diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg index a21fb69056..528ca47408 100644 --- a/docs/images/nf-core-bump-version.svg +++ b/docs/images/nf-core-bump-version.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core bump-version 1.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - 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' - - -ERROR    Could not find version number in assets/multiqc_config.yml: '('1\\.0dev', '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/releases/tag/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> - - <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 2.11 - 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.svg b/docs/images/nf-core-create.svg index 15a043a7aa..680fbe8ad2 100644 --- a/docs/images/nf-core-create.svg +++ b/docs/images/nf-core-create.svg @@ -19,104 +19,104 @@ font-weight: 700; } - .terminal-1329910358-matrix { + .terminal-1578160727-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1329910358-title { + .terminal-1578160727-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1329910358-r1 { fill: #c5c8c6 } -.terminal-1329910358-r2 { fill: #98a84b } -.terminal-1329910358-r3 { fill: #9a9b99 } -.terminal-1329910358-r4 { fill: #608ab1 } -.terminal-1329910358-r5 { fill: #d0b344 } -.terminal-1329910358-r6 { fill: #98729f } -.terminal-1329910358-r7 { fill: #ff2c7a } -.terminal-1329910358-r8 { fill: #98a84b;font-weight: bold } -.terminal-1329910358-r9 { fill: #1984e9;text-decoration: underline; } + .terminal-1578160727-r1 { fill: #c5c8c6 } +.terminal-1578160727-r2 { fill: #98a84b } +.terminal-1578160727-r3 { fill: #9a9b99 } +.terminal-1578160727-r4 { fill: #608ab1 } +.terminal-1578160727-r5 { fill: #d0b344 } +.terminal-1578160727-r6 { fill: #98729f } +.terminal-1578160727-r7 { fill: #ff2c7a } +.terminal-1578160727-r8 { fill: #98a84b;font-weight: bold } +.terminal-1578160727-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 2.10 - 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 2.11 - 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 d65d1e5571..0a327fbaa7 100644 --- a/docs/images/nf-core-download.svg +++ b/docs/images/nf-core-download.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - -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 2.11 - 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 05bb424160..53f80a26be 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-1709682129-matrix { + .terminal-1786293714-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1709682129-title { + .terminal-1786293714-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1709682129-r1 { fill: #c5c8c6 } -.terminal-1709682129-r2 { fill: #98a84b } -.terminal-1709682129-r3 { fill: #9a9b99 } -.terminal-1709682129-r4 { fill: #608ab1 } -.terminal-1709682129-r5 { fill: #d0b344 } -.terminal-1709682129-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1709682129-r7 { fill: #68a0b3;font-weight: bold } + .terminal-1786293714-r1 { fill: #c5c8c6 } +.terminal-1786293714-r2 { fill: #98a84b } +.terminal-1786293714-r3 { fill: #9a9b99 } +.terminal-1786293714-r4 { fill: #608ab1 } +.terminal-1786293714-r5 { fill: #d0b344 } +.terminal-1786293714-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1786293714-r7 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,24 +96,24 @@ - + - - $ nf-core launch rnaseq -r 3.8.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - 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 2.11 - 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 ee99ec8128..885973ea4a 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 2.10 - https://nf-co.re - - -INFO     Fetching licence information for 8 tools                                                    + + $ nf-core licences deepvariant + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - https://nf-co.re + + +INFO     Fetching licence information for 8 tools                                                    +INFO     Warning: This tool only prints licence information for the software tools packaged using    +         conda.                                                                                      +INFO     The pipeline may use other software and dependencies not described here.                    +┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓ +┃Package Name┃Version┃Licence┃ +┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩ +│ lbzip2       │ 2.5     │ GPL v3  │ +│ deepvariant  │ 0.7.0   │ MIT     │ +│ htslib       │ 1.9     │ MIT     │ +│ picard       │ 2.18.7  │ MIT     │ +│ pip          │ 10.0.1  │ MIT     │ +│ samtools     │ 1.9     │ MIT     │ +│ python       │ 2.7.15  │ PSF     │ +│ bzip2        │ 1.0.6   │ bzip2   │ +└──────────────┴─────────┴─────────┘ diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg index a10c597a23..84e8b387bc 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 2.10 - 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).│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - -╭─[!] 3 Module Test Warnings─────────────────────────────────────────────────────────────────────╮ -│                                           ╷                          ╷                           │ -│Module name                              │File path               │Test message             │ -│╶──────────────────────────────────────────┼──────────────────────────┼──────────────────────────╴│ -│custom/dumpsoftwareversions│modules/nf-core/custom/…│New version available│ -│fastqc│modules/nf-core/fastqc  │New version available│ -│multiqc│modules/nf-core/multiqc │New version available│ -│                                           ╵                          ╵                           │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────╮ -│LINT RESULTS SUMMARY │ -├───────────────────────┤ -│[✔] 183 Tests Passed│ -│[?]   1 Test Ignored│ -│[!]   4 Test Warnings│ -│[✗]   0 Tests Failed│ -╰───────────────────────╯ + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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│ +╰──────────────────────╯ diff --git a/docs/images/nf-core-list-rna.svg b/docs/images/nf-core-list-rna.svg index ea5cbae618..b5f6ba62c2 100644 --- a/docs/images/nf-core-list-rna.svg +++ b/docs/images/nf-core-list-rna.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core list rna rna-seq - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ scrnaseq             │    99 │            dev │   3 days ago │           - │ -                   │ -│ rnafusion            │   112 │            dev │   3 days ago │           - │ -                   │ -│ differentialabundan… │    26 │            dev │  2 weeks ago │           - │ -                   │ -│ dualrnaseq           │    13 │            dev │  2 weeks ago │           - │ -                   │ -│ smrnaseq             │    54 │            dev │  3 weeks ago │           - │ -                   │ -│ rnaseq               │   665 │            dev │ 1 months ago │           - │ -                   │ -│ marsseq              │     4 │            dev │ 2 months ago │           - │ -                   │ -│ spatialtranscriptom… │    27 │            dev │ 3 months ago │           - │ -                   │ -│ circrna              │    31 │            dev │ 8 months ago │           - │ -                   │ -│ lncpipe              │    26 │            dev │  1 years ago │           - │ -                   │ -│ scflow               │    20 │            dev │  2 years ago │           - │ -                   │ -└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ + + $ nf-core list rna rna-seq + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnafusion            │   119 │          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 │           - │ -                   │ +└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg index 067a8bc3b6..0d741d48ba 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-2093940179-matrix { + .terminal-2494560554-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2093940179-title { + .terminal-2494560554-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2093940179-r1 { fill: #c5c8c6 } -.terminal-2093940179-r2 { fill: #98a84b } -.terminal-2093940179-r3 { fill: #9a9b99 } -.terminal-2093940179-r4 { fill: #608ab1 } -.terminal-2093940179-r5 { fill: #d0b344 } -.terminal-2093940179-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2093940179-r7 { fill: #868887 } -.terminal-2093940179-r8 { fill: #868887;font-style: italic; } + .terminal-2494560554-r1 { fill: #c5c8c6 } +.terminal-2494560554-r2 { fill: #98a84b } +.terminal-2494560554-r3 { fill: #9a9b99 } +.terminal-2494560554-r4 { fill: #608ab1 } +.terminal-2494560554-r5 { fill: #d0b344 } +.terminal-2494560554-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-2494560554-r7 { fill: #868887 } +.terminal-2494560554-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -112,29 +112,29 @@ - + - - $ nf-core list -s stars - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq              │   665 │            dev │  1 months ago │           - │ -                   │ -│ sarek               │   273 │            dev │    6 days ago │           - │ -                   │ -│ chipseq             │   153 │            dev │  2 months ago │           - │ -                   │ -│ atacseq             │   147 │            dev │   3 weeks ago │           - │ -                   │ -[..truncated..] + + $ nf-core list -s stars + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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..] diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg index 7980f060fb..2d8873a082 100644 --- a/docs/images/nf-core-list.svg +++ b/docs/images/nf-core-list.svg @@ -19,91 +19,91 @@ font-weight: 700; } - .terminal-3744497940-matrix { + .terminal-1618644398-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3744497940-title { + .terminal-1618644398-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3744497940-r1 { fill: #c5c8c6 } -.terminal-3744497940-r2 { fill: #98a84b } -.terminal-3744497940-r3 { fill: #9a9b99 } -.terminal-3744497940-r4 { fill: #608ab1 } -.terminal-3744497940-r5 { fill: #d0b344 } -.terminal-3744497940-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3744497940-r7 { fill: #868887 } -.terminal-3744497940-r8 { fill: #868887;font-style: italic; } + .terminal-1618644398-r1 { fill: #c5c8c6 } +.terminal-1618644398-r2 { fill: #98a84b } +.terminal-1618644398-r3 { fill: #9a9b99 } +.terminal-1618644398-r4 { fill: #608ab1 } +.terminal-1618644398-r5 { fill: #d0b344 } +.terminal-1618644398-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1618644398-r7 { fill: #868887 } +.terminal-1618644398-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +115,30 @@ - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ bacass              │    45 │            dev │     yesterday │           - │ -                   │ -│ fetchngs            │    86 │            dev │    2 days ago │           - │ -                   │ -│ scrnaseq            │    99 │            dev │    3 days ago │           - │ -                   │ -│ rnafusion           │   112 │            dev │    3 days ago │           - │ -                   │ -│ metatdenovo         │     3 │            dev │    3 days ago │           - │ -                   │ -[..truncated..] + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ 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 │   5 hours ago │           - │ -                   │ +│ metaboigniter       │    11 │          2.0.0 │   4 hours ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index ec8c80dea8..8ac4ba322d 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-4248893410-matrix { + .terminal-200931299-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4248893410-title { + .terminal-200931299-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4248893410-r1 { fill: #c5c8c6 } -.terminal-4248893410-r2 { fill: #98a84b } -.terminal-4248893410-r3 { fill: #9a9b99 } -.terminal-4248893410-r4 { fill: #608ab1 } -.terminal-4248893410-r5 { fill: #d0b344 } -.terminal-4248893410-r6 { fill: #98a84b;font-weight: bold } -.terminal-4248893410-r7 { fill: #c5c8c6;font-weight: bold } + .terminal-200931299-r1 { fill: #c5c8c6 } +.terminal-200931299-r2 { fill: #98a84b } +.terminal-200931299-r3 { fill: #9a9b99 } +.terminal-200931299-r4 { fill: #608ab1 } +.terminal-200931299-r5 { fill: #d0b344 } +.terminal-200931299-r6 { fill: #98a84b;font-weight: bold } +.terminal-200931299-r7 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -114,30 +114,30 @@ - + - - $ nf-core modules bump-versions fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - 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 2.11 - https://nf-co.re + + + + +╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ +│[!] 1 Module version up to date.│ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ +│Module name                             │Update Message                                       │ +├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ +│ fastqc                                   │ Module version up to date: fastqc                     │ +╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ diff --git a/docs/images/nf-core-modules-create-test.svg b/docs/images/nf-core-modules-create-test.svg deleted file mode 100644 index c171509599..0000000000 --- a/docs/images/nf-core-modules-create-test.svg +++ /dev/null @@ -1,132 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - $ nf-core modules create-test-yml fastqc --no-prompts --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -INFO     Looking for test workflow entry points: 'tests/modules/nf-core/fastqc/main.nf' -──────────────────────────────────────────────────────────────────────────────────────────────────── -INFO     Building test meta for entry point 'test_fastqc' -INFO     Running 'fastqc' test with command:                                                         -nextflow run ./tests/modules/nf-core/fastqc -entry test_fastqc -c  -./tests/config/nextflow.config --outdir /tmp/tmpnrlvr32x -work-dir /tmp/tmpyu2of3fe - - - - diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index 1114ebffb6..65d9c90131 100644 --- a/docs/images/nf-core-modules-create.svg +++ b/docs/images/nf-core-modules-create.svg @@ -19,106 +19,104 @@ font-weight: 700; } - .terminal-2353616836-matrix { + .terminal-95821698-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2353616836-title { + .terminal-95821698-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2353616836-r1 { fill: #c5c8c6 } -.terminal-2353616836-r2 { fill: #98a84b } -.terminal-2353616836-r3 { fill: #9a9b99 } -.terminal-2353616836-r4 { fill: #608ab1 } -.terminal-2353616836-r5 { fill: #d0b344 } -.terminal-2353616836-r6 { fill: #68a0b3;font-weight: bold } -.terminal-2353616836-r7 { fill: #98729f } -.terminal-2353616836-r8 { fill: #ff2c7a } + .terminal-95821698-r1 { fill: #c5c8c6 } +.terminal-95821698-r2 { fill: #98a84b } +.terminal-95821698-r3 { fill: #9a9b99 } +.terminal-95821698-r4 { fill: #608ab1 } +.terminal-95821698-r5 { fill: #d0b344 } +.terminal-95821698-r6 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -130,35 +128,35 @@ - + - - $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - 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 / edited following files:                                                           -           ./modules/nf-core/fastqc/main.nf -           ./modules/nf-core/fastqc/meta.yml -           ./tests/modules/nf-core/fastqc/main.nf -           ./tests/modules/nf-core/fastqc/test.yml -           ./tests/modules/nf-core/fastqc/nextflow.config -           ./tests/config/pytest_modules.yml + + $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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                                                 diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg index 0649779367..ea713ba23c 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-585364002-matrix { + .terminal-1933046224-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-585364002-title { + .terminal-1933046224-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-585364002-r1 { fill: #c5c8c6 } -.terminal-585364002-r2 { fill: #98a84b } -.terminal-585364002-r3 { fill: #9a9b99 } -.terminal-585364002-r4 { fill: #608ab1 } -.terminal-585364002-r5 { fill: #d0b344 } -.terminal-585364002-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-585364002-r7 { fill: #98a84b;font-weight: bold } -.terminal-585364002-r8 { fill: #868887 } -.terminal-585364002-r9 { fill: #d08442 } -.terminal-585364002-r10 { fill: #868887;font-style: italic; } -.terminal-585364002-r11 { fill: #98729f } + .terminal-1933046224-r1 { fill: #c5c8c6 } +.terminal-1933046224-r2 { fill: #98a84b } +.terminal-1933046224-r3 { fill: #9a9b99 } +.terminal-1933046224-r4 { fill: #608ab1 } +.terminal-1933046224-r5 { fill: #d0b344 } +.terminal-1933046224-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1933046224-r7 { fill: #98a84b;font-weight: bold } +.terminal-1933046224-r8 { fill: #868887 } +.terminal-1933046224-r9 { fill: #d08442 } +.terminal-1933046224-r10 { fill: #868887;font-style: italic; } +.terminal-1933046224-r11 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -187,53 +187,53 @@ - + - - $ nf-core modules info abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ -│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ -│ 🔧 Tools: abacas                                                                                 │ -│ 📖 Description: contiguate draft genome assembly                                                 │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -                  ╷                                                                   ╷              -📥 Inputs        │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} -                  ╵                                                                   ╵              -                  ╷                                                                   ╷              -📤 Outputs       │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - results  (files)│List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* -                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ -                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ -                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ -                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - versions  (file)│File containing software versions                                  │versions.yml -                  ╵                                                                   ╵              - - 💻  Installation command: nf-core modules install abacas - + + $ nf-core modules info abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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 3e53a93b38..9ebfbce6d7 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-2562821165-matrix { + .terminal-2637794350-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2562821165-title { + .terminal-2637794350-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2562821165-r1 { fill: #c5c8c6 } -.terminal-2562821165-r2 { fill: #98a84b } -.terminal-2562821165-r3 { fill: #9a9b99 } -.terminal-2562821165-r4 { fill: #608ab1 } -.terminal-2562821165-r5 { fill: #d0b344 } + .terminal-2637794350-r1 { fill: #c5c8c6 } +.terminal-2637794350-r2 { fill: #98a84b } +.terminal-2637794350-r3 { fill: #9a9b99 } +.terminal-2637794350-r4 { fill: #608ab1 } +.terminal-2637794350-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core modules install abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - 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 2.11 - 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 a7f87b39c9..9c364ea5b3 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 2.10 - https://nf-co.re - - - -INFO     Linting modules repo: '.' -INFO     Linting module: 'multiqc' + + + + $ nf-core modules lint multiqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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│ +╰──────────────────────╯ diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index a8b366dddf..5d592084ac 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-1258228559-matrix { + .terminal-3570470079-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1258228559-title { + .terminal-3570470079-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1258228559-r1 { fill: #c5c8c6 } -.terminal-1258228559-r2 { fill: #98a84b } -.terminal-1258228559-r3 { fill: #9a9b99 } -.terminal-1258228559-r4 { fill: #608ab1 } -.terminal-1258228559-r5 { fill: #d0b344 } -.terminal-1258228559-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1258228559-r7 { fill: #868887;font-style: italic; } + .terminal-3570470079-r1 { fill: #c5c8c6 } +.terminal-3570470079-r2 { fill: #98a84b } +.terminal-3570470079-r3 { fill: #9a9b99 } +.terminal-3570470079-r4 { fill: #608ab1 } +.terminal-3570470079-r5 { fill: #d0b344 } +.terminal-3570470079-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3570470079-r7 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,36 +132,36 @@ - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -INFO     Modules installed in '.':                                                                   - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -┃Module Name        ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ custom/dumpsoftwar… │ https://github.co… │ 911696ea0b62df80e9… │ Remove quay from   │ 2023-05-04 │ -│                     │                    │                     │ biocontainers      │            │ -│                     │                    │                     │ (#3380)            │            │ -│ fastqc              │ https://github.co… │ bd8092b67b5103bdd5… │ Add                │ 2023-07-01 │ -│                     │                    │                     │ singularity.regis… │            │ -│                     │                    │                     │ = 'quay.io' for    │            │ -│                     │                    │                     │ tests (#3499)      │            │ -│ multiqc             │ https://github.co… │ 911696ea0b62df80e9… │ Remove quay from   │ 2023-05-04 │ -│                     │                    │                     │ biocontainers      │            │ -[..truncated..] + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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..] diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index 8156a97f4c..1bc0eb0ff1 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-2763676620-matrix { + .terminal-2130205015-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2763676620-title { + .terminal-2130205015-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2763676620-r1 { fill: #c5c8c6 } -.terminal-2763676620-r2 { fill: #98a84b } -.terminal-2763676620-r3 { fill: #9a9b99 } -.terminal-2763676620-r4 { fill: #608ab1 } -.terminal-2763676620-r5 { fill: #d0b344 } -.terminal-2763676620-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-2763676620-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-2763676620-r8 { fill: #868887;font-style: italic; } + .terminal-2130205015-r1 { fill: #c5c8c6 } +.terminal-2130205015-r2 { fill: #98a84b } +.terminal-2130205015-r3 { fill: #9a9b99 } +.terminal-2130205015-r4 { fill: #608ab1 } +.terminal-2130205015-r5 { fill: #d0b344 } +.terminal-2130205015-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-2130205015-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2130205015-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core modules list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -INFO     Modules available from https://github.com/nf-core/modules.git(master):                     - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Module Name                                          ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ abacas                                                │ -│ abricate/run                                          │ -│ abricate/summary                                      │ -│ adapterremoval                                        │ -│ adapterremovalfixprefix                               │ -│ admixture                                             │ -│ affy/justrma                                          │ -│ agat/convertspgff2gtf                                 │ -│ agat/convertspgxf2gxf                                 │ -[..truncated..] + + $ nf-core modules list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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 7e07e6fdd2..7c6973da2c 100644 --- a/docs/images/nf-core-modules-patch.svg +++ b/docs/images/nf-core-modules-patch.svg @@ -19,65 +19,65 @@ font-weight: 700; } - .terminal-3451393581-matrix { + .terminal-3925415502-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3451393581-title { + .terminal-3925415502-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3451393581-r1 { fill: #c5c8c6 } -.terminal-3451393581-r2 { fill: #98a84b } -.terminal-3451393581-r3 { fill: #9a9b99 } -.terminal-3451393581-r4 { fill: #608ab1 } -.terminal-3451393581-r5 { fill: #d0b344 } -.terminal-3451393581-r6 { fill: #cc555a;font-weight: bold } + .terminal-3925415502-r1 { fill: #c5c8c6 } +.terminal-3925415502-r2 { fill: #98a84b } +.terminal-3925415502-r3 { fill: #9a9b99 } +.terminal-3925415502-r4 { fill: #608ab1 } +.terminal-3925415502-r5 { fill: #d0b344 } +.terminal-3925415502-r6 { fill: #cc555a;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -89,22 +89,22 @@ - + - - $ nf-core modules patch fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -ERROR    Module 'modules/nf-core/fastqc' is unchanged. No patch to compute                           + + $ nf-core modules patch fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - https://nf-co.re + + + +ERROR    module 'modules/nf-core/fastqc' is unchanged. No patch to compute                           diff --git a/docs/images/nf-core-modules-remove.svg b/docs/images/nf-core-modules-remove.svg index aa232cbf40..c63303b6e8 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-3202493823-matrix { + .terminal-3245682048-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3202493823-title { + .terminal-3245682048-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3202493823-r1 { fill: #c5c8c6 } -.terminal-3202493823-r2 { fill: #98a84b } -.terminal-3202493823-r3 { fill: #9a9b99 } -.terminal-3202493823-r4 { fill: #608ab1 } -.terminal-3202493823-r5 { fill: #d0b344 } + .terminal-3245682048-r1 { fill: #c5c8c6 } +.terminal-3245682048-r2 { fill: #98a84b } +.terminal-3245682048-r3 { fill: #9a9b99 } +.terminal-3245682048-r4 { fill: #608ab1 } +.terminal-3245682048-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -88,22 +88,22 @@ - + - - $ nf-core modules remove abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -INFO     Removed files for 'abacas' and its dependencies 'abacas'.                                   + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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 ca5e1e151e..0c531cf929 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 samtools/view --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -────────────────────────────────────────── samtools/view ─────────────────────────────────────────── -WARNING  You have uncommitted changes. Make sure to commit last changes before running the tests.    -INFO     Running pytest for module 'samtools/view' + + $ nf-core modules test fastqc --no-prompts --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - https://nf-co.re + + + +Usage:nf-core modules test [OPTIONS] <tool> or <tool/subtool>                                      + +Try'nf-core modules test -h'for help +╭─ Error ──────────────────────────────────────────────────────────────────────────────────────────╮ +│ No such option: --force Did you mean --once?                                                     │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + diff --git a/docs/images/nf-core-modules-update.svg b/docs/images/nf-core-modules-update.svg index f10bf15c33..83def3a38b 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-3796124800-matrix { + .terminal-1647661905-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3796124800-title { + .terminal-1647661905-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3796124800-r1 { fill: #c5c8c6 } -.terminal-3796124800-r2 { fill: #98a84b } -.terminal-3796124800-r3 { fill: #9a9b99 } -.terminal-3796124800-r4 { fill: #608ab1 } -.terminal-3796124800-r5 { fill: #d0b344 } + .terminal-1647661905-r1 { fill: #c5c8c6 } +.terminal-1647661905-r2 { fill: #98a84b } +.terminal-1647661905-r3 { fill: #9a9b99 } +.terminal-1647661905-r4 { fill: #608ab1 } +.terminal-1647661905-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core modules update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -INFO    'modules/nf-core/abacas' is already up to date                                              -INFO     Updating 'nf-core/custom/dumpsoftwareversions' -INFO     Updating 'nf-core/fastqc' -INFO     Updating 'nf-core/multiqc' -INFO     Updates complete ✨                                                                         + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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 880a7b13ca..61249df24f 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-1769917115-matrix { + .terminal-1899547324-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1769917115-title { + .terminal-1899547324-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1769917115-r1 { fill: #c5c8c6 } -.terminal-1769917115-r2 { fill: #98a84b } -.terminal-1769917115-r3 { fill: #9a9b99 } -.terminal-1769917115-r4 { fill: #608ab1 } -.terminal-1769917115-r5 { fill: #d0b344 } -.terminal-1769917115-r6 { fill: #98a84b;font-weight: bold } -.terminal-1769917115-r7 { fill: #868887;font-weight: bold } -.terminal-1769917115-r8 { fill: #868887 } -.terminal-1769917115-r9 { fill: #4e707b;font-weight: bold } -.terminal-1769917115-r10 { fill: #68a0b3;font-weight: bold } + .terminal-1899547324-r1 { fill: #c5c8c6 } +.terminal-1899547324-r2 { fill: #98a84b } +.terminal-1899547324-r3 { fill: #9a9b99 } +.terminal-1899547324-r4 { fill: #608ab1 } +.terminal-1899547324-r5 { fill: #d0b344 } +.terminal-1899547324-r6 { fill: #98a84b;font-weight: bold } +.terminal-1899547324-r7 { fill: #868887;font-weight: bold } +.terminal-1899547324-r8 { fill: #868887 } +.terminal-1899547324-r9 { fill: #4e707b;font-weight: bold } +.terminal-1899547324-r10 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,23 +96,23 @@ - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - 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 2.11 - 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 1fa52d8f30..3d95deadf3 100644 --- a/docs/images/nf-core-schema-lint.svg +++ b/docs/images/nf-core-schema-lint.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - + - + - - $ nf-core schema lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - -WARNING [!] Default parameter 'outdir' is empty or null. It is advisable to remove the default from -the schema -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 31 params) + + $ nf-core schema lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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 c33cadae84..e3619757ff 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-2439576725-matrix { + .terminal-2578316438-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2439576725-title { + .terminal-2578316438-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2439576725-r1 { fill: #c5c8c6 } -.terminal-2439576725-r2 { fill: #98a84b } -.terminal-2439576725-r3 { fill: #9a9b99 } -.terminal-2439576725-r4 { fill: #608ab1 } -.terminal-2439576725-r5 { fill: #d0b344 } -.terminal-2439576725-r6 { fill: #98a84b;font-weight: bold } -.terminal-2439576725-r7 { fill: #868887;font-weight: bold } -.terminal-2439576725-r8 { fill: #868887 } -.terminal-2439576725-r9 { fill: #4e707b;font-weight: bold } + .terminal-2578316438-r1 { fill: #c5c8c6 } +.terminal-2578316438-r2 { fill: #98a84b } +.terminal-2578316438-r3 { fill: #9a9b99 } +.terminal-2578316438-r4 { fill: #608ab1 } +.terminal-2578316438-r5 { fill: #d0b344 } +.terminal-2578316438-r6 { fill: #98a84b;font-weight: bold } +.terminal-2578316438-r7 { fill: #868887;font-weight: bold } +.terminal-2578316438-r8 { fill: #868887 } +.terminal-2578316438-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 2.10 - 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 2.11 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 93 params) +INFO    [✓] Input parameters look valid diff --git a/docs/images/nf-core-subworkflows-create-test.svg b/docs/images/nf-core-subworkflows-create-test.svg deleted file mode 100644 index 04edf19367..0000000000 --- a/docs/images/nf-core-subworkflows-create-test.svg +++ /dev/null @@ -1,136 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - $ nf-core subworkflows create-test-yml bam_stats_samtools --no-prompts --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -INFO     Looking for test workflow entry points:                                                     -'tests/subworkflows/nf-core/bam_stats_samtools/main.nf' -──────────────────────────────────────────────────────────────────────────────────────────────────── -INFO     Building test meta for entry point 'test_bam_stats_samtools' -INFO     Running 'bam_stats_samtools' test with command:                                             -nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools --c ./tests/config/nextflow.config --outdir /tmp/tmpc5x73b37 -work-dir /tmp/tmpcka4vu1g - - - - diff --git a/docs/images/nf-core-subworkflows-create.svg b/docs/images/nf-core-subworkflows-create.svg index 1b6b3ad41b..be37e78473 100644 --- a/docs/images/nf-core-subworkflows-create.svg +++ b/docs/images/nf-core-subworkflows-create.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - + - + - - $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - 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 / edited following files:                                                           -           ./subworkflows/nf-core/bam_stats_samtools/main.nf -           ./subworkflows/nf-core/bam_stats_samtools/meta.yml -           ./tests/subworkflows/nf-core/bam_stats_samtools/main.nf -           ./tests/subworkflows/nf-core/bam_stats_samtools/test.yml -           ./tests/subworkflows/nf-core/bam_stats_samtools/nextflow.config -           ./tests/config/pytest_modules.yml + + $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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 d29a99bbef..f76ce03fe7 100644 --- a/docs/images/nf-core-subworkflows-info.svg +++ b/docs/images/nf-core-subworkflows-info.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - $ nf-core subworkflows info bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - 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                        │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -                       ╷                                                                   ╷         -📥 Inputs             │Description                                                        │Pattern -╺━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━╸ - meta  (map)          │Groovy Map containing sample information e.g. [ id:'test',         │ -                       │single_end:false ]                                                 │ -╶──────────────────────┼───────────────────────────────────────────────────────────────────┼───────╴ - bam  (file)          │BAM file to calculate statistics                                   │*.{bam} -╶──────────────────────┼───────────────────────────────────────────────────────────────────┼───────╴ - bai  (file)          │Index for input BAM file                                           │*.{bai} -╶──────────────────────┼───────────────────────────────────────────────────────────────────┼───────╴ - bed  (file)          │BED file for the reference gene model                              │*.{bed} -╶──────────────────────┼───────────────────────────────────────────────────────────────────┼───────╴ - rseqc_modules  (list)│List of rseqc modules to run e.g. [ 'bam_stat', 'infer_experiment' │ -                       │]                                                                  │ -                       ╵                                                                   ╵         -                                     ╷                                   ╷                           -📤 Outputs                          │Description                        │                  Pattern -╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━╸ - bamstat_txt  (file)                │bam statistics report              │           *.bam_stat.txt -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - innerdistance_distance  (file)     │the inner distances                │     *.inner_distance.txt -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - innerdistance_freq  (file)         │frequencies of different insert    │*.inner_distance_freq.txt -                                     │sizes                              │ -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - innerdistance_mean  (file)         │mean/median values of inner        │*.inner_distance_mean.txt -                                     │distances                          │ -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - innerdistance_pdf  (file)          │distribution plot of inner         │*.inner_distance_plot.pdf -                                     │distances                          │ -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - innerdistance_rscript  (file)      │script to reproduce the plot       │  *.inner_distance_plot.R -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - inferexperiment_txt  (file)        │infer_experiment results report    │   *.infer_experiment.txt -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - junctionannotation_bed  (file)     │bed file of annotated junctions    │           *.junction.bed -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - junctionannotation_interact_bed   │Interact bed file                  │           *.Interact.bed -(file)                              │                                   │ -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - junctionannotation_xls  (file)     │xls file with junction information │                    *.xls -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - junctionannotation_pdf  (file)     │junction plot                      │           *.junction.pdf -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - junctionannotation_events_pdf     │events plot                        │             *.events.pdf -(file)                              │                                   │ -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - junctionannotation_rscript  (file) │Rscript to reproduce the plots     │                      *.r -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - junctionannotation_log  (file)     │Log file generated by tool         │                    *.log -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - junctionsaturation_pdf  (file)     │Junction saturation report         │                    *.pdf -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - junctionsaturation_rscript  (file) │Junction saturation R-script       │                      *.r -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - readdistribution_txt  (file)       │the read distribution report       │  *.read_distribution.txt -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - readduplication_seq_xls  (file)    │Read duplication rate determined   │         *seq.DupRate.xls -                                     │from mapping position of read      │ -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - readduplication_pos_xls  (file)    │Read duplication rate determined   │         *pos.DupRate.xls -                                     │from sequence of read              │ -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - readduplication_pdf  (file)        │plot of duplication rate           │                    *.pdf -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - readduplication_rscript  (file)    │script to reproduce the plot       │                      *.R -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - tin_txt  (file)                    │TXT file containing tin.py results │                    *.txt -                                     │summary                            │ -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - versions  (file)                   │File containing software versions  │             versions.yml -                                     ╵                                   ╵                           - - 💻  Installation command: nf-core subworkflows install bam_rseqc - + + + + $ nf-core subworkflows info bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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                        │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +                       ╷                                                                   ╷         +📥 Inputs             │Description                                                        │Pattern +╺━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━╸ + meta  (map)          │Groovy Map containing sample information e.g. [ id:'test',         │ +                       │single_end:false ]                                                 │ +╶──────────────────────┼───────────────────────────────────────────────────────────────────┼───────╴ + bam  (file)          │BAM file to calculate statistics                                   │*.{bam} +╶──────────────────────┼───────────────────────────────────────────────────────────────────┼───────╴ + bai  (file)          │Index for input BAM file                                           │*.{bai} +╶──────────────────────┼───────────────────────────────────────────────────────────────────┼───────╴ + bed  (file)          │BED file for the reference gene model                              │*.{bed} +╶──────────────────────┼───────────────────────────────────────────────────────────────────┼───────╴ + rseqc_modules  (list)│List of rseqc modules to run e.g. [ 'bam_stat', 'infer_experiment' │ +                       │]                                                                  │ +                       ╵                                                                   ╵         +                                    ╷                                    ╷                           +📤 Outputs                         │Description                         │                  Pattern +╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━╸ + ch_bamstat  (file)                │bam statistics report               │           *.bam_stat.txt +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_innerdistance  (file)          │All the output files from           │            *.{txt,pdf,R} +                                    │RSEQC_INNERDISTANCE                 │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_innerdistance_distance  (file) │the inner distances                 │     *.inner_distance.txt +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_innerdistance_freq  (file)     │frequencies of different insert     │*.inner_distance_freq.txt +                                    │sizes                               │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_innerdistance_mean  (file)     │mean/median values of inner         │*.inner_distance_mean.txt +                                    │distances                           │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_innerdistance_pdf  (file)      │distribution plot of inner distances│*.inner_distance_plot.pdf +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_innerdistance_rscript  (file)  │script to reproduce the plot        │  *.inner_distance_plot.R +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_inferexperiment  (file)        │infer_experiment results report     │   *.infer_experiment.txt +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_junctionannotation  (file)     │All the output files from           │    *.{bed,xls,pdf,R,log} +                                    │RSEQC_JUNCTIONANNOTATION            │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_junctionannotation_bed  (file) │bed file of annotated junctions     │           *.junction.bed +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_junctionannotation_interact_bed│Interact bed file                   │           *.Interact.bed +(file)                             │                                    │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_junctionannotation_xls  (file) │xls file with junction information  │                    *.xls +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_junctionannotation_pdf  (file) │junction plot                       │           *.junction.pdf +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_junctionannotation_events_pdf │events plot                         │             *.events.pdf +(file)                             │                                    │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_junctionannotation_rscript    │Rscript to reproduce the plots      │                      *.r +(file)                             │                                    │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_junctionannotation_log  (file) │Log file generated by tool          │                    *.log +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_junctionsaturation  (file)     │All the output files from           │                *.{pdf,R} +                                    │RSEQC_JUNCTIONSATURATION            │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_junctionsaturation_pdf  (file) │Junction saturation report          │                    *.pdf +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_junctionsaturation_rscript    │Junction saturation R-script        │                      *.r +(file)                             │                                    │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_readdistribution  (file)       │the read distribution report        │  *.read_distribution.txt +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_readduplication  (file)        │All the output files from           │            *.{xls,pdf,R} +                                    │RSEQC_READDUPLICATION               │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_readduplication_seq_xls  (file)│Read duplication rate determined    │         *seq.DupRate.xls +                                    │from mapping position of read       │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_readduplication_pos_xls  (file)│Read duplication rate determined    │         *pos.DupRate.xls +                                    │from sequence of read               │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_readduplication_pdf  (file)    │plot of duplication rate            │                    *.pdf +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + 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 30edb594bb..3b303f44a4 100644 --- a/docs/images/nf-core-subworkflows-install.svg +++ b/docs/images/nf-core-subworkflows-install.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + - + - + - - $ nf-core subworkflows install bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -INFO     Installing 'bam_rseqc' + + $ nf-core subworkflows install bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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 b3dcea1c0c..48c4837788 100644 --- a/docs/images/nf-core-subworkflows-lint.svg +++ b/docs/images/nf-core-subworkflows-lint.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - $ nf-core subworkflows lint bam_stats_samtools - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -INFO     Linting modules repo: '.' -INFO     Linting subworkflow: 'bam_stats_samtools' - -╭─[!] 12 Subworkflow Test Warnings───────────────────────────────────────────────────────────────╮ -│                                           ╷                          ╷                           │ -│Subworkflow name                         │File path               │Test message             │ -│╶──────────────────────────────────────────┼──────────────────────────┼──────────────────────────╴│ -│bam_stats_samtools│subworkflows/nf-core/ba…│Included component │ -│││'SAMTOOLS_INDEX' versions│ -│││are not added in main.nf│ -│bam_stats_samtools│subworkflows/nf-core/ba…│Included component │ -│││'SAMTOOLS_SORT' versions │ -│││are not added in main.nf│ -│bam_stats_samtools│subworkflows/nf-core/ba…│TODO string in main.nf: A│ -│││subworkflow SHOULD import│ -│││at least two modules│ -│bam_stats_samtools│subworkflows/nf-core/ba…│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/ba…│TODO string in main.nf: │ -│││edit emitted channels│ -│bam_stats_samtools│subworkflows/nf-core/ba…│TODO string in main.nf: │ -│││edit input (take) │ -│││channels│ -│bam_stats_samtools│subworkflows/nf-core/ba…│TODO string in main.nf: │ -│││substitute modules here │ -│││for the modules of your │ -│││subworkflow│ -│bam_stats_samtools│subworkflows/nf-core/ba…│TODO string in meta.yml: │ -│││#Add a description of the│ -│││subworkflow and list │ -│││keywords│ -│bam_stats_samtools│subworkflows/nf-core/ba…│TODO string in meta.yml: │ -│││#Add a list of the │ -│││modules and/or │ -│││subworkflows used in the │ -│││subworkflow│ -│bam_stats_samtools│subworkflows/nf-core/ba…│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/ba…│TODO string in meta.yml: │ -│││#List all of the channels│ -│││used as output with a │ -│││descriptions and their │ -│││structure│ -│bam_stats_samtools│tests/subworkflows/nf-c…│TODO string in test.yml: │ -│││#Please run the following│ -│││command to build this │ -│││file:│ -│                                           ╵                          ╵                           │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─[✗] 4 Subworkflow Tests Failed─────────────────────────────────────────────────────────────────╮ -│                                           ╷                          ╷                           │ -│Subworkflow name                         │File path               │Test message             │ -│╶──────────────────────────────────────────┼──────────────────────────┼──────────────────────────╴│ -│bam_stats_samtools│subworkflows/nf-core/ba…│Deprecated section │ -│││'modules' not found in │ -│││meta.yml│ -│bam_stats_samtools│tests/subworkflows/nf-c…│Included │ -│││module/subworkflow │ -│││samtools/index missing in│ -│││test.yml│ -│bam_stats_samtools│tests/subworkflows/nf-c…│Included │ -│││module/subworkflow │ -│││samtools/sort missing in │ -│││test.yml│ -│bam_stats_samtools│tests/subworkflows/nf-c…│Included │ -│││module/subworkflow │ -│││samtools missing in │ -│││test.yml│ -│                                           ╵                          ╵                           │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────╮ -│LINT RESULTS SUMMARY│ -├───────────────────────┤ -│[✔]  22 Tests Passed │ -│[!]  12 Test Warnings│ -│[✗]   4 Tests Failed │ -╰───────────────────────╯ + + + + $ nf-core subworkflows lint bam_stats_samtools + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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 715c95f093..7d33c4a6c1 100644 --- a/docs/images/nf-core-subworkflows-list-local.svg +++ b/docs/images/nf-core-subworkflows-list-local.svg @@ -19,67 +19,67 @@ font-weight: 700; } - .terminal-334238752-matrix { + .terminal-372904993-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-334238752-title { + .terminal-372904993-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-334238752-r1 { fill: #c5c8c6 } -.terminal-334238752-r2 { fill: #98a84b } -.terminal-334238752-r3 { fill: #9a9b99 } -.terminal-334238752-r4 { fill: #608ab1 } -.terminal-334238752-r5 { fill: #d0b344 } + .terminal-372904993-r1 { fill: #c5c8c6 } +.terminal-372904993-r2 { fill: #98a84b } +.terminal-372904993-r3 { fill: #9a9b99 } +.terminal-372904993-r4 { fill: #608ab1 } +.terminal-372904993-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -91,23 +91,23 @@ - + - - $ nf-core subworkflows list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -INFO     No nf-core subworkflows found in '.' - + + $ nf-core subworkflows list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - https://nf-co.re + + + +INFO     No nf-core subworkflows found in '.' + diff --git a/docs/images/nf-core-subworkflows-list-remote.svg b/docs/images/nf-core-subworkflows-list-remote.svg index da584195cd..31d72d0d2d 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-929385462-matrix { + .terminal-2778221227-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-929385462-title { + .terminal-2778221227-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-929385462-r1 { fill: #c5c8c6 } -.terminal-929385462-r2 { fill: #98a84b } -.terminal-929385462-r3 { fill: #9a9b99 } -.terminal-929385462-r4 { fill: #608ab1 } -.terminal-929385462-r5 { fill: #d0b344 } -.terminal-929385462-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-929385462-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-929385462-r8 { fill: #868887;font-style: italic; } + .terminal-2778221227-r1 { fill: #c5c8c6 } +.terminal-2778221227-r2 { fill: #98a84b } +.terminal-2778221227-r3 { fill: #9a9b99 } +.terminal-2778221227-r4 { fill: #608ab1 } +.terminal-2778221227-r5 { fill: #d0b344 } +.terminal-2778221227-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-2778221227-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2778221227-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core subworkflows list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Subworkflow Name                             ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ 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                                     │ -│ bam_sort_stats_samtools                       │ -[..truncated..] + + $ nf-core subworkflows list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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 8c62f7f198..481490d4ef 100644 --- a/docs/images/nf-core-subworkflows-remove.svg +++ b/docs/images/nf-core-subworkflows-remove.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ nf-core subworkflows remove bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - 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 'bam_rseqc' and its dependencies 'bam_rseqc, rseqc_bamstat,  -rseqc_inferexperiment, rseqc_innerdistance'.                                                + + $ nf-core subworkflows remove bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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 fd30636860..909b3c00d8 100644 --- a/docs/images/nf-core-subworkflows-test.svg +++ b/docs/images/nf-core-subworkflows-test.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ nf-core subworkflows test bam_rseqc --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -──────────────────────────────────────────── bam_rseqc ───────────────────────────────────────────── -WARNING  You have uncommitted changes. Make sure to commit last changes before running the tests.    -INFO     Running pytest for subworkflow 'bam_rseqc' + + $ nf-core subworkflows test bam_rseqc --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - https://nf-co.re + + + +INFO     Generating nf-test snapshot                                                                 +╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/utils.py:315 in      │ +│run_cmd│ +││ +│ 312 │   full_cmd = f"{executable}{cmd}"│ +│ 313 │   log.debug(f"Running command: {full_cmd}")                                             │ +│ 314 │   try:                                                                                  │ +│❱  315 │   │   proc = subprocess.run(shlex.split(full_cmd), stdout=subprocess.PIPE, stderr=subp  │ +│ 316 │   │   return (proc.stdout, proc.stderr)                                                 │ +│ 317 │   exceptOSErroras e:                                                                  │ +│ 318 │   │   if e.errno == errno.ENOENT:                                                       │ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/subprocess.py:548 in run│ +││ +│ 545 │   │   kwargs['stdout'] = PIPE                                                           │ +│ 546 │   │   kwargs['stderr'] = PIPE                                                           │ +│ 547 │   │ +│❱  548 │   with Popen(*popenargs, **kwargs) as process:                                          │ +│ 549 │   │   try:                                                                              │ +│ 550 │   │   │   stdout, stderr = process.communicate(input, timeout=timeout)                  │ +│ 551 │   │   except TimeoutExpired as exc:                                                     │ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/subprocess.py:1026 in __init__│ +││ +│1023 │   │   │   │   │   self.stderr = io.TextIOWrapper(self.stderr,                           │ +│1024 │   │   │   │   │   │   │   encoding=encoding, errors=errors)                             │ +│1025 │   │   │   │ +│❱ 1026 │   │   │   self._execute_child(args, executable, preexec_fn, close_fds,                  │ +│1027 │   │   │   │   │   │   │   │   pass_fds, cwd, env,                                       │ +│1028 │   │   │   │   │   │   │   │   startupinfo, creationflags, shell,                        │ +│1029 │   │   │   │   │   │   │   │   p2cread, p2cwrite,                                        │ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/subprocess.py:1950 in _execute_child│ +││ +│1947 │   │   │   │   │   │   err_filename = orig_executable                                    │ +│1948 │   │   │   │   │   if errno_num != 0:                                                    │ +│1949 │   │   │   │   │   │   err_msg = os.strerror(errno_num)                                  │ +│❱ 1950 │   │   │   │   │   raise child_exception_type(errno_num, err_msg, err_filename)          │ +│1951 │   │   │   │   raise child_exception_type(err_msg)                                       │ +│1952 │ +│1953 │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +FileNotFoundError: [Errno 2] No such file or directory: 'nf-test' + +During handling of the above exception, another exception occurred: + +╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ +│/opt/hostedtoolcache/Python/3.12.1/x64/bin/nf-core:8 in <module>│ +││ +│5 fromnf_core.__main__import run_nf_core                                                     │ +│6 if__name__ == '__main__':                                                                   │ +│7 │   sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])                         │ +│❱ 8 │   sys.exit(run_nf_core())                                                                  │ +│9 │ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/__main__.py:111 in   │ +│run_nf_core│ +││ +│ 108 │   │   │   log.debug(f"Could not check latest version: {e}")                             │ +│ 109 │   │   stderr.print("\n")                                                                │ +│ 110 │   # Launch the click cli│ +│❱  111 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │ +│ 112 │ +│ 113 │ +│ 114 @click.group(context_settings=dict(help_option_names=["-h", "--help"]))                   │ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/click/core.py:1157 in        │ +│__call__│ +││ +│1154 │   │ +│1155 │   def__call__(self, *args: t.Any, **kwargs: t.Any) -> t.Any:                           │ +│1156 │   │   """Alias for :meth:`main`."""│ +│❱ 1157 │   │   returnself.main(*args, **kwargs)                                                 │ +│1158 │ +│1159 │ +│1160 classCommand(BaseCommand):                                                               │ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/rich_click/rich_command.py:1│ +│26 in main│ +││ +│123 │   │   try:                                                                               │ +│124 │   │   │   try:                                                                           │ +│125 │   │   │   │   withself.make_context(prog_name, args, **extra) as ctx:                   │ +│❱ 126 │   │   │   │   │   rv = self.invoke(ctx)                                                  │ +│127 │   │   │   │   │   ifnot standalone_mode:                                                │ +│128 │   │   │   │   │   │   return rv                                                          │ +│129 │   │   │   │   │   # it's not safe to `ctx.exit(rv)` here!│ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/click/core.py:1688 in invoke│ +││ +│1685 │   │   │   │   super().invoke(ctx)                                                       │ +│1686 │   │   │   │   sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)                    │ +│1687 │   │   │   │   with sub_ctx:                                                             │ +│❱ 1688 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │ +│1689 │   │   │ +│1690 │   │   # In chain mode we create the contexts step by step, but after the│ +│1691 │   │   # base command has been invoked.  Because at that point we do not│ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/click/core.py:1688 in invoke│ +││ +│1685 │   │   │   │   super().invoke(ctx)                                                       │ +│1686 │   │   │   │   sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)                    │ +│1687 │   │   │   │   with sub_ctx:                                                             │ +│❱ 1688 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │ +│1689 │   │   │ +│1690 │   │   # In chain mode we create the contexts step by step, but after the│ +│1691 │   │   # base command has been invoked.  Because at that point we do not│ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/click/core.py:1434 in invoke│ +││ +│1431 │   │   │   echo(style(message, fg="red"), err=True)                                      │ +│1432 │   │   │ +│1433 │   │   ifself.callback isnotNone:                                                     │ +│❱ 1434 │   │   │   return ctx.invoke(self.callback, **ctx.params)                                │ +│1435 │   │ +│1436 │   defshell_complete(self, ctx: Context, incomplete: str) -> t.List["CompletionItem"]:  │ +│1437 │   │   """Return a list of completions for the incomplete value. Looks│ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/click/core.py:783 in invoke│ +││ +│ 780 │   │   │ +│ 781 │   │   with augment_usage_errors(__self):                                                │ +│ 782 │   │   │   with ctx:                                                                     │ +│❱  783 │   │   │   │   return __callback(*args, **kwargs)                                        │ +│ 784 │   │ +│ 785 │   defforward(                                                                          │ +│ 786 │   │   __self, __cmd: "Command", *args: t.Any, **kwargs: t.Any  # noqa: B902│ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/click/decorators.py:33 in    │ +│new_func│ +││ +│ 30 │   """│ +│ 31 │   │ +│ 32 │   defnew_func(*args: "P.args", **kwargs: "P.kwargs") -> "R":                            │ +│❱  33 │   │   return f(get_current_context(), *args, **kwargs)                                   │ +│ 34 │   │ +│ 35 │   return update_wrapper(new_func, f)                                                     │ +│ 36 │ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/__main__.py:1101 in  │ +│test_subworkflow│ +││ +│1098 │   │   │   branch=ctx.obj["modules_repo_branch"],                                        │ +│1099 │   │   │   verbose=ctx.obj["verbose"],                                                   │ +│1100 │   │   )                                                                                 │ +│❱ 1101 │   │   sw_tester.run()                                                                   │ +│1102 │   except (UserWarning, LookupError) as e:                                               │ +│1103 │   │   log.critical(e)                                                                   │ +│1104 │   │   sys.exit(1)                                                                       │ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/components/component│ +│s_test.py:94 in run│ +││ +│ 91 │   │   │   "NFT_DIFF_ARGS"│ +│ 92 │   │   ] = "--line-numbers --expand-tabs=2"# taken from https://code.askimed.com/nf-t│ +│ 93 │   │   with nf_core.utils.set_wd(Path(self.dir)):                                         │ +│❱  94 │   │   │   self.check_snapshot_stability()                                                │ +│ 95 │   │   iflen(self.errors) > 0:                                                           │ +│ 96 │   │   │   errors = "\n - ".join(self.errors)                                             │ +│ 97 │   │   │   raiseUserWarning(f"Ran, but found errors:\n - {errors}")                      │ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/components/component│ +│s_test.py:226 in check_snapshot_stability│ +││ +│223 │   defcheck_snapshot_stability(self) -> bool:                                            │ +│224 │   │   """Run the nf-test twice and check if the snapshot changes"""│ +│225 │   │   log.info("Generating nf-test snapshot")                                            │ +│❱ 226 │   │   ifnotself.generate_snapshot():                                                   │ +│227 │   │   │   returnFalse# stop here if the first run failed│ +│228 │   │   elifself.once:                                                                    │ +│229 │   │   │   returnTrue# stop here if the test should be run only once│ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/components/component│ +│s_test.py:194 in generate_snapshot│ +││ +│191 │   │   self.update = False# reset self.update to False to test if the new snapshot is│ +│192 │   │   tag = f"subworkflows/{self.component_name}"ifself.component_type == "subworkfl│ +│193 │   │   │ +│❱ 194 │   │   result = nf_core.utils.run_cmd(                                                    │ +│195 │   │   │   "nf-test",                                                                     │ +│196 │   │   │   f"test --tag {tag} --profile {os.environ['PROFILE']}{verbose}{update}",      │ +│197 │   │   )                                                                                  │ +││ +│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/utils.py:319 in      │ +│run_cmd│ +││ +│ 316 │   │   return (proc.stdout, proc.stderr)                                                 │ +│ 317 │   exceptOSErroras e:                                                                  │ +│ 318 │   │   if e.errno == errno.ENOENT:                                                       │ +│❱  319 │   │   │   raiseRuntimeError(                                                           │ +│ 320 │   │   │   │   f"It looks like {executable} is not installed. Please ensure it is avail│ +│ 321 │   │   │   )                                                                             │ +│ 322 │   │   else:                                                                             │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +RuntimeError: It looks like nf-test is not installed. Please ensure it is available in your PATH. diff --git a/docs/images/nf-core-subworkflows-update.svg b/docs/images/nf-core-subworkflows-update.svg index 87a3b96706..2594a2fa65 100644 --- a/docs/images/nf-core-subworkflows-update.svg +++ b/docs/images/nf-core-subworkflows-update.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core subworkflows update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.10 - https://nf-co.re - - - -ERROR   'rseqc/junctionannotation' + + $ nf-core subworkflows update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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 df1a9b3843..6b1e13eb56 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 2.10 - https://nf-co.re - - -INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthing -INFO     Original pipeline repository branch is 'master' -INFO     Deleting all files in 'TEMPLATE' branch                                                     -INFO     Making a new template pipeline using pipeline variables                                     + + $ nf-core sync + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11 - 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