diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index 23b05de88a..55880e8130 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -42,8 +42,8 @@ jobs: sync: needs: get-pipelines - # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} + # use the github runner on release otherwise use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default + runs-on: ${{github.event_name == 'release' && 'self-hosted' || github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} strategy: matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}} fail-fast: false diff --git a/.github/workflows/update_components_template.yml b/.github/workflows/update_components_template.yml index 5ba513735e..e2ecebfcb4 100644 --- a/.github/workflows/update_components_template.yml +++ b/.github/workflows/update_components_template.yml @@ -22,11 +22,11 @@ jobs: run: pip install nf-core - name: Update modules - run: nf-core modules update --all + run: nf-core modules update --all --no-preview working-directory: nf_core/pipeline-template - name: Update subworkflows - run: nf-core subworkflows update --all + run: nf-core subworkflows update --all --no-preview working-directory: nf_core/pipeline-template # Commit the changes diff --git a/CHANGELOG.md b/CHANGELOG.md index a7eea54dd0..e130d3c37b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,17 @@ # nf-core/tools: Changelog -## [v2.14.0 - Tantalum Toad](https://github.com/nf-core/tools/releases/tag/2.14) - [2024-05-07] +## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] + +### Template + +- Don't cache pip in `linting.yml` ([#2961](https://github.com/nf-core/tools/pull/2961)) + +### General + +- Fix update github action for components in pipeline template ([#2968](https://github.com/nf-core/tools/pull/2968)) +- Run sync after release on self hosted runners ([#2970](https://github.com/nf-core/tools/pull/2970)) + +## [v2.14.0 - Tantalum Toad](https://github.com/nf-core/tools/releases/tag/2.14.0) - [2024-05-08] ### Template diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg index 8a7ad902f4..2ed97e79a8 100644 --- a/docs/images/nf-core-bump-version.svg +++ b/docs/images/nf-core-bump-version.svg @@ -19,122 +19,122 @@ font-weight: 700; } - .terminal-3430835254-matrix { + .terminal-3649135671-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3430835254-title { + .terminal-3649135671-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3430835254-r1 { fill: #c5c8c6 } -.terminal-3430835254-r2 { fill: #98a84b } -.terminal-3430835254-r3 { fill: #9a9b99 } -.terminal-3430835254-r4 { fill: #608ab1 } -.terminal-3430835254-r5 { fill: #d0b344 } -.terminal-3430835254-r6 { fill: #cc555a } + .terminal-3649135671-r1 { fill: #c5c8c6 } +.terminal-3649135671-r2 { fill: #98a84b } +.terminal-3649135671-r3 { fill: #9a9b99 } +.terminal-3649135671-r4 { fill: #608ab1 } +.terminal-3649135671-r5 { fill: #d0b344 } +.terminal-3649135671-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -146,41 +146,41 @@ - + - - $ nf-core bump-version 1.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - -INFO     Changing version number from '1.0dev' to '1.1' -INFO     Updated version in 'nextflow.config' - - version         = '1.0dev' - + version         = '1.1' - - -INFO     Updated version in 'assets/multiqc_config.yml' - - This report has been generated by the <a  -href="https://github.com/nf-core/nextbigthing/tree/dev" target="_blank">nf-core/nextbigthing</a> - + This report has been generated by the <a  -href="https://github.com/nf-core/nextbigthing/releases/tag/1.1"  -target="_blank">nf-core/nextbigthing</a> - - -INFO     Updated version in 'assets/multiqc_config.yml' - - <a href="https://nf-co.re/nextbigthing/dev/docs/output"  -target="_blank">documentation</a>. - + <a href="https://nf-co.re/nextbigthing/1.1/docs/output"  -target="_blank">documentation</a>. - - + + $ nf-core bump-version 1.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +INFO     Changing version number from '1.0dev' to '1.1' +INFO     Updated version in 'nextflow.config' + - version         = '1.0dev' + + version         = '1.1' + + +INFO     Updated version in 'assets/multiqc_config.yml' + - This report has been generated by the <a  +href="https://github.com/nf-core/nextbigthing/tree/dev" target="_blank">nf-core/nextbigthing</a> + + This report has been generated by the <a  +href="https://github.com/nf-core/nextbigthing/releases/tag/1.1"  +target="_blank">nf-core/nextbigthing</a> + + +INFO     Updated version in 'assets/multiqc_config.yml' + - <a href="https://nf-co.re/nextbigthing/dev/docs/output"  +target="_blank">documentation</a>. + + <a href="https://nf-co.re/nextbigthing/1.1/docs/output"  +target="_blank">documentation</a>. + + diff --git a/docs/images/nf-core-create-logo.svg b/docs/images/nf-core-create-logo.svg index 50340ff44f..8313bf8a21 100644 --- a/docs/images/nf-core-create-logo.svg +++ b/docs/images/nf-core-create-logo.svg @@ -19,62 +19,62 @@ font-weight: 700; } - .terminal-2584807909-matrix { + .terminal-2620328422-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2584807909-title { + .terminal-2620328422-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2584807909-r1 { fill: #c5c8c6 } -.terminal-2584807909-r2 { fill: #98a84b } -.terminal-2584807909-r3 { fill: #9a9b99 } -.terminal-2584807909-r4 { fill: #608ab1 } -.terminal-2584807909-r5 { fill: #d0b344 } -.terminal-2584807909-r6 { fill: #98729f } + .terminal-2620328422-r1 { fill: #c5c8c6 } +.terminal-2620328422-r2 { fill: #98a84b } +.terminal-2620328422-r3 { fill: #9a9b99 } +.terminal-2620328422-r4 { fill: #608ab1 } +.terminal-2620328422-r5 { fill: #d0b344 } +.terminal-2620328422-r6 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + @@ -86,21 +86,21 @@ - + - - $ nf-core create-logo nextbigthing - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - -INFO     Created logo: nf-core-nextbigthing_logo_light.png + + $ nf-core create-logo nextbigthing + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +INFO     Created logo: nf-core-nextbigthing_logo_light.png diff --git a/docs/images/nf-core-create.svg b/docs/images/nf-core-create.svg index 70b281cd1c..cd25e8805c 100644 --- a/docs/images/nf-core-create.svg +++ b/docs/images/nf-core-create.svg @@ -19,104 +19,104 @@ font-weight: 700; } - .terminal-166056632-matrix { + .terminal-414307001-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-166056632-title { + .terminal-414307001-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-166056632-r1 { fill: #c5c8c6 } -.terminal-166056632-r2 { fill: #98a84b } -.terminal-166056632-r3 { fill: #9a9b99 } -.terminal-166056632-r4 { fill: #608ab1 } -.terminal-166056632-r5 { fill: #d0b344 } -.terminal-166056632-r6 { fill: #98729f } -.terminal-166056632-r7 { fill: #ff2c7a } -.terminal-166056632-r8 { fill: #98a84b;font-weight: bold } -.terminal-166056632-r9 { fill: #1984e9;text-decoration: underline; } + .terminal-414307001-r1 { fill: #c5c8c6 } +.terminal-414307001-r2 { fill: #98a84b } +.terminal-414307001-r3 { fill: #9a9b99 } +.terminal-414307001-r4 { fill: #608ab1 } +.terminal-414307001-r5 { fill: #d0b344 } +.terminal-414307001-r6 { fill: #98729f } +.terminal-414307001-r7 { fill: #ff2c7a } +.terminal-414307001-r8 { fill: #98a84b;font-weight: bold } +.terminal-414307001-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 2.14.0 - 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 2.14.1 - https://nf-co.re + + +INFO     Creating new nf-core pipeline: 'nf-core/nextbigthing' +INFO     Initialising pipeline git repository                                                        +INFO     Done. Remember to add a remote and push to GitHub:                                          + cd /home/runner/work/tools/tools/tmp/nf-core-nextbigthing + git remote add origin git@github.com:USERNAME/REPO_NAME.git  + git push --all origin                                        +INFO     This will also push your newly created dev branch and the TEMPLATE branch for syncing.      +INFO    !!!!!! IMPORTANT !!!!!! + +If you are interested in adding your pipeline to the nf-core community, +PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE! + +Please read: https://nf-co.re/developers/adding_pipelines#join-the-community diff --git a/docs/images/nf-core-download.svg b/docs/images/nf-core-download.svg index e7511c8f54..98e99944e1 100644 --- a/docs/images/nf-core-download.svg +++ b/docs/images/nf-core-download.svg @@ -19,86 +19,86 @@ font-weight: 700; } - .terminal-2899897808-matrix { + .terminal-3049975249-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2899897808-title { + .terminal-3049975249-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2899897808-r1 { fill: #c5c8c6 } -.terminal-2899897808-r2 { fill: #98a84b } -.terminal-2899897808-r3 { fill: #9a9b99 } -.terminal-2899897808-r4 { fill: #608ab1 } -.terminal-2899897808-r5 { fill: #d0b344 } -.terminal-2899897808-r6 { fill: #cc555a } + .terminal-3049975249-r1 { fill: #c5c8c6 } +.terminal-3049975249-r2 { fill: #98a84b } +.terminal-3049975249-r3 { fill: #9a9b99 } +.terminal-3049975249-r4 { fill: #608ab1 } +.terminal-3049975249-r5 { fill: #d0b344 } +.terminal-3049975249-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -110,29 +110,29 @@ - + - - $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - -WARNING  Could not find GitHub authentication token. Some API requests may fail.                     -INFO     Saving 'nf-core/rnaseq' -          Pipeline revision: '3.8' -          Use containers: 'none' -          Container library: 'quay.io' -          Output directory: 'nf-core-rnaseq' -          Include default institutional configuration: 'True' -INFO     Downloading centralised configs from GitHub                                                 -INFO     Downloading workflow files from GitHub                                                      + + $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +WARNING  Could not find GitHub authentication token. Some API requests may fail.                     +INFO     Saving 'nf-core/rnaseq' +          Pipeline revision: '3.8' +          Use containers: 'none' +          Container library: 'quay.io' +          Output directory: 'nf-core-rnaseq' +          Include default institutional configuration: 'True' +INFO     Downloading centralised configs from GitHub                                                 +INFO     Downloading workflow files from GitHub                                                      diff --git a/docs/images/nf-core-launch-rnaseq.svg b/docs/images/nf-core-launch-rnaseq.svg index ef0cfc2ba8..0b191ff2eb 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-3860180531-matrix { + .terminal-3936792116-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3860180531-title { + .terminal-3936792116-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3860180531-r1 { fill: #c5c8c6 } -.terminal-3860180531-r2 { fill: #98a84b } -.terminal-3860180531-r3 { fill: #9a9b99 } -.terminal-3860180531-r4 { fill: #608ab1 } -.terminal-3860180531-r5 { fill: #d0b344 } -.terminal-3860180531-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3860180531-r7 { fill: #68a0b3;font-weight: bold } + .terminal-3936792116-r1 { fill: #c5c8c6 } +.terminal-3936792116-r2 { fill: #98a84b } +.terminal-3936792116-r3 { fill: #9a9b99 } +.terminal-3936792116-r4 { fill: #608ab1 } +.terminal-3936792116-r5 { fill: #d0b344 } +.terminal-3936792116-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3936792116-r7 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,24 +96,24 @@ - + - - $ nf-core launch rnaseq -r 3.8.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - 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 2.14.1 - https://nf-co.re + + +INFO     NOTE: This tool ignores any pipeline parameter defaults overwritten by Nextflow config      +         files or profiles                                                                           + +INFO     Downloading workflow: nf-core/rnaseq (3.8.1) diff --git a/docs/images/nf-core-licences.svg b/docs/images/nf-core-licences.svg index d8aa9b03a3..74aab4fa8e 100644 --- a/docs/images/nf-core-licences.svg +++ b/docs/images/nf-core-licences.svg @@ -19,62 +19,62 @@ font-weight: 700; } - .terminal-918751615-matrix { + .terminal-954993024-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-918751615-title { + .terminal-954993024-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-918751615-r1 { fill: #c5c8c6 } -.terminal-918751615-r2 { fill: #98a84b } -.terminal-918751615-r3 { fill: #9a9b99 } -.terminal-918751615-r4 { fill: #608ab1 } -.terminal-918751615-r5 { fill: #d0b344 } -.terminal-918751615-r6 { fill: #68a0b3;font-weight: bold } + .terminal-954993024-r1 { fill: #c5c8c6 } +.terminal-954993024-r2 { fill: #98a84b } +.terminal-954993024-r3 { fill: #9a9b99 } +.terminal-954993024-r4 { fill: #608ab1 } +.terminal-954993024-r5 { fill: #d0b344 } +.terminal-954993024-r6 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + @@ -86,21 +86,21 @@ - + - - $ nf-core licences deepvariant - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - -INFO     Fetching licence information for 8 tools                                                    + + $ nf-core licences deepvariant + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +INFO     Fetching licence information for 8 tools                                                    diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg index 9276638e99..bb7b6b879e 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 2.14.0 - https://nf-co.re - - - -INFO     Testing pipeline: . - -╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ -│/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/requests/models.py:971 in    │ -│json│ -││ -│ 968 │   │   │   │   │   raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)                    │ -│ 969 │   │   │ -│ 970 │   │   try:                                                                              │ -│❱  971 │   │   │   return complexjson.loads(self.text, **kwargs)                                 │ -│ 972 │   │   except JSONDecodeError as e:                                                      │ -│ 973 │   │   │   # Catch JSON-related errors and raise as requests.JSONDecodeError│ -│ 974 │   │   │   # This aliases json.JSONDecodeError and simplejson.JSONDecodeError│ -││ -│/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/json/__init__.py:346 in loads│ -││ -│343 │   if (clsisNoneand object_hook isNoneand│ -│344 │   │   │   parse_int isNoneand parse_float isNoneand│ -│345 │   │   │   parse_constant isNoneand object_pairs_hook isNoneandnot kw):              │ -│❱ 346 │   │   return _default_decoder.decode(s)                                                  │ -│347 │   ifclsisNone:                                                                        │ -│348 │   │   cls = JSONDecoder                                                                  │ -│349 │   if object_hook isnotNone:                                                            │ -││ -│/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/json/decoder.py:337 in decode│ -││ -│334 │   │   containing a JSON document).│ -│335 │   │   │ -│336 │   │   """│ -│❱ 337 │   │   obj, end = self.raw_decode(s, idx=_w(s, 0).end())                                  │ -│338 │   │   end = _w(s, end).end()                                                             │ -│339 │   │   if end != len(s):                                                                  │ -│340 │   │   │   raise JSONDecodeError("Extra data", s, end)                                    │ -││ -│/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/json/decoder.py:355 in raw_decode│ -││ -│352 │   │   try:                                                                               │ -│353 │   │   │   obj, end = self.scan_once(s, idx)                                              │ -│354 │   │   exceptStopIterationas err:                                                       │ -│❱ 355 │   │   │   raise JSONDecodeError("Expecting value", s, err.value) fromNone│ -│356 │   │   return obj, end                                                                    │ -│357 │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -JSONDecodeError: Expecting value: line 1 column 1(char 0) - -During handling of the above exception, another exception occurred: - -╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ -│/opt/hostedtoolcache/Python/3.12.3/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/3.12.3/x64/lib/python3.12/site-packages/nf_core/__main__.py:150 in   │ -│run_nf_core│ -││ -│ 147 │   │   │   log.debug(f"Could not check latest version: {e}")                             │ -│ 148 │   │   stderr.print("\n")                                                                │ -│ 149 │   # Launch the click cli│ -│❱  150 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │ -│ 151 │ -│ 152 │ -│ 153 @tui()                                                                                    │ -││ -│/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/rich_click/rich_command.py:3│ -│67 in __call__│ -││ -│364 │   │   # Include this here because I run into a false warning│ -│365 │   │   # in the PyCharm IDE otherwise; for some reason PyCharm doesn't│ -│366 │   │   # seem to think RichGroups are callable. (No issues with Mypy, though.)│ -│❱ 367 │   │   returnsuper().__call__(*args, **kwargs)                                           │ -│368 │ -│369 │ -│370 classRichCommandCollection(CommandCollection, RichGroup):                                 │ -││ -│/opt/hostedtoolcache/Python/3.12.3/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/3.12.3/x64/lib/python3.12/site-packages/rich_click/rich_command.py:1│ -│52 in main│ -││ -│149 │   │   try:                                                                               │ -│150 │   │   │   try:                                                                           │ -│151 │   │   │   │   withself.make_context(prog_name, args, **extra) as ctx:                   │ -│❱ 152 │   │   │   │   │   rv = self.invoke(ctx)                                                  │ -│153 │   │   │   │   │   ifnot standalone_mode:                                                │ -│154 │   │   │   │   │   │   return rv                                                          │ -│155 │   │   │   │   │   # it's not safe to `ctx.exit(rv)` here!│ -││ -│/opt/hostedtoolcache/Python/3.12.3/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/3.12.3/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/3.12.3/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/3.12.3/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/3.12.3/x64/lib/python3.12/site-packages/nf_core/__main__.py:635 in   │ -│lint│ -││ -│ 632 │   │ -│ 633 │   # Run the lint tests!│ -│ 634 │   try:                                                                                  │ -│❱  635 │   │   lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting(                    │ -│ 636 │   │   │   dir,                                                                          │ -│ 637 │   │   │   release,                                                                      │ -│ 638 │   │   │   fix,                                                                          │ -││ -│/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/nf_core/lint/__init__.py:603│ -│ in run_linting│ -││ -│600 │   │ -│601 │   # Run the pipeline linting tests│ -│602 │   try:                                                                                   │ -│❱ 603 │   │   lint_obj._lint_pipeline()                                                          │ -│604 │   exceptAssertionErroras e:                                                            │ -│605 │   │   log.critical(f"Critical error: {e}")                                               │ -│606 │   │   log.info("Stopping tests...")                                                      │ -││ -│/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/nf_core/lint/__init__.py:228│ -│ in _lint_pipeline│ -││ -│225 │   │   │   │   │   continue│ -│226 │   │   │   │   self.progress_bar.update(lint_progress, advance=1, test_name=test_name)    │ -│227 │   │   │   │   log.debug(f"Running lint test: {test_name}")                               │ -│❱ 228 │   │   │   │   test_results = getattr(self, test_name)()                                  │ -│229 │   │   │   │   for test in test_results.get("passed", []):                                │ -│230 │   │   │   │   │   self.passed.append((test_name, test))                                  │ -│231 │   │   │   │   for test in test_results.get("ignored", []):                               │ -││ -│/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/nf_core/lint/actions_schema_│ -│validation.py:31 in actions_schema_validation│ -││ -│28 │   │ -│29 │   # Load the GitHub workflow schema│ -│30 │   r = requests.get("https://json.schemastore.org/github-workflow", allow_redirects=Tru│ -│❱ 31 │   schema = r.json()                                                                       │ -│32 │   │ -│33 │   # Validate all workflows against the schema│ -│34 │   for wf_path in action_workflows:                                                        │ -││ -│/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/requests/models.py:975 in    │ -│json│ -││ -│ 972 │   │   except JSONDecodeError as e:                                                      │ -│ 973 │   │   │   # Catch JSON-related errors and raise as requests.JSONDecodeError│ -│ 974 │   │   │   # This aliases json.JSONDecodeError and simplejson.JSONDecodeError│ -│❱  975 │   │   │   raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)                            │ -│ 976 │   │ -│ 977 │   @property│ -│ 978 │   deflinks(self):                                                                      │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -JSONDecodeError: Expecting value: line 1 column 1(char 0) + + + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Testing pipeline: . + + +╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ +││ +│pipeline_todos: pipeline_todos                                                                  │ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─[!] 1 Pipeline Test Warning────────────────────────────────────────────────────────────────────╮ +││ +│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │ +│doi (after the first release).                                                                  │ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + + +╭──────────────────────╮ +│LINT RESULTS SUMMARY│ +├──────────────────────┤ +│[✔] 194 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 26d224ddc2..c2bc73b4e9 100644 --- a/docs/images/nf-core-list-rna.svg +++ b/docs/images/nf-core-list-rna.svg @@ -19,114 +19,114 @@ font-weight: 700; } - .terminal-3988802752-matrix { + .terminal-4017179797-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3988802752-title { + .terminal-4017179797-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3988802752-r1 { fill: #c5c8c6 } -.terminal-3988802752-r2 { fill: #98a84b } -.terminal-3988802752-r3 { fill: #9a9b99 } -.terminal-3988802752-r4 { fill: #608ab1 } -.terminal-3988802752-r5 { fill: #d0b344 } -.terminal-3988802752-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3988802752-r7 { fill: #868887 } + .terminal-4017179797-r1 { fill: #c5c8c6 } +.terminal-4017179797-r2 { fill: #98a84b } +.terminal-4017179797-r3 { fill: #9a9b99 } +.terminal-4017179797-r4 { fill: #608ab1 } +.terminal-4017179797-r5 { fill: #d0b344 } +.terminal-4017179797-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-4017179797-r7 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -138,38 +138,38 @@ - + - - $ nf-core list rna rna-seq - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ differentialabunda… │    45 │          1.4.0 │  5 months ago │           - │ -                   │ -│ smrnaseq            │    68 │          2.3.1 │   3 weeks ago │           - │ -                   │ -│ rnaseq              │   784 │         3.14.0 │  4 months ago │           - │ -                   │ -│ spatialvi           │    39 │            dev │     yesterday │           - │ -                   │ -│ scnanoseq           │     5 │            dev │    1 week ago │           - │ -                   │ -│ scrnaseq            │   169 │          2.6.0 │  18 hours ago │           - │ -                   │ -│ circrna             │    40 │            dev │   2 weeks ago │           - │ -                   │ -│ rnafusion           │   129 │          3.0.2 │   4 weeks ago │           - │ -                   │ -│ rnasplice           │    33 │          1.0.3 │  2 months ago │           - │ -                   │ -│ dualrnaseq          │    16 │          1.0.0 │   3 years ago │           - │ -                   │ -│ marsseq             │     5 │          1.0.3 │ 10 months ago │           - │ -                   │ -│ lncpipe             │    30 │            dev │   2 years ago │           - │ -                   │ -│ scflow              │    24 │            dev │   3 years ago │           - │ -                   │ -└─────────────────────┴───────┴────────────────┴───────────────┴─────────────┴─────────────────────┘ + + $ nf-core list rna rna-seq + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ differentialabunda… │    45 │          1.5.0 │     yesterday │           - │ -                   │ +│ smrnaseq            │    68 │          2.3.1 │   3 weeks ago │           - │ -                   │ +│ rnaseq              │   785 │         3.14.0 │  4 months ago │           - │ -                   │ +│ spatialvi           │    39 │            dev │    3 days ago │           - │ -                   │ +│ scnanoseq           │     5 │            dev │   1 weeks ago │           - │ -                   │ +│ scrnaseq            │   169 │          2.6.0 │     yesterday │           - │ -                   │ +│ circrna             │    40 │            dev │   2 weeks ago │           - │ -                   │ +│ rnafusion           │   129 │          3.0.2 │   4 weeks ago │           - │ -                   │ +│ rnasplice           │    33 │          1.0.3 │  2 months ago │           - │ -                   │ +│ dualrnaseq          │    16 │          1.0.0 │   3 years ago │           - │ -                   │ +│ marsseq             │     5 │          1.0.3 │ 10 months ago │           - │ -                   │ +│ lncpipe             │    30 │            dev │   2 years ago │           - │ -                   │ +│ scflow              │    24 │            dev │   3 years ago │           - │ -                   │ +└─────────────────────┴───────┴────────────────┴───────────────┴─────────────┴─────────────────────┘ diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg index be2b84287b..70cb20a716 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-358676910-matrix { + .terminal-4091738593-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-358676910-title { + .terminal-4091738593-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-358676910-r1 { fill: #c5c8c6 } -.terminal-358676910-r2 { fill: #98a84b } -.terminal-358676910-r3 { fill: #9a9b99 } -.terminal-358676910-r4 { fill: #608ab1 } -.terminal-358676910-r5 { fill: #d0b344 } -.terminal-358676910-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-358676910-r7 { fill: #868887 } -.terminal-358676910-r8 { fill: #868887;font-style: italic; } + .terminal-4091738593-r1 { fill: #c5c8c6 } +.terminal-4091738593-r2 { fill: #98a84b } +.terminal-4091738593-r3 { fill: #9a9b99 } +.terminal-4091738593-r4 { fill: #608ab1 } +.terminal-4091738593-r5 { fill: #d0b344 } +.terminal-4091738593-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-4091738593-r7 { fill: #868887 } +.terminal-4091738593-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -112,29 +112,29 @@ - + - - $ nf-core list -s stars - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq              │   784 │         3.14.0 │  4 months ago │           - │ -                   │ -│ sarek               │   340 │          3.4.2 │  20 hours ago │           - │ -                   │ -│ mag                 │   182 │          2.5.4 │  3 months ago │           - │ -                   │ -│ chipseq             │   172 │          2.0.0 │   2 years ago │           - │ -                   │ -[..truncated..] + + $ nf-core list -s stars + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq              │   785 │         3.14.0 │  4 months ago │           - │ -                   │ +│ sarek               │   340 │          3.4.2 │     yesterday │           - │ -                   │ +│ mag                 │   182 │          2.5.4 │  3 months ago │           - │ -                   │ +│ chipseq             │   173 │          2.0.0 │   2 years ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg index 6857db79f9..32680c6142 100644 --- a/docs/images/nf-core-list.svg +++ b/docs/images/nf-core-list.svg @@ -19,91 +19,91 @@ font-weight: 700; } - .terminal-4024274838-matrix { + .terminal-187731172-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4024274838-title { + .terminal-187731172-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4024274838-r1 { fill: #c5c8c6 } -.terminal-4024274838-r2 { fill: #98a84b } -.terminal-4024274838-r3 { fill: #9a9b99 } -.terminal-4024274838-r4 { fill: #608ab1 } -.terminal-4024274838-r5 { fill: #d0b344 } -.terminal-4024274838-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-4024274838-r7 { fill: #868887 } -.terminal-4024274838-r8 { fill: #868887;font-style: italic; } + .terminal-187731172-r1 { fill: #c5c8c6 } +.terminal-187731172-r2 { fill: #98a84b } +.terminal-187731172-r3 { fill: #9a9b99 } +.terminal-187731172-r4 { fill: #608ab1 } +.terminal-187731172-r5 { fill: #d0b344 } +.terminal-187731172-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-187731172-r7 { fill: #868887 } +.terminal-187731172-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +115,30 @@ - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ differentialabunda… │    45 │          1.4.0 │  5 months ago │           - │ -                   │ -│ smrnaseq            │    68 │          2.3.1 │   3 weeks ago │           - │ -                   │ -│ sarek               │   340 │          3.4.2 │  20 hours ago │           - │ -                   │ -│ variantbenchmarking │     4 │            dev │  19 hours ago │           - │ -                   │ -│ meerpipe            │     0 │            dev │     yesterday │           - │ -                   │ -[..truncated..] + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ oncoanalyser        │    14 │            dev │  11 hours ago │           - │ -                   │ +│ metapep             │     6 │            dev │  20 hours ago │           - │ -                   │ +│ reportho            │     1 │            dev │     yesterday │           - │ -                   │ +│ differentialabunda… │    45 │          1.5.0 │     yesterday │           - │ -                   │ +│ smrnaseq            │    68 │          2.3.1 │   3 weeks ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index 4c342507a3..c71a3091f8 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-1669199940-matrix { + .terminal-1915222085-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1669199940-title { + .terminal-1915222085-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1669199940-r1 { fill: #c5c8c6 } -.terminal-1669199940-r2 { fill: #98a84b } -.terminal-1669199940-r3 { fill: #9a9b99 } -.terminal-1669199940-r4 { fill: #608ab1 } -.terminal-1669199940-r5 { fill: #d0b344 } -.terminal-1669199940-r6 { fill: #98a84b;font-weight: bold } -.terminal-1669199940-r7 { fill: #c5c8c6;font-weight: bold } + .terminal-1915222085-r1 { fill: #c5c8c6 } +.terminal-1915222085-r2 { fill: #98a84b } +.terminal-1915222085-r3 { fill: #9a9b99 } +.terminal-1915222085-r4 { fill: #608ab1 } +.terminal-1915222085-r5 { fill: #d0b344 } +.terminal-1915222085-r6 { fill: #98a84b;font-weight: bold } +.terminal-1915222085-r7 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -114,30 +114,30 @@ - + - - $ nf-core modules bump-versions fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - 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 2.14.1 - https://nf-co.re + + + + +╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ +│[!] 1 Module version up to date.│ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ +│Module name                             │Update Message                                       │ +├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ +│ fastqc                                   │ Module version up to date: fastqc                     │ +╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index 6cd7e15b66..973d5eed03 100644 --- a/docs/images/nf-core-modules-create.svg +++ b/docs/images/nf-core-modules-create.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + - - $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -INFO     Repository type: modules -INFO    Press enter to use default values (shown in brackets)or type your own responses.  -ctrl+click underlined text to open links. -INFO     Using Bioconda package: 'bioconda::fastqc=0.12.1' -INFO     Using Docker container: 'biocontainers/fastqc:0.12.1--hdfd78af_0' -INFO     Using Singularity container:                                                                -'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' -INFO     Created component template: 'fastqc' -INFO     Created following files:                                                                    -           modules/nf-core/fastqc/main.nf                                                            -           modules/nf-core/fastqc/meta.yml                                                           -           modules/nf-core/fastqc/environment.yml                                                    -           modules/nf-core/fastqc/tests/tags.yml                                                     -           modules/nf-core/fastqc/tests/main.nf.test                                                 + + $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Repository type: modules +INFO    Press enter to use default values (shown in brackets)or type your own responses.  +ctrl+click underlined text to open links. +INFO     Using Bioconda package: 'bioconda::fastqc=0.12.1' diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg index 92d19331ab..cc0cf02fdf 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-1309733425-matrix { + .terminal-1889661490-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1309733425-title { + .terminal-1889661490-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1309733425-r1 { fill: #c5c8c6 } -.terminal-1309733425-r2 { fill: #98a84b } -.terminal-1309733425-r3 { fill: #9a9b99 } -.terminal-1309733425-r4 { fill: #608ab1 } -.terminal-1309733425-r5 { fill: #d0b344 } -.terminal-1309733425-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1309733425-r7 { fill: #98a84b;font-weight: bold } -.terminal-1309733425-r8 { fill: #868887 } -.terminal-1309733425-r9 { fill: #d08442 } -.terminal-1309733425-r10 { fill: #868887;font-style: italic; } -.terminal-1309733425-r11 { fill: #98729f } + .terminal-1889661490-r1 { fill: #c5c8c6 } +.terminal-1889661490-r2 { fill: #98a84b } +.terminal-1889661490-r3 { fill: #9a9b99 } +.terminal-1889661490-r4 { fill: #608ab1 } +.terminal-1889661490-r5 { fill: #d0b344 } +.terminal-1889661490-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1889661490-r7 { fill: #98a84b;font-weight: bold } +.terminal-1889661490-r8 { fill: #868887 } +.terminal-1889661490-r9 { fill: #d08442 } +.terminal-1889661490-r10 { fill: #868887;font-style: italic; } +.terminal-1889661490-r11 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -187,53 +187,53 @@ - + - - $ nf-core modules info abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ -│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ -│ 🔧 Tools: abacas                                                                                 │ -│ 📖 Description: contiguate draft genome assembly                                                 │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -                  ╷                                                                   ╷              -📥 Inputs        │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} -                  ╵                                                                   ╵              -                  ╷                                                                   ╷              -📤 Outputs       │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - results  (file) │List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* -                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ -                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ -                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ -                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - versions  (file)│File containing software versions                                  │versions.yml -                  ╵                                                                   ╵              - - 💻  Installation command: nf-core modules install abacas - + + $ nf-core modules info abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ +│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ +│ 🔧 Tools: abacas                                                                                 │ +│ 📖 Description: contiguate draft genome assembly                                                 │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +                  ╷                                                                   ╷              +📥 Inputs        │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} +                  ╵                                                                   ╵              +                  ╷                                                                   ╷              +📤 Outputs       │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + results  (file) │List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* +                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ +                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ +                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ +                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + versions  (file)│File containing software versions                                  │versions.yml +                  ╵                                                                   ╵              + + 💻  Installation command: nf-core modules install abacas + diff --git a/docs/images/nf-core-modules-install.svg b/docs/images/nf-core-modules-install.svg index 51487ef6a5..975938bdc9 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-311069839-matrix { + .terminal-386043024-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-311069839-title { + .terminal-386043024-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-311069839-r1 { fill: #c5c8c6 } -.terminal-311069839-r2 { fill: #98a84b } -.terminal-311069839-r3 { fill: #9a9b99 } -.terminal-311069839-r4 { fill: #608ab1 } -.terminal-311069839-r5 { fill: #d0b344 } + .terminal-386043024-r1 { fill: #c5c8c6 } +.terminal-386043024-r2 { fill: #98a84b } +.terminal-386043024-r3 { fill: #9a9b99 } +.terminal-386043024-r4 { fill: #608ab1 } +.terminal-386043024-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core modules install abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - 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 2.14.1 - https://nf-co.re + + + +INFO     Installing 'abacas' +INFO     Use the following statement to include this module:                                         + + include { ABACAS } from '../modules/nf-core/abacas/main'                                            + diff --git a/docs/images/nf-core-modules-lint.svg b/docs/images/nf-core-modules-lint.svg index 355ca8d32d..692069b4f6 100644 --- a/docs/images/nf-core-modules-lint.svg +++ b/docs/images/nf-core-modules-lint.svg @@ -19,67 +19,67 @@ font-weight: 700; } - .terminal-1680563020-matrix { + .terminal-1737251661-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1680563020-title { + .terminal-1737251661-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1680563020-r1 { fill: #c5c8c6 } -.terminal-1680563020-r2 { fill: #98a84b } -.terminal-1680563020-r3 { fill: #9a9b99 } -.terminal-1680563020-r4 { fill: #608ab1 } -.terminal-1680563020-r5 { fill: #d0b344 } + .terminal-1737251661-r1 { fill: #c5c8c6 } +.terminal-1737251661-r2 { fill: #98a84b } +.terminal-1737251661-r3 { fill: #9a9b99 } +.terminal-1737251661-r4 { fill: #608ab1 } +.terminal-1737251661-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -91,23 +91,23 @@ - + - - $ nf-core modules lint multiqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -INFO     Linting modules repo: '.' -INFO     Linting module: 'multiqc' + + $ nf-core modules lint multiqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Linting modules repo: '.' +INFO     Linting module: 'multiqc' diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index 4956396bcf..ab9cc28c00 100644 --- a/docs/images/nf-core-modules-list-local.svg +++ b/docs/images/nf-core-modules-list-local.svg @@ -19,89 +19,89 @@ font-weight: 700; } - .terminal-1170249876-matrix { + .terminal-1390188693-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1170249876-title { + .terminal-1390188693-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1170249876-r1 { fill: #c5c8c6 } -.terminal-1170249876-r2 { fill: #98a84b } -.terminal-1170249876-r3 { fill: #9a9b99 } -.terminal-1170249876-r4 { fill: #608ab1 } -.terminal-1170249876-r5 { fill: #d0b344 } -.terminal-1170249876-r6 { fill: #c5c8c6;font-weight: bold } + .terminal-1390188693-r1 { fill: #c5c8c6 } +.terminal-1390188693-r2 { fill: #98a84b } +.terminal-1390188693-r3 { fill: #9a9b99 } +.terminal-1390188693-r4 { fill: #608ab1 } +.terminal-1390188693-r5 { fill: #d0b344 } +.terminal-1390188693-r6 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -113,30 +113,30 @@ - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -INFO     Repository type: pipeline -INFO     Modules installed in '.':                                                                   - -┏━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -┃Module Name┃Repository     ┃Version SHA┃Message                             ┃Date      ┃ -┡━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ fastqc      │ nf-core/modules │ 285a505     │ Fix FastQC memory allocation (#5432) │ 2024-04-05 │ -│ multiqc     │ nf-core/modules │ b7ebe95     │ Update MQC container (#5006)         │ 2024-02-29 │ -└─────────────┴─────────────────┴─────────────┴──────────────────────────────────────┴────────────┘ + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Repository type: pipeline +INFO     Modules installed in '.':                                                                   + +┏━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +┃Module Name┃Repository     ┃Version SHA┃Message                             ┃Date      ┃ +┡━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ fastqc      │ nf-core/modules │ 285a505     │ Fix FastQC memory allocation (#5432) │ 2024-04-05 │ +│ multiqc     │ nf-core/modules │ b7ebe95     │ Update MQC container (#5006)         │ 2024-02-29 │ +└─────────────┴─────────────────┴─────────────┴──────────────────────────────────────┴────────────┘ diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index b6e6fb3a8e..dce6553c9a 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-2384681400-matrix { + .terminal-2530892217-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2384681400-title { + .terminal-2530892217-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2384681400-r1 { fill: #c5c8c6 } -.terminal-2384681400-r2 { fill: #98a84b } -.terminal-2384681400-r3 { fill: #9a9b99 } -.terminal-2384681400-r4 { fill: #608ab1 } -.terminal-2384681400-r5 { fill: #d0b344 } -.terminal-2384681400-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-2384681400-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-2384681400-r8 { fill: #868887;font-style: italic; } + .terminal-2530892217-r1 { fill: #c5c8c6 } +.terminal-2530892217-r2 { fill: #98a84b } +.terminal-2530892217-r3 { fill: #9a9b99 } +.terminal-2530892217-r4 { fill: #608ab1 } +.terminal-2530892217-r5 { fill: #d0b344 } +.terminal-2530892217-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-2530892217-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2530892217-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core modules list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -INFO     Modules available from https://github.com/nf-core/modules.git(master):                     - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Module Name                                          ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ abacas                                                │ -│ abricate/run                                          │ -│ abricate/summary                                      │ -│ abritamr/run                                          │ -│ adapterremoval                                        │ -│ adapterremovalfixprefix                               │ -│ admixture                                             │ -│ affy/justrma                                          │ -│ agat/convertspgff2gtf                                 │ -[..truncated..] + + $ nf-core modules list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Modules available from https://github.com/nf-core/modules.git(master):                     + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Module Name                                          ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ abacas                                                │ +│ abricate/run                                          │ +│ abricate/summary                                      │ +│ abritamr/run                                          │ +│ adapterremoval                                        │ +│ adapterremovalfixprefix                               │ +│ admixture                                             │ +│ affy/justrma                                          │ +│ agat/convertspgff2gtf                                 │ +[..truncated..] diff --git a/docs/images/nf-core-modules-patch.svg b/docs/images/nf-core-modules-patch.svg index 34d9c8dfb7..73358ec2f6 100644 --- a/docs/images/nf-core-modules-patch.svg +++ b/docs/images/nf-core-modules-patch.svg @@ -19,127 +19,127 @@ font-weight: 700; } - .terminal-2649828425-matrix { + .terminal-3003919434-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2649828425-title { + .terminal-3003919434-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2649828425-r1 { fill: #c5c8c6 } -.terminal-2649828425-r2 { fill: #98a84b } -.terminal-2649828425-r3 { fill: #9a9b99 } -.terminal-2649828425-r4 { fill: #608ab1 } -.terminal-2649828425-r5 { fill: #d0b344 } -.terminal-2649828425-r6 { fill: #ff2627 } -.terminal-2649828425-r7 { fill: #00823d } -.terminal-2649828425-r8 { fill: #ff2c7a;font-weight: bold } + .terminal-3003919434-r1 { fill: #c5c8c6 } +.terminal-3003919434-r2 { fill: #98a84b } +.terminal-3003919434-r3 { fill: #9a9b99 } +.terminal-3003919434-r4 { fill: #608ab1 } +.terminal-3003919434-r5 { fill: #d0b344 } +.terminal-3003919434-r6 { fill: #ff2627 } +.terminal-3003919434-r7 { fill: #00823d } +.terminal-3003919434-r8 { fill: #ff2c7a;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -151,42 +151,42 @@ - + - - $ nf-core modules patch fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -INFO     Changes in module 'nf-core/fastqc' -INFO     Changes in 'fastqc/main.nf':                                                                - ---- modules/nf-core/fastqc/main.nf -+++ modules/nf-core/fastqc/main.nf -@@ -1,6 +1,6 @@ -process FASTQC {                                                                                   -    tag "$meta.id"                                                                                 --    label 'process_medium' -+    label 'process_low' - -    conda "${moduleDir}/environment.yml"                                                           -    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_  - - -INFO    'modules/nf-core/fastqc/meta.yml' is unchanged                                              -INFO    'modules/nf-core/fastqc/environment.yml' is unchanged                                       -INFO    'modules/nf-core/fastqc/tests/tags.yml' is unchanged                                        -INFO    'modules/nf-core/fastqc/tests/main.nf.test.snap' is unchanged                               -INFO    'modules/nf-core/fastqc/tests/main.nf.test' is unchanged                                    -INFO     Patch file of 'modules/nf-core/fastqc' written to 'modules/nf-core/fastqc/fastqc.diff' + + $ nf-core modules patch fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Changes in module 'nf-core/fastqc' +INFO     Changes in 'fastqc/main.nf':                                                                + +--- modules/nf-core/fastqc/main.nf ++++ modules/nf-core/fastqc/main.nf +@@ -1,6 +1,6 @@ +process FASTQC {                                                                                   +    tag "$meta.id"                                                                                 +-    label 'process_medium' ++    label 'process_low' + +    conda "${moduleDir}/environment.yml"                                                           +    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_  + + +INFO    'modules/nf-core/fastqc/meta.yml' is unchanged                                              +INFO    'modules/nf-core/fastqc/environment.yml' is unchanged                                       +INFO    'modules/nf-core/fastqc/tests/tags.yml' is unchanged                                        +INFO    'modules/nf-core/fastqc/tests/main.nf.test.snap' is unchanged                               +INFO    'modules/nf-core/fastqc/tests/main.nf.test' is unchanged                                    +INFO     Patch file of 'modules/nf-core/fastqc' written to 'modules/nf-core/fastqc/fastqc.diff' diff --git a/docs/images/nf-core-modules-remove.svg b/docs/images/nf-core-modules-remove.svg index af35fe2d31..7c2db60311 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-2116038113-matrix { + .terminal-2159226338-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2116038113-title { + .terminal-2159226338-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2116038113-r1 { fill: #c5c8c6 } -.terminal-2116038113-r2 { fill: #98a84b } -.terminal-2116038113-r3 { fill: #9a9b99 } -.terminal-2116038113-r4 { fill: #608ab1 } -.terminal-2116038113-r5 { fill: #d0b344 } + .terminal-2159226338-r1 { fill: #c5c8c6 } +.terminal-2159226338-r2 { fill: #98a84b } +.terminal-2159226338-r3 { fill: #9a9b99 } +.terminal-2159226338-r4 { fill: #608ab1 } +.terminal-2159226338-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -88,22 +88,22 @@ - + - - $ nf-core modules remove abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -INFO     Removed files for 'abacas' and its dependencies 'abacas'.                                   + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Removed files for 'abacas' and its dependencies 'abacas'.                                   diff --git a/docs/images/nf-core-modules-test.svg b/docs/images/nf-core-modules-test.svg index cb1304e879..f72c920ef0 100644 --- a/docs/images/nf-core-modules-test.svg +++ b/docs/images/nf-core-modules-test.svg @@ -19,64 +19,64 @@ font-weight: 700; } - .terminal-9302271-matrix { + .terminal-40300800-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-9302271-title { + .terminal-40300800-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-9302271-r1 { fill: #c5c8c6 } -.terminal-9302271-r2 { fill: #98a84b } -.terminal-9302271-r3 { fill: #9a9b99 } -.terminal-9302271-r4 { fill: #608ab1 } -.terminal-9302271-r5 { fill: #d0b344 } + .terminal-40300800-r1 { fill: #c5c8c6 } +.terminal-40300800-r2 { fill: #98a84b } +.terminal-40300800-r3 { fill: #9a9b99 } +.terminal-40300800-r4 { fill: #608ab1 } +.terminal-40300800-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -88,22 +88,22 @@ - + - - $ nf-core modules test fastqc --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -INFO     Generating nf-test snapshot                                                                 + + $ nf-core modules test fastqc --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Generating nf-test snapshot                                                                 diff --git a/docs/images/nf-core-modules-update.svg b/docs/images/nf-core-modules-update.svg index 46983bf5ea..c4800530ef 100644 --- a/docs/images/nf-core-modules-update.svg +++ b/docs/images/nf-core-modules-update.svg @@ -19,73 +19,73 @@ font-weight: 700; } - .terminal-2984310290-matrix { + .terminal-3074160147-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2984310290-title { + .terminal-3074160147-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2984310290-r1 { fill: #c5c8c6 } -.terminal-2984310290-r2 { fill: #98a84b } -.terminal-2984310290-r3 { fill: #9a9b99 } -.terminal-2984310290-r4 { fill: #608ab1 } -.terminal-2984310290-r5 { fill: #d0b344 } + .terminal-3074160147-r1 { fill: #c5c8c6 } +.terminal-3074160147-r2 { fill: #98a84b } +.terminal-3074160147-r3 { fill: #9a9b99 } +.terminal-3074160147-r4 { fill: #608ab1 } +.terminal-3074160147-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -97,25 +97,25 @@ - + - - $ nf-core modules update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -INFO    'modules/nf-core/abacas' is already up to date                                              -INFO    'modules/nf-core/fastqc' is already up to date                                              -INFO    'modules/nf-core/multiqc' is already up to date                                             -INFO     Updates complete ✨                                                                         + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO    'modules/nf-core/abacas' is already up to date                                              +INFO    'modules/nf-core/fastqc' is already up to date                                              +INFO    'modules/nf-core/multiqc' is already up to date                                             +INFO     Updates complete ✨                                                                         diff --git a/docs/images/nf-core-schema-build.svg b/docs/images/nf-core-schema-build.svg index 6d3e448b04..646243917b 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-1038338818-matrix { + .terminal-1167969027-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1038338818-title { + .terminal-1167969027-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1038338818-r1 { fill: #c5c8c6 } -.terminal-1038338818-r2 { fill: #98a84b } -.terminal-1038338818-r3 { fill: #9a9b99 } -.terminal-1038338818-r4 { fill: #608ab1 } -.terminal-1038338818-r5 { fill: #d0b344 } -.terminal-1038338818-r6 { fill: #98a84b;font-weight: bold } -.terminal-1038338818-r7 { fill: #868887;font-weight: bold } -.terminal-1038338818-r8 { fill: #868887 } -.terminal-1038338818-r9 { fill: #4e707b;font-weight: bold } -.terminal-1038338818-r10 { fill: #68a0b3;font-weight: bold } + .terminal-1167969027-r1 { fill: #c5c8c6 } +.terminal-1167969027-r2 { fill: #98a84b } +.terminal-1167969027-r3 { fill: #9a9b99 } +.terminal-1167969027-r4 { fill: #608ab1 } +.terminal-1167969027-r5 { fill: #d0b344 } +.terminal-1167969027-r6 { fill: #98a84b;font-weight: bold } +.terminal-1167969027-r7 { fill: #868887;font-weight: bold } +.terminal-1167969027-r8 { fill: #868887 } +.terminal-1167969027-r9 { fill: #4e707b;font-weight: bold } +.terminal-1167969027-r10 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,23 +96,23 @@ - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 31 params) -INFO     Writing schema with 32 params: 'nextflow_schema.json' + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 31 params) +INFO     Writing schema with 32 params: 'nextflow_schema.json' diff --git a/docs/images/nf-core-schema-lint.svg b/docs/images/nf-core-schema-lint.svg index 1b1a836556..538c162a55 100644 --- a/docs/images/nf-core-schema-lint.svg +++ b/docs/images/nf-core-schema-lint.svg @@ -19,68 +19,68 @@ font-weight: 700; } - .terminal-3582544776-matrix { + .terminal-3685763977-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3582544776-title { + .terminal-3685763977-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3582544776-r1 { fill: #c5c8c6 } -.terminal-3582544776-r2 { fill: #98a84b } -.terminal-3582544776-r3 { fill: #9a9b99 } -.terminal-3582544776-r4 { fill: #608ab1 } -.terminal-3582544776-r5 { fill: #d0b344 } -.terminal-3582544776-r6 { fill: #98a84b;font-weight: bold } -.terminal-3582544776-r7 { fill: #868887;font-weight: bold } -.terminal-3582544776-r8 { fill: #868887 } -.terminal-3582544776-r9 { fill: #4e707b;font-weight: bold } + .terminal-3685763977-r1 { fill: #c5c8c6 } +.terminal-3685763977-r2 { fill: #98a84b } +.terminal-3685763977-r3 { fill: #9a9b99 } +.terminal-3685763977-r4 { fill: #608ab1 } +.terminal-3685763977-r5 { fill: #d0b344 } +.terminal-3685763977-r6 { fill: #98a84b;font-weight: bold } +.terminal-3685763977-r7 { fill: #868887;font-weight: bold } +.terminal-3685763977-r8 { fill: #868887 } +.terminal-3685763977-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -92,22 +92,22 @@ - + - - $ nf-core schema lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 32 params) + + $ nf-core schema lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 32 params) diff --git a/docs/images/nf-core-schema-validate.svg b/docs/images/nf-core-schema-validate.svg index 94663e3812..71de9f6609 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-2456354039-matrix { + .terminal-2595093752-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2456354039-title { + .terminal-2595093752-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2456354039-r1 { fill: #c5c8c6 } -.terminal-2456354039-r2 { fill: #98a84b } -.terminal-2456354039-r3 { fill: #9a9b99 } -.terminal-2456354039-r4 { fill: #608ab1 } -.terminal-2456354039-r5 { fill: #d0b344 } -.terminal-2456354039-r6 { fill: #98a84b;font-weight: bold } -.terminal-2456354039-r7 { fill: #868887;font-weight: bold } -.terminal-2456354039-r8 { fill: #868887 } -.terminal-2456354039-r9 { fill: #4e707b;font-weight: bold } + .terminal-2595093752-r1 { fill: #c5c8c6 } +.terminal-2595093752-r2 { fill: #98a84b } +.terminal-2595093752-r3 { fill: #9a9b99 } +.terminal-2595093752-r4 { fill: #608ab1 } +.terminal-2595093752-r5 { fill: #d0b344 } +.terminal-2595093752-r6 { fill: #98a84b;font-weight: bold } +.terminal-2595093752-r7 { fill: #868887;font-weight: bold } +.terminal-2595093752-r8 { fill: #868887 } +.terminal-2595093752-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 2.14.0 - 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 2.14.1 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 93 params) +INFO    [✓] Input parameters look valid diff --git a/docs/images/nf-core-subworkflows-create.svg b/docs/images/nf-core-subworkflows-create.svg index 52d5e7c39f..ddf50e89fd 100644 --- a/docs/images/nf-core-subworkflows-create.svg +++ b/docs/images/nf-core-subworkflows-create.svg @@ -19,89 +19,89 @@ font-weight: 700; } - .terminal-695111068-matrix { + .terminal-870288797-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-695111068-title { + .terminal-870288797-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-695111068-r1 { fill: #c5c8c6 } -.terminal-695111068-r2 { fill: #98a84b } -.terminal-695111068-r3 { fill: #9a9b99 } -.terminal-695111068-r4 { fill: #608ab1 } -.terminal-695111068-r5 { fill: #d0b344 } -.terminal-695111068-r6 { fill: #68a0b3;font-weight: bold } + .terminal-870288797-r1 { fill: #c5c8c6 } +.terminal-870288797-r2 { fill: #98a84b } +.terminal-870288797-r3 { fill: #9a9b99 } +.terminal-870288797-r4 { fill: #608ab1 } +.terminal-870288797-r5 { fill: #d0b344 } +.terminal-870288797-r6 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -113,30 +113,30 @@ - + - - $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -INFO     Repository type: modules -INFO    Press enter to use default values (shown in brackets)or type your own responses.  -ctrl+click underlined text to open links. -INFO     Created component template: 'bam_stats_samtools' -INFO     Created following files:                                                                    -           subworkflows/nf-core/bam_stats_samtools/main.nf                                           -           subworkflows/nf-core/bam_stats_samtools/meta.yml                                          -           subworkflows/nf-core/bam_stats_samtools/tests/tags.yml                                    -           subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test                                + + $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Repository type: modules +INFO    Press enter to use default values (shown in brackets)or type your own responses.  +ctrl+click underlined text to open links. +INFO     Created component template: 'bam_stats_samtools' +INFO     Created following files:                                                                    +           subworkflows/nf-core/bam_stats_samtools/main.nf                                           +           subworkflows/nf-core/bam_stats_samtools/meta.yml                                          +           subworkflows/nf-core/bam_stats_samtools/tests/tags.yml                                    +           subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test                                diff --git a/docs/images/nf-core-subworkflows-info.svg b/docs/images/nf-core-subworkflows-info.svg index e2c828102c..83eda7387e 100644 --- a/docs/images/nf-core-subworkflows-info.svg +++ b/docs/images/nf-core-subworkflows-info.svg @@ -19,112 +19,112 @@ font-weight: 700; } - .terminal-1309324417-matrix { + .terminal-1569305730-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1309324417-title { + .terminal-1569305730-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1309324417-r1 { fill: #c5c8c6 } -.terminal-1309324417-r2 { fill: #98a84b } -.terminal-1309324417-r3 { fill: #9a9b99 } -.terminal-1309324417-r4 { fill: #608ab1 } -.terminal-1309324417-r5 { fill: #d0b344 } -.terminal-1309324417-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1309324417-r7 { fill: #98a84b;font-weight: bold } -.terminal-1309324417-r8 { fill: #868887 } -.terminal-1309324417-r9 { fill: #868887;font-style: italic; } -.terminal-1309324417-r10 { fill: #d08442 } -.terminal-1309324417-r11 { fill: #98729f } + .terminal-1569305730-r1 { fill: #c5c8c6 } +.terminal-1569305730-r2 { fill: #98a84b } +.terminal-1569305730-r3 { fill: #9a9b99 } +.terminal-1569305730-r4 { fill: #608ab1 } +.terminal-1569305730-r5 { fill: #d0b344 } +.terminal-1569305730-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1569305730-r7 { fill: #98a84b;font-weight: bold } +.terminal-1569305730-r8 { fill: #868887 } +.terminal-1569305730-r9 { fill: #868887;font-style: italic; } +.terminal-1569305730-r10 { fill: #d08442 } +.terminal-1569305730-r11 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -136,36 +136,36 @@ - + - - $ nf-core subworkflows info bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -╭─ Subworkflow: bam_rseqc  ────────────────────────────────────────────────────────────────────────╮ -│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ -│ 📖 Description: Subworkflow to run multiple commands in the RSeqC package                        │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -[..truncated..] - readduplication_rscript  (file)    │script to reproduce the plot       │                      *.R -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - tin_txt  (file)                    │TXT file containing tin.py results │                    *.txt -                                     │summary                            │ -╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ - versions  (file)                   │File containing software versions  │             versions.yml -                                     ╵                                   ╵                           - - 💻  Installation command: nf-core subworkflows install bam_rseqc - + + $ nf-core subworkflows info bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +╭─ Subworkflow: bam_rseqc  ────────────────────────────────────────────────────────────────────────╮ +│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ +│ 📖 Description: Subworkflow to run multiple commands in the RSeqC package                        │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +[..truncated..] + readduplication_rscript  (file)    │script to reproduce the plot       │                      *.R +╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ + tin_txt  (file)                    │TXT file containing tin.py results │                    *.txt +                                     │summary                            │ +╶────────────────────────────────────┼───────────────────────────────────┼─────────────────────────╴ + versions  (file)                   │File containing software versions  │             versions.yml +                                     ╵                                   ╵                           + + 💻  Installation command: nf-core subworkflows install bam_rseqc + diff --git a/docs/images/nf-core-subworkflows-install.svg b/docs/images/nf-core-subworkflows-install.svg index 628ed9fef0..ee5ef0ec21 100644 --- a/docs/images/nf-core-subworkflows-install.svg +++ b/docs/images/nf-core-subworkflows-install.svg @@ -19,64 +19,64 @@ font-weight: 700; } - .terminal-3596750067-matrix { + .terminal-3633843444-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3596750067-title { + .terminal-3633843444-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3596750067-r1 { fill: #c5c8c6 } -.terminal-3596750067-r2 { fill: #98a84b } -.terminal-3596750067-r3 { fill: #9a9b99 } -.terminal-3596750067-r4 { fill: #608ab1 } -.terminal-3596750067-r5 { fill: #d0b344 } + .terminal-3633843444-r1 { fill: #c5c8c6 } +.terminal-3633843444-r2 { fill: #98a84b } +.terminal-3633843444-r3 { fill: #9a9b99 } +.terminal-3633843444-r4 { fill: #608ab1 } +.terminal-3633843444-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -88,22 +88,22 @@ - + - - $ nf-core subworkflows install bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -INFO     Installing 'bam_rseqc' + + $ nf-core subworkflows install bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Installing 'bam_rseqc' diff --git a/docs/images/nf-core-subworkflows-lint.svg b/docs/images/nf-core-subworkflows-lint.svg index a4497c6cd2..08135d4e7c 100644 --- a/docs/images/nf-core-subworkflows-lint.svg +++ b/docs/images/nf-core-subworkflows-lint.svg @@ -19,242 +19,242 @@ font-weight: 700; } - .terminal-3131507105-matrix { + .terminal-2452554146-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3131507105-title { + .terminal-2452554146-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3131507105-r1 { fill: #c5c8c6 } -.terminal-3131507105-r2 { fill: #98a84b } -.terminal-3131507105-r3 { fill: #9a9b99 } -.terminal-3131507105-r4 { fill: #608ab1 } -.terminal-3131507105-r5 { fill: #d0b344 } -.terminal-3131507105-r6 { fill: #d0b344;font-weight: bold } -.terminal-3131507105-r7 { fill: #8d7b39 } -.terminal-3131507105-r8 { fill: #68a0b3;font-weight: bold } -.terminal-3131507105-r9 { fill: #d0b344;font-style: italic; } -.terminal-3131507105-r10 { fill: #c5c8c6;font-weight: bold } -.terminal-3131507105-r11 { fill: #98a84b;font-weight: bold } -.terminal-3131507105-r12 { fill: #cc555a } + .terminal-2452554146-r1 { fill: #c5c8c6 } +.terminal-2452554146-r2 { fill: #98a84b } +.terminal-2452554146-r3 { fill: #9a9b99 } +.terminal-2452554146-r4 { fill: #608ab1 } +.terminal-2452554146-r5 { fill: #d0b344 } +.terminal-2452554146-r6 { fill: #d0b344;font-weight: bold } +.terminal-2452554146-r7 { fill: #8d7b39 } +.terminal-2452554146-r8 { fill: #68a0b3;font-weight: bold } +.terminal-2452554146-r9 { fill: #d0b344;font-style: italic; } +.terminal-2452554146-r10 { fill: #c5c8c6;font-weight: bold } +.terminal-2452554146-r11 { fill: #98a84b;font-weight: bold } +.terminal-2452554146-r12 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -266,79 +266,79 @@ - + - - $ nf-core subworkflows lint bam_stats_samtools - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -INFO     Linting modules repo: '.' -INFO     Linting subworkflow: 'bam_stats_samtools' - -╭─[!] 15 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│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│versions not found in snapshot file │ -│                     ╵                                     ╵                                      │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────╮ -│LINT RESULTS SUMMARY│ -├───────────────────────┤ -│[✔]  42 Tests Passed │ -│[!]  15 Test Warnings│ -│[✗]   0 Tests Failed │ -╰───────────────────────╯ + + $ nf-core subworkflows lint bam_stats_samtools + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Linting modules repo: '.' +INFO     Linting subworkflow: 'bam_stats_samtools' + +╭─[!] 15 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│ +│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│versions not found in snapshot file │ +│                     ╵                                     ╵                                      │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭───────────────────────╮ +│LINT RESULTS SUMMARY│ +├───────────────────────┤ +│[✔]  42 Tests Passed │ +│[!]  15 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 50072fb6df..85b5237f63 100644 --- a/docs/images/nf-core-subworkflows-list-local.svg +++ b/docs/images/nf-core-subworkflows-list-local.svg @@ -19,108 +19,108 @@ font-weight: 700; } - .terminal-1791436705-matrix { + .terminal-2066032546-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1791436705-title { + .terminal-2066032546-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1791436705-r1 { fill: #c5c8c6 } -.terminal-1791436705-r2 { fill: #98a84b } -.terminal-1791436705-r3 { fill: #9a9b99 } -.terminal-1791436705-r4 { fill: #608ab1 } -.terminal-1791436705-r5 { fill: #d0b344 } -.terminal-1791436705-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1791436705-r7 { fill: #868887;font-style: italic; } + .terminal-2066032546-r1 { fill: #c5c8c6 } +.terminal-2066032546-r2 { fill: #98a84b } +.terminal-2066032546-r3 { fill: #9a9b99 } +.terminal-2066032546-r4 { fill: #608ab1 } +.terminal-2066032546-r5 { fill: #d0b344 } +.terminal-2066032546-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-2066032546-r7 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,36 +132,36 @@ - + - - $ nf-core subworkflows list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -INFO     Repository type: pipeline -INFO     Subworkflows installed in '.':                                                              - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -┃Subworkflow Name        ┃Repository     ┃Version SHA┃Message                 ┃Date      ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ utils_nextflow_pipeline  │ nf-core/modules │ 5caf764     │ remove params.outdir     │ 2024-02-28 │ -│                          │                 │             │ from modules and         │            │ -│                          │                 │             │ subworfklows tests       │            │ -│                          │                 │             │ (#5007)                  │            │ -│ utils_nfcore_pipeline    │ nf-core/modules │ 92de218     │ handle multiple DOIs     │ 2024-05-02 │ -│                          │                 │             │ (#5556)                  │            │ -│ utils_nfvalidation_plug… │ nf-core/modules │ 5caf764     │ remove params.outdir     │ 2024-02-28 │ -│                          │                 │             │ from modules and         │            │ -[..truncated..] + + $ nf-core subworkflows list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Repository type: pipeline +INFO     Subworkflows installed in '.':                                                              + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +┃Subworkflow Name        ┃Repository     ┃Version SHA┃Message                 ┃Date      ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ utils_nextflow_pipeline  │ nf-core/modules │ 5caf764     │ remove params.outdir     │ 2024-02-28 │ +│                          │                 │             │ from modules and         │            │ +│                          │                 │             │ subworfklows tests       │            │ +│                          │                 │             │ (#5007)                  │            │ +│ utils_nfcore_pipeline    │ nf-core/modules │ 92de218     │ handle multiple DOIs     │ 2024-05-02 │ +│                          │                 │             │ (#5556)                  │            │ +│ utils_nfvalidation_plug… │ nf-core/modules │ 5caf764     │ remove params.outdir     │ 2024-02-28 │ +│                          │                 │             │ from modules and         │            │ +[..truncated..] diff --git a/docs/images/nf-core-subworkflows-list-remote.svg b/docs/images/nf-core-subworkflows-list-remote.svg index b2c9fcb327..8b7d4e803c 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-1181242108-matrix { + .terminal-1319064317-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1181242108-title { + .terminal-1319064317-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1181242108-r1 { fill: #c5c8c6 } -.terminal-1181242108-r2 { fill: #98a84b } -.terminal-1181242108-r3 { fill: #9a9b99 } -.terminal-1181242108-r4 { fill: #608ab1 } -.terminal-1181242108-r5 { fill: #d0b344 } -.terminal-1181242108-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-1181242108-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-1181242108-r8 { fill: #868887;font-style: italic; } + .terminal-1319064317-r1 { fill: #c5c8c6 } +.terminal-1319064317-r2 { fill: #98a84b } +.terminal-1319064317-r3 { fill: #9a9b99 } +.terminal-1319064317-r4 { fill: #608ab1 } +.terminal-1319064317-r5 { fill: #d0b344 } +.terminal-1319064317-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-1319064317-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-1319064317-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core subworkflows list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - 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_umicollapse          │ -│ bam_dedup_stats_samtools_umitools             │ -│ bam_docounts_contamination_angsd              │ -│ bam_markduplicates_picard                     │ -│ bam_markduplicates_samtools                   │ -│ bam_ngscheckmate                              │ -│ bam_qc_picard                                 │ -[..truncated..] + + $ nf-core subworkflows list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Subworkflow Name                             ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ bam_cnv_wisecondorx                           │ +│ bam_create_som_pon_gatk                       │ +│ bam_dedup_stats_samtools_umicollapse          │ +│ bam_dedup_stats_samtools_umitools             │ +│ bam_docounts_contamination_angsd              │ +│ bam_markduplicates_picard                     │ +│ bam_markduplicates_samtools                   │ +│ bam_ngscheckmate                              │ +│ bam_qc_picard                                 │ +[..truncated..] diff --git a/docs/images/nf-core-subworkflows-remove.svg b/docs/images/nf-core-subworkflows-remove.svg index 0fa3b40f89..9da9135085 100644 --- a/docs/images/nf-core-subworkflows-remove.svg +++ b/docs/images/nf-core-subworkflows-remove.svg @@ -19,82 +19,82 @@ font-weight: 700; } - .terminal-3759247281-matrix { + .terminal-3928723378-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3759247281-title { + .terminal-3928723378-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3759247281-r1 { fill: #c5c8c6 } -.terminal-3759247281-r2 { fill: #98a84b } -.terminal-3759247281-r3 { fill: #9a9b99 } -.terminal-3759247281-r4 { fill: #608ab1 } -.terminal-3759247281-r5 { fill: #d0b344 } + .terminal-3928723378-r1 { fill: #c5c8c6 } +.terminal-3928723378-r2 { fill: #98a84b } +.terminal-3928723378-r3 { fill: #9a9b99 } +.terminal-3928723378-r4 { fill: #608ab1 } +.terminal-3928723378-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -106,28 +106,28 @@ - + - - $ nf-core subworkflows remove bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - 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 'bam_rseqc' and its dependencies 'bam_rseqc, rseqc_bamstat,  -rseqc_inferexperiment, rseqc_innerdistance, rseqc_junctionannotation'.                      + + $ nf-core subworkflows remove bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Removed files for 'rseqc/bamstat' and its dependencies 'rseqc/bamstat'.                     +INFO     Removed files for 'rseqc/inferexperiment' and its dependencies 'rseqc/inferexperiment'.     +INFO     Removed files for 'rseqc/innerdistance' and its dependencies 'rseqc/innerdistance'.         +INFO     Removed files for 'rseqc/junctionannotation' and its dependencies                           +'rseqc/junctionannotation'.                                                                 +INFO     Removed files for 'bam_rseqc' and its dependencies 'bam_rseqc, rseqc_bamstat,  +rseqc_inferexperiment, rseqc_innerdistance, rseqc_junctionannotation'.                      diff --git a/docs/images/nf-core-subworkflows-test.svg b/docs/images/nf-core-subworkflows-test.svg index a497ee900d..cbd67278ad 100644 --- a/docs/images/nf-core-subworkflows-test.svg +++ b/docs/images/nf-core-subworkflows-test.svg @@ -19,64 +19,64 @@ font-weight: 700; } - .terminal-1767306345-matrix { + .terminal-1798304874-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1767306345-title { + .terminal-1798304874-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1767306345-r1 { fill: #c5c8c6 } -.terminal-1767306345-r2 { fill: #98a84b } -.terminal-1767306345-r3 { fill: #9a9b99 } -.terminal-1767306345-r4 { fill: #608ab1 } -.terminal-1767306345-r5 { fill: #d0b344 } + .terminal-1798304874-r1 { fill: #c5c8c6 } +.terminal-1798304874-r2 { fill: #98a84b } +.terminal-1798304874-r3 { fill: #9a9b99 } +.terminal-1798304874-r4 { fill: #608ab1 } +.terminal-1798304874-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -88,22 +88,22 @@ - + - - $ nf-core subworkflows test bam_rseqc --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -INFO     Generating nf-test snapshot                                                                 + + $ nf-core subworkflows test bam_rseqc --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Generating nf-test snapshot                                                                 diff --git a/docs/images/nf-core-subworkflows-update.svg b/docs/images/nf-core-subworkflows-update.svg index bff01d365b..d6da3d97ab 100644 --- a/docs/images/nf-core-subworkflows-update.svg +++ b/docs/images/nf-core-subworkflows-update.svg @@ -19,65 +19,65 @@ font-weight: 700; } - .terminal-795743372-matrix { + .terminal-833557645-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-795743372-title { + .terminal-833557645-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-795743372-r1 { fill: #c5c8c6 } -.terminal-795743372-r2 { fill: #98a84b } -.terminal-795743372-r3 { fill: #9a9b99 } -.terminal-795743372-r4 { fill: #608ab1 } -.terminal-795743372-r5 { fill: #d0b344 } -.terminal-795743372-r6 { fill: #cc555a;font-weight: bold } + .terminal-833557645-r1 { fill: #c5c8c6 } +.terminal-833557645-r2 { fill: #98a84b } +.terminal-833557645-r3 { fill: #9a9b99 } +.terminal-833557645-r4 { fill: #608ab1 } +.terminal-833557645-r5 { fill: #d0b344 } +.terminal-833557645-r6 { fill: #cc555a;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -89,22 +89,22 @@ - + - - $ nf-core subworkflows update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - https://nf-co.re - - - -ERROR   'rseqc/junctionsaturation' + + $ nf-core subworkflows update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +ERROR   'rseqc/junctionsaturation' diff --git a/docs/images/nf-core-sync.svg b/docs/images/nf-core-sync.svg index 3a198f5713..d5c5b666c4 100644 --- a/docs/images/nf-core-sync.svg +++ b/docs/images/nf-core-sync.svg @@ -19,70 +19,70 @@ font-weight: 700; } - .terminal-967031034-matrix { + .terminal-1040562427-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-967031034-title { + .terminal-1040562427-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-967031034-r1 { fill: #c5c8c6 } -.terminal-967031034-r2 { fill: #98a84b } -.terminal-967031034-r3 { fill: #9a9b99 } -.terminal-967031034-r4 { fill: #608ab1 } -.terminal-967031034-r5 { fill: #d0b344 } -.terminal-967031034-r6 { fill: #cc555a } -.terminal-967031034-r7 { fill: #98729f } -.terminal-967031034-r8 { fill: #ff2c7a } + .terminal-1040562427-r1 { fill: #c5c8c6 } +.terminal-1040562427-r2 { fill: #98a84b } +.terminal-1040562427-r3 { fill: #9a9b99 } +.terminal-1040562427-r4 { fill: #608ab1 } +.terminal-1040562427-r5 { fill: #d0b344 } +.terminal-1040562427-r6 { fill: #cc555a } +.terminal-1040562427-r7 { fill: #98729f } +.terminal-1040562427-r8 { fill: #ff2c7a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -94,23 +94,23 @@ - + - - $ nf-core sync - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.0 - 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' + + $ nf-core sync + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +WARNING  Could not find GitHub authentication token. Some API requests may fail.                     +INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthing +INFO     Original pipeline repository branch is 'master' diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml index d1ecae12b7..b2cde075fe 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -20,7 +20,6 @@ jobs: uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: python-version: "3.12" - cache: "pip" - name: Install pre-commit run: pip install pre-commit diff --git a/setup.py b/setup.py index 1ebf4a6b38..47137cde70 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import find_packages, setup -version = "2.14.0" +version = "2.14.1" with open("README.md") as f: readme = f.read()