight: bold } +.terminal-446953444-r7 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -114,30 +114,30 @@ - + - - $ nf-core modules bump-versions fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - 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 2.12 - https://nf-co.re + + + + +╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ +│[!] 1 Module version up to date.│ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ +│Module name                             │Update Message                                       │ +├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ +│ fastqc                                   │ Module version up to date: fastqc                     │ +╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index 7cf8b9ca99..17fb2e365e 100644 --- a/docs/images/nf-core-modules-create.svg +++ b/docs/images/nf-core-modules-create.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - + - + - - $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     Repository type: modules -INFO    Press enter to use default values (shown in brackets)or type your own responses.  -ctrl+click underlined text to open links. -INFO     Using Bioconda package: 'bioconda::fastqc=0.12.1' -INFO     Using Docker container: 'biocontainers/fastqc:0.12.1--hdfd78af_0' -INFO     Using Singularity container:                                                                -'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' -INFO     Created component template: 'fastqc' -INFO     Created following files:                                                                    -           modules/nf-core/fastqc/main.nf                                                            -           modules/nf-core/fastqc/meta.yml                                                           -           modules/nf-core/fastqc/environment.yml                                                    -           modules/nf-core/fastqc/tests/tags.yml                                                     -           modules/nf-core/fastqc/tests/main.nf.test                                                 + + $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Repository type: modules +INFO    Press enter to use default values (shown in brackets)or type your own responses.  +ctrl+click underlined text to open links. +INFO     Using Bioconda package: 'bioconda::fastqc=0.12.1' +INFO     Could not find a Docker/Singularity container (Unexpected response code `503` for           +https://api.biocontainers.pro/ga4gh/trs/v2/tools/fastqc/versions/fastqc-0.12.1) +INFO     Created component template: 'fastqc' +INFO     Created following files:                                                                    +           modules/nf-core/fastqc/main.nf                                                            +           modules/nf-core/fastqc/meta.yml                                                           +           modules/nf-core/fastqc/environment.yml                                                    +           modules/nf-core/fastqc/tests/tags.yml                                                     +           modules/nf-core/fastqc/tests/main.nf.test                                                 diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg index b604cb3f7b..65b3256542 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-149484079-matrix { + .terminal-2512974289-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-149484079-title { + .terminal-2512974289-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-149484079-r1 { fill: #c5c8c6 } -.terminal-149484079-r2 { fill: #98a84b } -.terminal-149484079-r3 { fill: #9a9b99 } -.terminal-149484079-r4 { fill: #608ab1 } -.terminal-149484079-r5 { fill: #d0b344 } -.terminal-149484079-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-149484079-r7 { fill: #98a84b;font-weight: bold } -.terminal-149484079-r8 { fill: #868887 } -.terminal-149484079-r9 { fill: #d08442 } -.terminal-149484079-r10 { fill: #868887;font-style: italic; } -.terminal-149484079-r11 { fill: #98729f } + .terminal-2512974289-r1 { fill: #c5c8c6 } +.terminal-2512974289-r2 { fill: #98a84b } +.terminal-2512974289-r3 { fill: #9a9b99 } +.terminal-2512974289-r4 { fill: #608ab1 } +.terminal-2512974289-r5 { fill: #d0b344 } +.terminal-2512974289-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-2512974289-r7 { fill: #98a84b;font-weight: bold } +.terminal-2512974289-r8 { fill: #868887 } +.terminal-2512974289-r9 { fill: #d08442 } +.terminal-2512974289-r10 { fill: #868887;font-style: italic; } +.terminal-2512974289-r11 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -187,53 +187,53 @@ - + - - $ nf-core modules info abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ -│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ -│ 🔧 Tools: abacas                                                                                 │ -│ 📖 Description: contiguate draft genome assembly                                                 │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -                  ╷                                                                   ╷              -📥 Inputs        │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} -                  ╵                                                                   ╵              -                  ╷                                                                   ╷              -📤 Outputs       │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - results  (file) │List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* -                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ -                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ -                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ -                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - versions  (file)│File containing software versions                                  │versions.yml -                  ╵                                                                   ╵              - - 💻  Installation command: nf-core modules install abacas - + + $ nf-core modules info abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ +│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ +│ 🔧 Tools: abacas                                                                                 │ +│ 📖 Description: contiguate draft genome assembly                                                 │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +                  ╷                                                                   ╷              +📥 Inputs        │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} +                  ╵                                                                   ╵              +                  ╷                                                                   ╷              +📤 Outputs       │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + results  (file) │List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* +                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ +                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ +                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ +                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + versions  (file)│File containing software versions                                  │versions.yml +                  ╵                                                                   ╵              + + 💻  Installation command: nf-core modules install abacas + diff --git a/docs/images/nf-core-modules-install.svg b/docs/images/nf-core-modules-install.svg index f444190f32..8e5ba2ee29 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-160730253-matrix { + .terminal-2712767535-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-160730253-title { + .terminal-2712767535-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-160730253-r1 { fill: #c5c8c6 } -.terminal-160730253-r2 { fill: #98a84b } -.terminal-160730253-r3 { fill: #9a9b99 } -.terminal-160730253-r4 { fill: #608ab1 } -.terminal-160730253-r5 { fill: #d0b344 } + .terminal-2712767535-r1 { fill: #c5c8c6 } +.terminal-2712767535-r2 { fill: #98a84b } +.terminal-2712767535-r3 { fill: #9a9b99 } +.terminal-2712767535-r4 { fill: #608ab1 } +.terminal-2712767535-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core modules install abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - 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 2.12 - 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 03edcaf551..1ef2c54aed 100644 --- a/docs/images/nf-core-modules-lint.svg +++ b/docs/images/nf-core-modules-lint.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - $ nf-core modules lint multiqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     Linting modules repo: '.' -INFO     Linting module: 'multiqc' -INFO     Found 4 inputs in modules/nf-core/multiqc/main.nf                                           -INFO     Found 4 outputs in modules/nf-core/multiqc/main.nf                                          - -╭─[!] 1 Module Test Warning──────────────────────────────────────────────────────────────────────╮ -│              ╷                                 ╷                                                 │ -│Module name │File path                      │Test message                                   │ -│╶─────────────┼─────────────────────────────────┼────────────────────────────────────────────────╴│ -│multiqc│modules/nf-core/multiqc/main.nf│Conda update: bioconda::multiqc 1.18 -> 1.19│ -│              ╵                                 ╵                                                 │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭──────────────────────╮ -│LINT RESULTS SUMMARY│ -├──────────────────────┤ -│[✔]  50 Tests Passed│ -│[!]   1 Test Warning│ -│[✗]   0 Tests Failed│ -╰──────────────────────╯ + + + + $ nf-core modules lint multiqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Linting modules repo: '.' +INFO     Linting module: 'multiqc' diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index a1b2806467..a94545663b 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-1750863134-matrix { + .terminal-114288408-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1750863134-title { + .terminal-114288408-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1750863134-r1 { fill: #c5c8c6 } -.terminal-1750863134-r2 { fill: #98a84b } -.terminal-1750863134-r3 { fill: #9a9b99 } -.terminal-1750863134-r4 { fill: #608ab1 } -.terminal-1750863134-r5 { fill: #d0b344 } -.terminal-1750863134-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1750863134-r7 { fill: #868887;font-style: italic; } + .terminal-114288408-r1 { fill: #c5c8c6 } +.terminal-114288408-r2 { fill: #98a84b } +.terminal-114288408-r3 { fill: #9a9b99 } +.terminal-114288408-r4 { fill: #608ab1 } +.terminal-114288408-r5 { fill: #d0b344 } +.terminal-114288408-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-114288408-r7 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,36 +132,36 @@ - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     Modules installed in '.':                                                                   - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -┃Module Name        ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ custom/dumpsoftwar… │ https://github.co… │ bba7e362e4afead706… │ add                │ 2023-11-14 │ -│                     │                    │                     │ environment-schem… │            │ -│                     │                    │                     │ rename yaml-schema │            │ -│                     │                    │                     │ to meta-schema     │            │ -│                     │                    │                     │ (#4323)            │            │ -│ fastqc              │ https://github.co… │ 65ad3e0b9a4099592e… │ Update version     │ 2023-12-08 │ -│                     │                    │                     │ strings (#4556)    │            │ -│ multiqc             │ https://github.co… │ 4ab13872435962dadc… │ Pull multiqc       │ 2023-12-05 │ -│                     │                    │                     │ static multiqc     │            │ -[..truncated..] + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Modules installed in '.':                                                                   + +self.repo_type='pipeline' +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +┃Module Name        ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ custom/dumpsoftwar… │ https://github.co… │ 8ec825f465b9c17f9d… │ Bump MultiQC       │ 2024-01-10 │ +│                     │                    │                     │ version to 1.19    │            │ +│                     │                    │                     │ (#4705)            │            │ +│ fastqc              │ https://github.co… │ c9488585ce7bd35ccd… │ CHORES: update     │ 2024-01-18 │ +│                     │                    │                     │ fasqc tests with   │            │ +│                     │                    │                     │ new data           │            │ +│                     │                    │                     │ organisation       │            │ +│                     │                    │                     │ (#4760)            │            │ +[..truncated..] diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index 28be0b24ee..f8a16874f3 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-2091866550-matrix { + .terminal-2276415832-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2091866550-title { + .terminal-2276415832-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2091866550-r1 { fill: #c5c8c6 } -.terminal-2091866550-r2 { fill: #98a84b } -.terminal-2091866550-r3 { fill: #9a9b99 } -.terminal-2091866550-r4 { fill: #608ab1 } -.terminal-2091866550-r5 { fill: #d0b344 } -.terminal-2091866550-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-2091866550-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-2091866550-r8 { fill: #868887;font-style: italic; } + .terminal-2276415832-r1 { fill: #c5c8c6 } +.terminal-2276415832-r2 { fill: #98a84b } +.terminal-2276415832-r3 { fill: #9a9b99 } +.terminal-2276415832-r4 { fill: #608ab1 } +.terminal-2276415832-r5 { fill: #d0b344 } +.terminal-2276415832-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-2276415832-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2276415832-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core modules list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     Modules available from https://github.com/nf-core/modules.git(master):                     - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Module Name                                          ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ abacas                                                │ -│ abricate/run                                          │ -│ abricate/summary                                      │ -│ abritamr/run                                          │ -│ adapterremoval                                        │ -│ adapterremovalfixprefix                               │ -│ admixture                                             │ -│ affy/justrma                                          │ -│ agat/convertspgff2gtf                                 │ -[..truncated..] + + $ nf-core modules list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Modules available from https://github.com/nf-core/modules.git(master):                     + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Module Name                                          ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ abacas                                                │ +│ abricate/run                                          │ +│ abricate/summary                                      │ +│ abritamr/run                                          │ +│ adapterremoval                                        │ +│ adapterremovalfixprefix                               │ +│ admixture                                             │ +│ affy/justrma                                          │ +│ agat/convertspgff2gtf                                 │ +[..truncated..] diff --git a/docs/images/nf-core-modules-patch.svg b/docs/images/nf-core-modules-patch.svg index 25033c107a..70dc93a8a3 100644 --- a/docs/images/nf-core-modules-patch.svg +++ b/docs/images/nf-core-modules-patch.svg @@ -19,127 +19,127 @@ font-weight: 700; } - .terminal-1129851975-matrix { + .terminal-3232574441-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1129851975-title { + .terminal-3232574441-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1129851975-r1 { fill: #c5c8c6 } -.terminal-1129851975-r2 { fill: #98a84b } -.terminal-1129851975-r3 { fill: #9a9b99 } -.terminal-1129851975-r4 { fill: #608ab1 } -.terminal-1129851975-r5 { fill: #d0b344 } -.terminal-1129851975-r6 { fill: #ff2627 } -.terminal-1129851975-r7 { fill: #00823d } -.terminal-1129851975-r8 { fill: #ff2c7a;font-weight: bold } + .terminal-3232574441-r1 { fill: #c5c8c6 } +.terminal-3232574441-r2 { fill: #98a84b } +.terminal-3232574441-r3 { fill: #9a9b99 } +.terminal-3232574441-r4 { fill: #608ab1 } +.terminal-3232574441-r5 { fill: #d0b344 } +.terminal-3232574441-r6 { fill: #ff2627 } +.terminal-3232574441-r7 { fill: #00823d } +.terminal-3232574441-r8 { fill: #ff2c7a;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -151,42 +151,42 @@ - + - - $ nf-core modules patch fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     Changes in module 'nf-core/fastqc' -INFO    'modules/nf-core/fastqc/environment.yml' is unchanged                                       -INFO    'modules/nf-core/fastqc/meta.yml' is unchanged                                              -INFO     Changes in 'fastqc/main.nf':                                                                - ---- modules/nf-core/fastqc/main.nf -+++ modules/nf-core/fastqc/main.nf -@@ -1,6 +1,6 @@ -process FASTQC {                                                                                   -    tag "$meta.id"                                                                                 --    label 'process_medium' -+    label 'process_low' - -    conda "${moduleDir}/environment.yml"                                                           -    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_  - - -INFO    'modules/nf-core/fastqc/tests/tags.yml' is unchanged                                        -INFO    'modules/nf-core/fastqc/tests/main.nf.test' is unchanged                                    -INFO    'modules/nf-core/fastqc/tests/main.nf.test.snap' is unchanged                               -INFO     Patch file of 'modules/nf-core/fastqc' written to 'modules/nf-core/fastqc/fastqc.diff' + + $ nf-core modules patch fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Changes in module 'nf-core/fastqc' +INFO    'modules/nf-core/fastqc/meta.yml' is unchanged                                              +INFO     Changes in 'fastqc/main.nf':                                                                + +--- modules/nf-core/fastqc/main.nf ++++ modules/nf-core/fastqc/main.nf +@@ -1,6 +1,6 @@ +process FASTQC {                                                                                   +    tag "$meta.id"                                                                                 +-    label 'process_medium' ++    label 'process_low' + +    conda "${moduleDir}/environment.yml"                                                           +    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_  + + +INFO    'modules/nf-core/fastqc/environment.yml' is unchanged                                       +INFO    'modules/nf-core/fastqc/tests/main.nf.test.snap' is unchanged                               +INFO    'modules/nf-core/fastqc/tests/tags.yml' is unchanged                                        +INFO    'modules/nf-core/fastqc/tests/main.nf.test' is unchanged                                    +INFO     Patch file of 'modules/nf-core/fastqc' written to 'modules/nf-core/fastqc/fastqc.diff' diff --git a/docs/images/nf-core-modules-remove.svg b/docs/images/nf-core-modules-remove.svg index b1dafc6753..910e57fb3c 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-2029268447-matrix { + .terminal-3288870273-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2029268447-title { + .terminal-3288870273-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2029268447-r1 { fill: #c5c8c6 } -.terminal-2029268447-r2 { fill: #98a84b } -.terminal-2029268447-r3 { fill: #9a9b99 } -.terminal-2029268447-r4 { fill: #608ab1 } -.terminal-2029268447-r5 { fill: #d0b344 } + .terminal-3288870273-r1 { fill: #c5c8c6 } +.terminal-3288870273-r2 { fill: #98a84b } +.terminal-3288870273-r3 { fill: #9a9b99 } +.terminal-3288870273-r4 { fill: #608ab1 } +.terminal-3288870273-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -88,22 +88,22 @@ - + - - $ nf-core modules remove abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     Removed files for 'abacas' and its dependencies 'abacas'.                                   + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Removed files for 'abacas' and its dependencies 'abacas'.                                   diff --git a/docs/images/nf-core-modules-test.svg b/docs/images/nf-core-modules-test.svg index 3416c21bc0..475a31db2b 100644 --- a/docs/images/nf-core-modules-test.svg +++ b/docs/images/nf-core-modules-test.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - $ nf-core modules test fastqc --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     Generating nf-test snapshot                                                                 -╭───────────────────────────────────────── nf-test output ─────────────────────────────────────────╮ -│                                                                                                  │ -│ 🚀 nf-test 0.8.2                                                                                 │ -│ https://code.askimed.com/nf-test                                                                 │ -│ (c) 2021 - 2023 Lukas Forer and Sebastian Schoenherr                                             │ -│                                                                                                  │ -│ Found 1 files in test directory.                                                                 │ -│                                                                                                  │ -│ Test Process FASTQC                                                                              │ -│                                                                                                  │ -│   Test [9cf5f580] 'sarscov2 - bam' FAILED (5.818s)                                               │ -│                                                                                                  │ -│   Assertion failed:                                                                              │ -│                                                                                                  │ -│   2 of 2 assertions failed                                                                       │ -│                                                                                                  │ -│   Nextflow stdout:                                                                               │ -│                                                                                                  │ -│   Process `FASTQC` declares 1 input channel but 2 were specified                                 │ -│                                                                                                  │ -│    -- Check script 'meta/mock.nf' at line: 41 or see                                             │ -│ '/home/runner/work/tools/tools/tmp/modules/.nf-test/tests/9cf5f5804db49395806e612d2a2c23ca/meta/ │ -│ nextflow.log' file for more details                                                              │ -│   Nextflow stderr:                                                                               │ -│                                                                                                  │ -│                                                                                                  │ -│                                                                                                  │ -│   Test [a2de5162] 'sarscov2 - bam - stub' FAILED (4.637s)                                        │ -│                                                                                                  │ -│   Assertion failed:                                                                              │ -│                                                                                                  │ -│   2 of 2 assertions failed                                                                       │ -│                                                                                                  │ -│   Nextflow stdout:                                                                               │ -│                                                                                                  │ -│   Process `FASTQC` declares 1 input channel but 2 were specified                                 │ -│                                                                                                  │ -│    -- Check script 'meta/mock.nf' at line: 41 or see                                             │ -│ '/home/runner/work/tools/tools/tmp/modules/.nf-test/tests/a2de51628f1d36119180ba630b7026a2/meta/ │ -│ nextflow.log' file for more details                                                              │ -│   Nextflow stderr:                                                                               │ -│                                                                                                  │ -│                                                                                                  │ -│                                                                                                  │ -│                                                                                                  │ -│ Test Workflow FASTQ_FASTQC_UMITOOLS_FASTP                                                        │ -│                                                                                                  │ -│   Test [19e7efa0] 'sarscov2 paired-end [fastq]' FAILED (5.439s)                                  │ -│                                                                                                  │ -│   Assertion failed:                                                                              │ -│                                                                                                  │ -│   14 of 14 assertions failed                                                                     │ -│                                                                                                  │ -│   Nextflow stdout:                                                                               │ -│                                                                                                  │ -│   ERROR ~ No such variable: Exception evaluating property 'html' for nextflow.script.ChannelOut, │ -│ Reason: groovy.lang.MissingPropertyException: No such property: html for class:                  │ -│ groovyx.gpars.dataflow.DataflowBroadcast                                                         │ -│   Possible solutions: head                                                                       │ -│                                                                                                  │ -│    -- Check script                                                                               │ -│ '/home/runner/work/tools/tools/tmp/modules/./subworkflows/nf-core/fastq_fastqc_umitools_fastp/te │ -│ sts/../main.nf' at line: 115 or see                                                              │ -│ '/home/runner/work/tools/tools/tmp/modules/.nf-test/tests/19e7efa075a613f6b4da77288e1c9f33/meta/ │ -│ nextflow.log' file for more details                                                              │ -│   Nextflow stderr:                                                                               │ -│                                                                                                  │ -│                                                                                                  │ -│                                                                                                  │ -│                                                                                                  │ -│                                                                                                  │ -│ FAILURE: Executed 3 tests in 15.898s (3 failed)                                                  │ -│                                                                                                  │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────────────────────── nf-test error ──────────────────────────────────────────╮ -│ Assertion failed:                                                                                │ -│                                                                                                  │ -│ assert process.success                                                                           │ -│        |       |                                                                                 │ -│        FASTQC  false                                                                             │ -│                                                                                                  │ -│ java.lang.RuntimeException: Process has no output channels. process.out can not be used.         │ -│ Assertion failed:                                                                                │ -│                                                                                                  │ -│ assert process.success                                                                           │ -│        |       |                                                                                 │ -│        FASTQC  false                                                                             │ -│                                                                                                  │ -│ java.lang.RuntimeException: Process has no output channels. process.out can not be used.         │ -│ Assertion failed:                                                                                │ -│                                                                                                  │ -│ assert workflow.success                                                                          │ -│        |        |                                                                                │ -│        workflow false                                                                            │ -│                                                                                                  │ -│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ -│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ -│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ -│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ -│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ -│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ -│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ -│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ -│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ -│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ -│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ -│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ -│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ -│                                                                                                  │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -CRITICAL Ran, but found errors:                                                                      -          - nf-test failed                                                                           + + + + $ nf-core modules test fastqc --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Generating nf-test snapshot                                                                 diff --git a/docs/images/nf-core-modules-update.svg b/docs/images/nf-core-modules-update.svg index 6169857b74..400b4470c1 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-2555794352-matrix { + .terminal-1757107026-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2555794352-title { + .terminal-1757107026-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2555794352-r1 { fill: #c5c8c6 } -.terminal-2555794352-r2 { fill: #98a84b } -.terminal-2555794352-r3 { fill: #9a9b99 } -.terminal-2555794352-r4 { fill: #608ab1 } -.terminal-2555794352-r5 { fill: #d0b344 } + .terminal-1757107026-r1 { fill: #c5c8c6 } +.terminal-1757107026-r2 { fill: #98a84b } +.terminal-1757107026-r3 { fill: #9a9b99 } +.terminal-1757107026-r4 { fill: #608ab1 } +.terminal-1757107026-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core modules update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - 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 ✨                                                                         + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - 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 deb06cbf36..e3404658f0 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-343853851-matrix { + .terminal-2029177533-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-343853851-title { + .terminal-2029177533-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-343853851-r1 { fill: #c5c8c6 } -.terminal-343853851-r2 { fill: #98a84b } -.terminal-343853851-r3 { fill: #9a9b99 } -.terminal-343853851-r4 { fill: #608ab1 } -.terminal-343853851-r5 { fill: #d0b344 } -.terminal-343853851-r6 { fill: #98a84b;font-weight: bold } -.terminal-343853851-r7 { fill: #868887;font-weight: bold } -.terminal-343853851-r8 { fill: #868887 } -.terminal-343853851-r9 { fill: #4e707b;font-weight: bold } -.terminal-343853851-r10 { fill: #68a0b3;font-weight: bold } + .terminal-2029177533-r1 { fill: #c5c8c6 } +.terminal-2029177533-r2 { fill: #98a84b } +.terminal-2029177533-r3 { fill: #9a9b99 } +.terminal-2029177533-r4 { fill: #608ab1 } +.terminal-2029177533-r5 { fill: #d0b344 } +.terminal-2029177533-r6 { fill: #98a84b;font-weight: bold } +.terminal-2029177533-r7 { fill: #868887;font-weight: bold } +.terminal-2029177533-r8 { fill: #868887 } +.terminal-2029177533-r9 { fill: #4e707b;font-weight: bold } +.terminal-2029177533-r10 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,23 +96,23 @@ - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 30 params) -INFO     Writing schema with 31 params: './nextflow_schema.json' + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - 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 f8ca82b271..34b71e7f47 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-3360246661-matrix { + .terminal-3400157991-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3360246661-title { + .terminal-3400157991-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3360246661-r1 { fill: #c5c8c6 } -.terminal-3360246661-r2 { fill: #98a84b } -.terminal-3360246661-r3 { fill: #9a9b99 } -.terminal-3360246661-r4 { fill: #608ab1 } -.terminal-3360246661-r5 { fill: #d0b344 } -.terminal-3360246661-r6 { fill: #98a84b;font-weight: bold } -.terminal-3360246661-r7 { fill: #868887;font-weight: bold } -.terminal-3360246661-r8 { fill: #868887 } -.terminal-3360246661-r9 { fill: #4e707b;font-weight: bold } + .terminal-3400157991-r1 { fill: #c5c8c6 } +.terminal-3400157991-r2 { fill: #98a84b } +.terminal-3400157991-r3 { fill: #9a9b99 } +.terminal-3400157991-r4 { fill: #608ab1 } +.terminal-3400157991-r5 { fill: #d0b344 } +.terminal-3400157991-r6 { fill: #98a84b;font-weight: bold } +.terminal-3400157991-r7 { fill: #868887;font-weight: bold } +.terminal-3400157991-r8 { fill: #868887 } +.terminal-3400157991-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -92,22 +92,22 @@ - + - - $ nf-core schema lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 31 params) + + $ nf-core schema lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - 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 2eb5093ede..048289f30e 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-2178481397-matrix { + .terminal-2717056151-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2178481397-title { + .terminal-2717056151-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2178481397-r1 { fill: #c5c8c6 } -.terminal-2178481397-r2 { fill: #98a84b } -.terminal-2178481397-r3 { fill: #9a9b99 } -.terminal-2178481397-r4 { fill: #608ab1 } -.terminal-2178481397-r5 { fill: #d0b344 } -.terminal-2178481397-r6 { fill: #98a84b;font-weight: bold } -.terminal-2178481397-r7 { fill: #868887;font-weight: bold } -.terminal-2178481397-r8 { fill: #868887 } -.terminal-2178481397-r9 { fill: #4e707b;font-weight: bold } + .terminal-2717056151-r1 { fill: #c5c8c6 } +.terminal-2717056151-r2 { fill: #98a84b } +.terminal-2717056151-r3 { fill: #9a9b99 } +.terminal-2717056151-r4 { fill: #608ab1 } +.terminal-2717056151-r5 { fill: #d0b344 } +.terminal-2717056151-r6 { fill: #98a84b;font-weight: bold } +.terminal-2717056151-r7 { fill: #868887;font-weight: bold } +.terminal-2717056151-r8 { fill: #868887 } +.terminal-2717056151-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -95,23 +95,23 @@ - + - - $ nf-core schema validate nf-core-rnaseq/3_8 nf-params.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - 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/3_8 nf-params.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 93 params) +INFO    [✓] Input parameters look valid diff --git a/docs/images/nf-core-subworkflows-create.svg b/docs/images/nf-core-subworkflows-create.svg index 21edf7370b..d559a8819d 100644 --- a/docs/images/nf-core-subworkflows-create.svg +++ b/docs/images/nf-core-subworkflows-create.svg @@ -19,89 +19,89 @@ font-weight: 700; } - .terminal-344362394-matrix { + .terminal-1494453564-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-344362394-title { + .terminal-1494453564-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-344362394-r1 { fill: #c5c8c6 } -.terminal-344362394-r2 { fill: #98a84b } -.terminal-344362394-r3 { fill: #9a9b99 } -.terminal-344362394-r4 { fill: #608ab1 } -.terminal-344362394-r5 { fill: #d0b344 } -.terminal-344362394-r6 { fill: #68a0b3;font-weight: bold } + .terminal-1494453564-r1 { fill: #c5c8c6 } +.terminal-1494453564-r2 { fill: #98a84b } +.terminal-1494453564-r3 { fill: #9a9b99 } +.terminal-1494453564-r4 { fill: #608ab1 } +.terminal-1494453564-r5 { fill: #d0b344 } +.terminal-1494453564-r6 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -113,30 +113,30 @@ - + - - $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     Repository type: modules -INFO    Press enter to use default values (shown in brackets)or type your own responses.  -ctrl+click underlined text to open links. -INFO     Created component template: 'bam_stats_samtools' -INFO     Created following files:                                                                    -           subworkflows/nf-core/bam_stats_samtools/main.nf                                           -           subworkflows/nf-core/bam_stats_samtools/meta.yml                                          -           subworkflows/nf-core/bam_stats_samtools/tests/tags.yml                                    -           subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test                                + + $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Repository type: modules +INFO    Press enter to use default values (shown in brackets)or type your own responses.  +ctrl+click underlined text to open links. +INFO     Created component template: 'bam_stats_samtools' +INFO     Created following files:                                                                    +           subworkflows/nf-core/bam_stats_samtools/main.nf                                           +           subworkflows/nf-core/bam_stats_samtools/meta.yml                                          +           subworkflows/nf-core/bam_stats_samtools/tests/tags.yml                                    +           subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test                                diff --git a/docs/images/nf-core-subworkflows-info.svg b/docs/images/nf-core-subworkflows-info.svg index d21f2e2b51..86d8ff7970 100644 --- a/docs/images/nf-core-subworkflows-info.svg +++ b/docs/images/nf-core-subworkflows-info.svg @@ -19,112 +19,112 @@ font-weight: 700; } - .terminal-2172892372-matrix { + .terminal-139834486-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2172892372-title { + .terminal-139834486-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2172892372-r1 { fill: #c5c8c6 } -.terminal-2172892372-r2 { fill: #98a84b } -.terminal-2172892372-r3 { fill: #9a9b99 } -.terminal-2172892372-r4 { fill: #608ab1 } -.terminal-2172892372-r5 { fill: #d0b344 } -.terminal-2172892372-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2172892372-r7 { fill: #98a84b;font-weight: bold } -.terminal-2172892372-r8 { fill: #868887 } -.terminal-2172892372-r9 { fill: #868887;font-style: italic; } -.terminal-2172892372-r10 { fill: #d08442 } -.terminal-2172892372-r11 { fill: #98729f } + .terminal-139834486-r1 { fill: #c5c8c6 } +.terminal-139834486-r2 { fill: #98a84b } +.terminal-139834486-r3 { fill: #9a9b99 } +.terminal-139834486-r4 { fill: #608ab1 } +.terminal-139834486-r5 { fill: #d0b344 } +.terminal-139834486-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-139834486-r7 { fill: #98a84b;font-weight: bold } +.terminal-139834486-r8 { fill: #868887 } +.terminal-139834486-r9 { fill: #868887;font-style: italic; } +.terminal-139834486-r10 { fill: #d08442 } +.terminal-139834486-r11 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -136,36 +136,36 @@ - + - - $ nf-core subworkflows info bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -╭─ Subworkflow: bam_rseqc  ────────────────────────────────────────────────────────────────────────╮ -│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ -│ 📖 Description: Subworkflow to run multiple commands in the RSeqC package                        │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -[..truncated..] - ch_readduplication_rscript  (file)│script to reproduce the plot        │                      *.R -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_tin  (file)                    │TXT file containing tin.py results  │                    *.txt -                                    │summary                             │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - versions  (file)                  │File containing software versions   │             versions.yml -                                    ╵                                    ╵                           - - 💻  Installation command: nf-core subworkflows install bam_rseqc - + + $ nf-core subworkflows info bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +╭─ Subworkflow: bam_rseqc  ────────────────────────────────────────────────────────────────────────╮ +│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ +│ 📖 Description: Subworkflow to run multiple commands in the RSeqC package                        │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +[..truncated..] + ch_readduplication_rscript  (file)│script to reproduce the plot        │                      *.R +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_tin  (file)                    │TXT file containing tin.py results  │                    *.txt +                                    │summary                             │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + versions  (file)                  │File containing software versions   │             versions.yml +                                    ╵                                    ╵                           + + 💻  Installation command: nf-core subworkflows install bam_rseqc + diff --git a/docs/images/nf-core-subworkflows-install.svg b/docs/images/nf-core-subworkflows-install.svg index 4e1c3d29a9..344150cbf2 100644 --- a/docs/images/nf-core-subworkflows-install.svg +++ b/docs/images/nf-core-subworkflows-install.svg @@ -19,76 +19,76 @@ font-weight: 700; } - .terminal-1280284146-matrix { + .terminal-3712652692-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1280284146-title { + .terminal-3712652692-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1280284146-r1 { fill: #c5c8c6 } -.terminal-1280284146-r2 { fill: #98a84b } -.terminal-1280284146-r3 { fill: #9a9b99 } -.terminal-1280284146-r4 { fill: #608ab1 } -.terminal-1280284146-r5 { fill: #d0b344 } + .terminal-3712652692-r1 { fill: #c5c8c6 } +.terminal-3712652692-r2 { fill: #98a84b } +.terminal-3712652692-r3 { fill: #9a9b99 } +.terminal-3712652692-r4 { fill: #608ab1 } +.terminal-3712652692-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core subworkflows install bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     Installing 'bam_rseqc' -INFO     Use the following statement to include this subworkflow:                                    - - include { BAM_RSEQC } from '../subworkflows/nf-core/bam_rseqc/main'                                 - + + $ nf-core subworkflows install bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Installing 'bam_rseqc' +INFO     Use the following statement to include this subworkflow:                                    + + include { BAM_RSEQC } from '../subworkflows/nf-core/bam_rseqc/main'                                 + diff --git a/docs/images/nf-core-subworkflows-lint.svg b/docs/images/nf-core-subworkflows-lint.svg index ce3299a21f..3b84645270 100644 --- a/docs/images/nf-core-subworkflows-lint.svg +++ b/docs/images/nf-core-subworkflows-lint.svg @@ -19,239 +19,239 @@ font-weight: 700; } - .terminal-4099828428-matrix { + .terminal-1652488611-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4099828428-title { + .terminal-1652488611-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4099828428-r1 { fill: #c5c8c6 } -.terminal-4099828428-r2 { fill: #98a84b } -.terminal-4099828428-r3 { fill: #9a9b99 } -.terminal-4099828428-r4 { fill: #608ab1 } -.terminal-4099828428-r5 { fill: #d0b344 } -.terminal-4099828428-r6 { fill: #d0b344;font-weight: bold } -.terminal-4099828428-r7 { fill: #8d7b39 } -.terminal-4099828428-r8 { fill: #fdfdc5 } -.terminal-4099828428-r9 { fill: #d0b344;font-style: italic; } -.terminal-4099828428-r10 { fill: #c5c8c6;font-weight: bold } -.terminal-4099828428-r11 { fill: #98a84b;font-weight: bold } -.terminal-4099828428-r12 { fill: #cc555a } + .terminal-1652488611-r1 { fill: #c5c8c6 } +.terminal-1652488611-r2 { fill: #98a84b } +.terminal-1652488611-r3 { fill: #9a9b99 } +.terminal-1652488611-r4 { fill: #608ab1 } +.terminal-1652488611-r5 { fill: #d0b344 } +.terminal-1652488611-r6 { fill: #d0b344;font-weight: bold } +.terminal-1652488611-r7 { fill: #8d7b39 } +.terminal-1652488611-r8 { fill: #68a0b3;font-weight: bold } +.terminal-1652488611-r9 { fill: #d0b344;font-style: italic; } +.terminal-1652488611-r10 { fill: #c5c8c6;font-weight: bold } +.terminal-1652488611-r11 { fill: #98a84b;font-weight: bold } +.terminal-1652488611-r12 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -263,78 +263,78 @@ - + - - $ nf-core subworkflows lint bam_stats_samtools - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     Linting modules repo: '.' -INFO     Linting subworkflow: 'bam_stats_samtools' - -╭─[!] 14 Subworkflow Test Warnings───────────────────────────────────────────────────────────────╮ -│                     ╷                                     ╷                                      │ -│Subworkflow name   │File path                          │Test message                        │ -│╶────────────────────┼─────────────────────────────────────┼─────────────────────────────────────╴│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: //Add │ -│││all required assertions to verify │ -│││the test output.│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Add │ -│││tags for all modules used within │ -│││this subworkflow. Example:│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Change │ -│││the test name preferably indicating │ -│││the test-data and file-format used│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Once │ -│││you have added the required tests, │ -│││please run the following command to │ -│││build this file:│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: define │ -│││inputs of the workflow here. │ -│││Example:│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: A │ -│││subworkflow SHOULD import at least │ -│││two modules│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: If in doubt │ -│││look at other nf-core/subworkflows │ -│││to see how we are doing things! :)│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit emitted│ -│││channels│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit input │ -│││(take) channels│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: substitute │ -│││modules here for the modules of your│ -│││subworkflow│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a │ -│││description of the subworkflow and │ -│││list keywords│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a list│ -│││of the modules and/or subworkflows │ -│││used in the subworkflow│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ -│││of the channels used as input with a│ -│││description and their structure│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ -│││of the channels used as output with │ -│││a descriptions and their structure│ -│                     ╵                                     ╵                                      │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────╮ -│LINT RESULTS SUMMARY│ -├───────────────────────┤ -│[✔]  42 Tests Passed │ -│[!]  14 Test Warnings│ -│[✗]   0 Tests Failed │ -╰───────────────────────╯ + + $ nf-core subworkflows lint bam_stats_samtools + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Linting modules repo: '.' +INFO     Linting subworkflow: 'bam_stats_samtools' + +╭─[!] 14 Subworkflow Test Warnings───────────────────────────────────────────────────────────────╮ +│                     ╷                                     ╷                                      │ +│Subworkflow name   │File path                          │Test message                        │ +│╶────────────────────┼─────────────────────────────────────┼─────────────────────────────────────╴│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: //Add │ +│││all required assertions to verify │ +│││the test output.│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Add │ +│││tags for all modules used within │ +│││this subworkflow. Example:│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Change │ +│││the test name preferably indicating │ +│││the test-data and file-format used│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Once │ +│││you have added the required tests, │ +│││please run the following command to │ +│││build this file:│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: define │ +│││inputs of the workflow here. │ +│││Example:│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: A │ +│││subworkflow SHOULD import at least │ +│││two modules│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: If in doubt │ +│││look at other nf-core/subworkflows │ +│││to see how we are doing things! :)│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit emitted│ +│││channels│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit input │ +│││(take) channels│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: substitute │ +│││modules here for the modules of your│ +│││subworkflow│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a │ +│││description of the subworkflow and │ +│││list keywords│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a list│ +│││of the modules and/or subworkflows │ +│││used in the subworkflow│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ +│││of the channels used as input with a│ +│││description and their structure│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ +│││of the channels used as output with │ +│││a descriptions and their structure│ +│                     ╵                                     ╵                                      │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭───────────────────────╮ +│LINT RESULTS SUMMARY│ +├───────────────────────┤ +│[✔]  42 Tests Passed │ +│[!]  14 Test Warnings│ +│[✗]   0 Tests Failed │ +╰───────────────────────╯ diff --git a/docs/images/nf-core-subworkflows-list-local.svg b/docs/images/nf-core-subworkflows-list-local.svg index 47871a6f4d..b73f19d7e6 100644 --- a/docs/images/nf-core-subworkflows-list-local.svg +++ b/docs/images/nf-core-subworkflows-list-local.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core subworkflows list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     No nf-core subworkflows found in '.' - + + $ nf-core subworkflows list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     No nf-core subworkflows found in '.' +self.repo_type='pipeline' + diff --git a/docs/images/nf-core-subworkflows-list-remote.svg b/docs/images/nf-core-subworkflows-list-remote.svg index bdc5e51c7c..6df1eb00d9 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-2018331402-matrix { + .terminal-2916043436-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2018331402-title { + .terminal-2916043436-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2018331402-r1 { fill: #c5c8c6 } -.terminal-2018331402-r2 { fill: #98a84b } -.terminal-2018331402-r3 { fill: #9a9b99 } -.terminal-2018331402-r4 { fill: #608ab1 } -.terminal-2018331402-r5 { fill: #d0b344 } -.terminal-2018331402-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-2018331402-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-2018331402-r8 { fill: #868887;font-style: italic; } + .terminal-2916043436-r1 { fill: #c5c8c6 } +.terminal-2916043436-r2 { fill: #98a84b } +.terminal-2916043436-r3 { fill: #9a9b99 } +.terminal-2916043436-r4 { fill: #608ab1 } +.terminal-2916043436-r5 { fill: #d0b344 } +.terminal-2916043436-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-2916043436-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2916043436-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core subworkflows list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Subworkflow Name                             ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ bam_cnv_wisecondorx                           │ -│ bam_create_som_pon_gatk                       │ -│ bam_dedup_stats_samtools_umitools             │ -│ bam_docounts_contamination_angsd              │ -│ bam_markduplicates_picard                     │ -│ bam_markduplicates_samtools                   │ -│ bam_ngscheckmate                              │ -│ bam_qc_picard                                 │ -│ bam_rseqc                                     │ -[..truncated..] + + $ nf-core subworkflows list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Subworkflow Name                             ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ bam_cnv_wisecondorx                           │ +│ bam_create_som_pon_gatk                       │ +│ bam_dedup_stats_samtools_umitools             │ +│ bam_docounts_contamination_angsd              │ +│ bam_markduplicates_picard                     │ +│ bam_markduplicates_samtools                   │ +│ bam_ngscheckmate                              │ +│ bam_qc_picard                                 │ +│ bam_rseqc                                     │ +[..truncated..] diff --git a/docs/images/nf-core-subworkflows-remove.svg b/docs/images/nf-core-subworkflows-remove.svg index 28527bc299..5bf8048c3b 100644 --- a/docs/images/nf-core-subworkflows-remove.svg +++ b/docs/images/nf-core-subworkflows-remove.svg @@ -19,100 +19,100 @@ font-weight: 700; } - .terminal-1022880614-matrix { + .terminal-4184599304-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1022880614-title { + .terminal-4184599304-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1022880614-r1 { fill: #c5c8c6 } -.terminal-1022880614-r2 { fill: #98a84b } -.terminal-1022880614-r3 { fill: #9a9b99 } -.terminal-1022880614-r4 { fill: #608ab1 } -.terminal-1022880614-r5 { fill: #d0b344 } + .terminal-4184599304-r1 { fill: #c5c8c6 } +.terminal-4184599304-r2 { fill: #98a84b } +.terminal-4184599304-r3 { fill: #9a9b99 } +.terminal-4184599304-r4 { fill: #608ab1 } +.terminal-4184599304-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -124,34 +124,34 @@ - + - - $ nf-core subworkflows remove bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     Removed files for 'rseqc/bamstat' and its dependencies 'rseqc/bamstat'.                     -INFO     Removed files for 'rseqc/inferexperiment' and its dependencies 'rseqc/inferexperiment'.     -INFO     Removed files for 'rseqc/innerdistance' and its dependencies 'rseqc/innerdistance'.         -INFO     Removed files for 'rseqc/junctionannotation' and its dependencies                           -'rseqc/junctionannotation'.                                                                 -INFO     Removed files for 'rseqc/junctionsaturation' and its dependencies                           -'rseqc/junctionsaturation'.                                                                 -INFO     Removed files for 'rseqc/readdistribution' and its dependencies 'rseqc/readdistribution'.   -INFO     Removed files for 'rseqc/readduplication' and its dependencies 'rseqc/readduplication'.     -INFO     Removed files for 'rseqc/tin' and its dependencies 'rseqc/tin'.                             -INFO     Removed files for 'bam_rseqc' and its dependencies 'bam_rseqc, rseqc_bamstat,  -rseqc_inferexperiment, rseqc_innerdistance, rseqc_junctionannotation,  -rseqc_junctionsaturation, rseqc_readdistribution, rseqc_readduplication, rseqc_tin'.        + + $ nf-core subworkflows remove bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Removed files for 'rseqc/bamstat' and its dependencies 'rseqc/bamstat'.                     +INFO     Removed files for 'rseqc/inferexperiment' and its dependencies 'rseqc/inferexperiment'.     +INFO     Removed files for 'rseqc/innerdistance' and its dependencies 'rseqc/innerdistance'.         +INFO     Removed files for 'rseqc/junctionannotation' and its dependencies                           +'rseqc/junctionannotation'.                                                                 +INFO     Removed files for 'rseqc/junctionsaturation' and its dependencies                           +'rseqc/junctionsaturation'.                                                                 +INFO     Removed files for 'rseqc/readdistribution' and its dependencies 'rseqc/readdistribution'.   +INFO     Removed files for 'rseqc/readduplication' and its dependencies 'rseqc/readduplication'.     +INFO     Removed files for 'rseqc/tin' and its dependencies 'rseqc/tin'.                             +INFO     Removed files for 'bam_rseqc' and its dependencies 'bam_rseqc, rseqc_bamstat,  +rseqc_inferexperiment, rseqc_innerdistance, rseqc_junctionannotation,  +rseqc_junctionsaturation, rseqc_readdistribution, rseqc_readduplication, rseqc_tin'.        diff --git a/docs/images/nf-core-subworkflows-test.svg b/docs/images/nf-core-subworkflows-test.svg index cbc724f546..8bcab4bda0 100644 --- a/docs/images/nf-core-subworkflows-test.svg +++ b/docs/images/nf-core-subworkflows-test.svg @@ -19,64 +19,64 @@ font-weight: 700; } - .terminal-1704916071-matrix { + .terminal-3863409673-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1704916071-title { + .terminal-3863409673-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1704916071-r1 { fill: #c5c8c6 } -.terminal-1704916071-r2 { fill: #98a84b } -.terminal-1704916071-r3 { fill: #9a9b99 } -.terminal-1704916071-r4 { fill: #608ab1 } -.terminal-1704916071-r5 { fill: #d0b344 } + .terminal-3863409673-r1 { fill: #c5c8c6 } +.terminal-3863409673-r2 { fill: #98a84b } +.terminal-3863409673-r3 { fill: #9a9b99 } +.terminal-3863409673-r4 { fill: #608ab1 } +.terminal-3863409673-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -88,22 +88,22 @@ - + - - $ nf-core subworkflows test bam_rseqc --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO     Generating nf-test snapshot                                                                 + + $ nf-core subworkflows test bam_rseqc --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO     Generating nf-test snapshot                                                                 diff --git a/docs/images/nf-core-subworkflows-update.svg b/docs/images/nf-core-subworkflows-update.svg index 0a9d9eceaf..285e5e569f 100644 --- a/docs/images/nf-core-subworkflows-update.svg +++ b/docs/images/nf-core-subworkflows-update.svg @@ -19,67 +19,67 @@ font-weight: 700; } - .terminal-2377731045-matrix { + .terminal-2735557511-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2377731045-title { + .terminal-2735557511-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2377731045-r1 { fill: #c5c8c6 } -.terminal-2377731045-r2 { fill: #98a84b } -.terminal-2377731045-r3 { fill: #9a9b99 } -.terminal-2377731045-r4 { fill: #608ab1 } -.terminal-2377731045-r5 { fill: #d0b344 } + .terminal-2735557511-r1 { fill: #c5c8c6 } +.terminal-2735557511-r2 { fill: #98a84b } +.terminal-2735557511-r3 { fill: #9a9b99 } +.terminal-2735557511-r4 { fill: #608ab1 } +.terminal-2735557511-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -91,23 +91,23 @@ - + - - $ nf-core subworkflows update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - - -INFO    'subworkflows/nf-core/bam_rseqc' is already up to date                                      -INFO     Updates complete ✨                                                                         + + $ nf-core subworkflows update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + + +INFO    'subworkflows/nf-core/bam_rseqc' is already up to date                                      +INFO     Updates complete ✨                                                                         diff --git a/docs/images/nf-core-sync.svg b/docs/images/nf-core-sync.svg index 18aa790e23..3d231e45f1 100644 --- a/docs/images/nf-core-sync.svg +++ b/docs/images/nf-core-sync.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + - + - + - - $ nf-core sync - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11.1 - https://nf-co.re - - -WARNING  Could not find GitHub authentication token. Some API requests may fail.                     -INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthing -INFO     Original pipeline repository branch is 'master' -INFO     Deleting all files in 'TEMPLATE' branch                                                     -INFO     Making a new template pipeline using pipeline variables                                     + + $ nf-core sync + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.12 - https://nf-co.re + + +WARNING  Could not find GitHub authentication token. Some API requests may fail.                     +INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthing +INFO     Original pipeline repository branch is 'master' +INFO     Deleting all files in 'TEMPLATE' branch                                                     +INFO     Making a new template pipeline using pipeline variables                                     +INFO     Committed changes to 'TEMPLATE' branch                                                      +INFO     Checking out original branch: 'master' +INFO     Now try to merge the updates in to your pipeline:                                           +           cd /home/runner/work/tools/tools/tmp/nf-core-nextbigthing +           git merge TEMPLATE