diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml index 8368255390..f5f289b73e 100644 --- a/.github/workflows/rich-codex.yml +++ b/.github/workflows/rich-codex.yml @@ -17,6 +17,21 @@ jobs: - name: Install Nextflow uses: nf-core/setup-nextflow@v1 + - name: Cache nf-test installation + id: cache-software + uses: actions/cache@v3 + with: + path: | + /usr/local/bin/nf-test + /home/runner/.nf-test/nf-test.jar + key: ${{ runner.os }}-nftest-${{ env.date }} + + - name: Install nf-test + if: steps.cache-software.outputs.cache-hit != 'true' + run: | + wget -qO- https://code.askimed.com/install/nf-test | bash + sudo mv nf-test /usr/local/bin/ + - name: Install nf-core/tools run: pip install git+https://github.com/nf-core/tools.git@dev diff --git a/CHANGELOG.md b/CHANGELOG.md index 9804e9e062..28c02ea066 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,17 @@ # nf-core/tools: Changelog -# [v2.11 - Magnesium Dragon](https://github.com/nf-core/tools/releases/tag/2.11) + [2023-12-19] +# [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20] + +### Template + +- Rename `release-announcments.yml` to `release-announcements.yml` ([#2610](https://github.com/nf-core/tools/pull/2610)) +- Fix `nextflow.config` `docker.runOptions` ([#2607](https://github.com/nf-core/tools/pull/2607)) + +### General + +- Only dump `modules.json` when it is modified ([#2609](https://github.com/nf-core/tools/pull/2609)) + +# [v2.11 - Magnesium Dragon](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-19] ### Template diff --git a/README.md b/README.md index ec58d668bd..653f5295ea 100644 --- a/README.md +++ b/README.md @@ -900,7 +900,7 @@ If you want to make a minor change to a locally installed module but still keep ![`nf-core modules patch fastqc`](docs/images/nf-core-modules-patch.svg) @@ -965,7 +965,7 @@ extra_env: PROFILE: 'conda' --> -![`nf-core modules test fastqc --no-prompts --force`](docs/images/nf-core-modules-test.svg) +![`nf-core modules test fastqc --no-prompts`](docs/images/nf-core-modules-test.svg) In case you changed something in the test and want to update the snapshot, run @@ -1076,6 +1076,9 @@ This shows documentation about the subworkflow on the command line, similar to w working_dir: tmp/nf-core-nextbigthing before_command: > echo "repository_type: pipeline" >> .nf-core.yml + +head: 15 +tail: 10 --> ![`nf-core subworkflows info bam_rseqc`](docs/images/nf-core-subworkflows-info.svg) diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg index 528ca47408..c57af953e3 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-541877205-matrix { + .terminal-2993841204-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-541877205-title { + .terminal-2993841204-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-541877205-r1 { fill: #c5c8c6 } -.terminal-541877205-r2 { fill: #98a84b } -.terminal-541877205-r3 { fill: #9a9b99 } -.terminal-541877205-r4 { fill: #608ab1 } -.terminal-541877205-r5 { fill: #d0b344 } -.terminal-541877205-r6 { fill: #cc555a } + .terminal-2993841204-r1 { fill: #c5c8c6 } +.terminal-2993841204-r2 { fill: #98a84b } +.terminal-2993841204-r3 { fill: #9a9b99 } +.terminal-2993841204-r4 { fill: #608ab1 } +.terminal-2993841204-r5 { fill: #d0b344 } +.terminal-2993841204-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -146,41 +146,41 @@ - + - - $ nf-core bump-version 1.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - -INFO     Changing version number from '1.0dev' to '1.1' -INFO     Updated version in 'nextflow.config' - - version         = '1.0dev' - + version         = '1.1' - - -INFO     Updated version in 'assets/multiqc_config.yml' - - This report has been generated by the <a  -href="https://github.com/nf-core/nextbigthing/tree/dev" target="_blank">nf-core/nextbigthing</a> - + This report has been generated by the <a  -href="https://github.com/nf-core/nextbigthing/releases/tag/1.1"  -target="_blank">nf-core/nextbigthing</a> - - -INFO     Updated version in 'assets/multiqc_config.yml' - - <a href="https://nf-co.re/nextbigthing/dev/docs/output"  -target="_blank">documentation</a>. - + <a href="https://nf-co.re/nextbigthing/1.1/docs/output"  -target="_blank">documentation</a>. - - + + $ nf-core bump-version 1.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + +INFO     Changing version number from '1.0dev' to '1.1' +INFO     Updated version in 'nextflow.config' + - version         = '1.0dev' + + version         = '1.1' + + +INFO     Updated version in 'assets/multiqc_config.yml' + - This report has been generated by the <a  +href="https://github.com/nf-core/nextbigthing/tree/dev" target="_blank">nf-core/nextbigthing</a> + + This report has been generated by the <a  +href="https://github.com/nf-core/nextbigthing/releases/tag/1.1"  +target="_blank">nf-core/nextbigthing</a> + + +INFO     Updated version in 'assets/multiqc_config.yml' + - <a href="https://nf-co.re/nextbigthing/dev/docs/output"  +target="_blank">documentation</a>. + + <a href="https://nf-co.re/nextbigthing/1.1/docs/output"  +target="_blank">documentation</a>. + + diff --git a/docs/images/nf-core-create.svg b/docs/images/nf-core-create.svg index 680fbe8ad2..99a7112fb4 100644 --- a/docs/images/nf-core-create.svg +++ b/docs/images/nf-core-create.svg @@ -19,104 +19,104 @@ font-weight: 700; } - .terminal-1578160727-matrix { + .terminal-3963146934-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1578160727-title { + .terminal-3963146934-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1578160727-r1 { fill: #c5c8c6 } -.terminal-1578160727-r2 { fill: #98a84b } -.terminal-1578160727-r3 { fill: #9a9b99 } -.terminal-1578160727-r4 { fill: #608ab1 } -.terminal-1578160727-r5 { fill: #d0b344 } -.terminal-1578160727-r6 { fill: #98729f } -.terminal-1578160727-r7 { fill: #ff2c7a } -.terminal-1578160727-r8 { fill: #98a84b;font-weight: bold } -.terminal-1578160727-r9 { fill: #1984e9;text-decoration: underline; } + .terminal-3963146934-r1 { fill: #c5c8c6 } +.terminal-3963146934-r2 { fill: #98a84b } +.terminal-3963146934-r3 { fill: #9a9b99 } +.terminal-3963146934-r4 { fill: #608ab1 } +.terminal-3963146934-r5 { fill: #d0b344 } +.terminal-3963146934-r6 { fill: #98729f } +.terminal-3963146934-r7 { fill: #ff2c7a } +.terminal-3963146934-r8 { fill: #98a84b;font-weight: bold } +.terminal-3963146934-r9 { fill: #1984e9;text-decoration: underline; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -128,34 +128,34 @@ - + - - $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique"  --a "Big Steve" --plain - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - -INFO     Creating new nf-core pipeline: 'nf-core/nextbigthing' -INFO     Initialising pipeline git repository                                                        -INFO     Done. Remember to add a remote and push to GitHub:                                          - cd /home/runner/work/tools/tools/tmp/nf-core-nextbigthing - git remote add origin git@github.com:USERNAME/REPO_NAME.git  - git push --all origin                                        -INFO     This will also push your newly created dev branch and the TEMPLATE branch for syncing.      -INFO    !!!!!! IMPORTANT !!!!!! - -If you are interested in adding your pipeline to the nf-core community, -PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE! - -Please read: https://nf-co.re/developers/adding_pipelines#join-the-community + + $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique"  +-a "Big Steve" --plain + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - 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 0a327fbaa7..cc6b17ebfd 100644 --- a/docs/images/nf-core-download.svg +++ b/docs/images/nf-core-download.svg @@ -19,86 +19,86 @@ font-weight: 700; } - .terminal-1787882863-matrix { + .terminal-2599349710-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1787882863-title { + .terminal-2599349710-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1787882863-r1 { fill: #c5c8c6 } -.terminal-1787882863-r2 { fill: #98a84b } -.terminal-1787882863-r3 { fill: #9a9b99 } -.terminal-1787882863-r4 { fill: #608ab1 } -.terminal-1787882863-r5 { fill: #d0b344 } -.terminal-1787882863-r6 { fill: #cc555a } + .terminal-2599349710-r1 { fill: #c5c8c6 } +.terminal-2599349710-r2 { fill: #98a84b } +.terminal-2599349710-r3 { fill: #9a9b99 } +.terminal-2599349710-r4 { fill: #608ab1 } +.terminal-2599349710-r5 { fill: #d0b344 } +.terminal-2599349710-r6 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -110,29 +110,29 @@ - + - - $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - 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 2.11.1 - https://nf-co.re + + +WARNING  Could not find GitHub authentication token. Some API requests may fail.                     +INFO     Saving 'nf-core/rnaseq' +          Pipeline revision: '3.8' +          Use containers: 'none' +          Container library: 'quay.io' +          Output directory: 'nf-core-rnaseq' +          Include default institutional configuration: 'True' +INFO     Downloading centralised configs from GitHub                                                 +INFO     Downloading workflow files from GitHub                                                      diff --git a/docs/images/nf-core-launch-rnaseq.svg b/docs/images/nf-core-launch-rnaseq.svg index 53f80a26be..b76e4893c5 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-1786293714-matrix { + .terminal-3706564145-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1786293714-title { + .terminal-3706564145-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1786293714-r1 { fill: #c5c8c6 } -.terminal-1786293714-r2 { fill: #98a84b } -.terminal-1786293714-r3 { fill: #9a9b99 } -.terminal-1786293714-r4 { fill: #608ab1 } -.terminal-1786293714-r5 { fill: #d0b344 } -.terminal-1786293714-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1786293714-r7 { fill: #68a0b3;font-weight: bold } + .terminal-3706564145-r1 { fill: #c5c8c6 } +.terminal-3706564145-r2 { fill: #98a84b } +.terminal-3706564145-r3 { fill: #9a9b99 } +.terminal-3706564145-r4 { fill: #608ab1 } +.terminal-3706564145-r5 { fill: #d0b344 } +.terminal-3706564145-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-3706564145-r7 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,24 +96,24 @@ - + - - $ nf-core launch rnaseq -r 3.8.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - -INFO     NOTE: This tool ignores any pipeline parameter defaults overwritten by Nextflow config      -         files or profiles                                                                           - -INFO     Downloading workflow: nf-core/rnaseq (3.8.1) + + $ nf-core launch rnaseq -r 3.8.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + +INFO     NOTE: This tool ignores any pipeline parameter defaults overwritten by Nextflow config      +         files or profiles                                                                           + +INFO     Downloading workflow: nf-core/rnaseq (3.8.1) diff --git a/docs/images/nf-core-licences.svg b/docs/images/nf-core-licences.svg index 885973ea4a..934458cf62 100644 --- a/docs/images/nf-core-licences.svg +++ b/docs/images/nf-core-licences.svg @@ -19,108 +19,108 @@ font-weight: 700; } - .terminal-2300693057-matrix { + .terminal-3498363552-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2300693057-title { + .terminal-3498363552-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2300693057-r1 { fill: #c5c8c6 } -.terminal-2300693057-r2 { fill: #98a84b } -.terminal-2300693057-r3 { fill: #9a9b99 } -.terminal-2300693057-r4 { fill: #608ab1 } -.terminal-2300693057-r5 { fill: #d0b344 } -.terminal-2300693057-r6 { fill: #68a0b3;font-weight: bold } -.terminal-2300693057-r7 { fill: #c5c8c6;font-weight: bold } + .terminal-3498363552-r1 { fill: #c5c8c6 } +.terminal-3498363552-r2 { fill: #98a84b } +.terminal-3498363552-r3 { fill: #9a9b99 } +.terminal-3498363552-r4 { fill: #608ab1 } +.terminal-3498363552-r5 { fill: #d0b344 } +.terminal-3498363552-r6 { fill: #68a0b3;font-weight: bold } +.terminal-3498363552-r7 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,36 +132,36 @@ - + - - $ nf-core licences deepvariant - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - -INFO     Fetching licence information for 8 tools                                                    -INFO     Warning: This tool only prints licence information for the software tools packaged using    -         conda.                                                                                      -INFO     The pipeline may use other software and dependencies not described here.                    -┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓ -┃Package Name┃Version┃Licence┃ -┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩ -│ lbzip2       │ 2.5     │ GPL v3  │ -│ deepvariant  │ 0.7.0   │ MIT     │ -│ htslib       │ 1.9     │ MIT     │ -│ picard       │ 2.18.7  │ MIT     │ -│ pip          │ 10.0.1  │ MIT     │ -│ samtools     │ 1.9     │ MIT     │ -│ python       │ 2.7.15  │ PSF     │ -│ bzip2        │ 1.0.6   │ bzip2   │ -└──────────────┴─────────┴─────────┘ + + $ nf-core licences deepvariant + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + +INFO     Fetching licence information for 8 tools                                                    +INFO     Warning: This tool only prints licence information for the software tools packaged using    +         conda.                                                                                      +INFO     The pipeline may use other software and dependencies not described here.                    +┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓ +┃Package Name┃Version┃Licence┃ +┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩ +│ lbzip2       │ 2.5     │ GPL v3  │ +│ deepvariant  │ 0.7.0   │ MIT     │ +│ htslib       │ 1.9     │ MIT     │ +│ picard       │ 2.18.7  │ MIT     │ +│ pip          │ 10.0.1  │ MIT     │ +│ samtools     │ 1.9     │ MIT     │ +│ python       │ 2.7.15  │ PSF     │ +│ bzip2        │ 1.0.6   │ bzip2   │ +└──────────────┴─────────┴─────────┘ diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg index 84e8b387bc..1c6f1dd1b0 100644 --- a/docs/images/nf-core-lint.svg +++ b/docs/images/nf-core-lint.svg @@ -19,136 +19,136 @@ font-weight: 700; } - .terminal-2427817567-matrix { + .terminal-1032032314-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2427817567-title { + .terminal-1032032314-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2427817567-r1 { fill: #c5c8c6 } -.terminal-2427817567-r2 { fill: #98a84b } -.terminal-2427817567-r3 { fill: #9a9b99 } -.terminal-2427817567-r4 { fill: #608ab1 } -.terminal-2427817567-r5 { fill: #d0b344 } -.terminal-2427817567-r6 { fill: #98729f } -.terminal-2427817567-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-2427817567-r8 { fill: #1984e9 } -.terminal-2427817567-r9 { fill: #d0b344;font-weight: bold } -.terminal-2427817567-r10 { fill: #fdfdc5 } -.terminal-2427817567-r11 { fill: #cc555a } + .terminal-1032032314-r1 { fill: #c5c8c6 } +.terminal-1032032314-r2 { fill: #98a84b } +.terminal-1032032314-r3 { fill: #9a9b99 } +.terminal-1032032314-r4 { fill: #608ab1 } +.terminal-1032032314-r5 { fill: #d0b344 } +.terminal-1032032314-r6 { fill: #98729f } +.terminal-1032032314-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-1032032314-r8 { fill: #1984e9 } +.terminal-1032032314-r9 { fill: #d0b344;font-weight: bold } +.terminal-1032032314-r10 { fill: #fdfdc5 } +.terminal-1032032314-r11 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -160,44 +160,44 @@ - + - - $ nf-core lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     Testing pipeline: . - - -╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ -││ -│pipeline_todos: pipeline_todos│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─[!] 1 Pipeline Test Warning────────────────────────────────────────────────────────────────────╮ -││ -│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │ -│doi (after the first release).│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - -╭──────────────────────╮ -│LINT RESULTS SUMMARY│ -├──────────────────────┤ -│[✔] 192 Tests Passed│ -│[?]   1 Test Ignored│ -│[!]   1 Test Warning│ -│[✗]   0 Tests Failed│ -╰──────────────────────╯ + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Testing pipeline: . + + +╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ +││ +│pipeline_todos: pipeline_todos│ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─[!] 1 Pipeline Test Warning────────────────────────────────────────────────────────────────────╮ +││ +│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │ +│doi (after the first release).│ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + +╭──────────────────────╮ +│LINT RESULTS SUMMARY│ +├──────────────────────┤ +│[✔] 192 Tests Passed│ +│[?]   1 Test Ignored│ +│[!]   1 Test Warning│ +│[✗]   0 Tests Failed│ +╰──────────────────────╯ diff --git a/docs/images/nf-core-list-rna.svg b/docs/images/nf-core-list-rna.svg index b5f6ba62c2..ed22bfbc6f 100644 --- a/docs/images/nf-core-list-rna.svg +++ b/docs/images/nf-core-list-rna.svg @@ -19,111 +19,111 @@ font-weight: 700; } - .terminal-874370221-matrix { + .terminal-1199297796-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-874370221-title { + .terminal-1199297796-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-874370221-r1 { fill: #c5c8c6 } -.terminal-874370221-r2 { fill: #98a84b } -.terminal-874370221-r3 { fill: #9a9b99 } -.terminal-874370221-r4 { fill: #608ab1 } -.terminal-874370221-r5 { fill: #d0b344 } -.terminal-874370221-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-874370221-r7 { fill: #868887 } + .terminal-1199297796-r1 { fill: #c5c8c6 } +.terminal-1199297796-r2 { fill: #98a84b } +.terminal-1199297796-r3 { fill: #9a9b99 } +.terminal-1199297796-r4 { fill: #608ab1 } +.terminal-1199297796-r5 { fill: #d0b344 } +.terminal-1199297796-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1199297796-r7 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -135,37 +135,37 @@ - + - - $ nf-core list rna rna-seq - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnafusion            │   119 │          3.0.1 │  3 weeks ago │           - │ -                   │ -│ rnaseq               │   704 │         3.13.2 │  4 weeks ago │           - │ -                   │ -│ differentialabundan… │    32 │          1.4.0 │  3 weeks ago │           - │ -                   │ -│ spatialtranscriptom… │    31 │            dev │  3 weeks ago │           - │ -                   │ -│ circrna              │    33 │            dev │  3 weeks ago │           - │ -                   │ -│ rnasplice            │    14 │          1.0.1 │ 1 months ago │           - │ -                   │ -│ smrnaseq             │    60 │          2.2.4 │ 2 months ago │           - │ -                   │ -│ scrnaseq             │   110 │          2.4.1 │ 3 months ago │           - │ -                   │ -│ dualrnaseq           │    13 │          1.0.0 │  3 years ago │           - │ -                   │ -│ marsseq              │     4 │          1.0.3 │ 5 months ago │           - │ -                   │ -│ lncpipe              │    26 │            dev │  1 years ago │           - │ -                   │ -│ scflow               │    22 │            dev │  2 years ago │           - │ -                   │ -└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ + + $ nf-core list rna rna-seq + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name       ┃Stars┃Latest Release┃    Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnafusion            │   120 │          3.0.1 │  3 weeks ago │           - │ -                   │ +│ rnaseq               │   704 │         3.13.2 │  4 weeks ago │           - │ -                   │ +│ differentialabundan… │    32 │          1.4.0 │  3 weeks ago │           - │ -                   │ +│ spatialtranscriptom… │    31 │            dev │  3 weeks ago │           - │ -                   │ +│ circrna              │    33 │            dev │  3 weeks ago │           - │ -                   │ +│ rnasplice            │    14 │          1.0.1 │ 1 months ago │           - │ -                   │ +│ smrnaseq             │    60 │          2.2.4 │ 2 months ago │           - │ -                   │ +│ scrnaseq             │   110 │          2.4.1 │ 3 months ago │           - │ -                   │ +│ dualrnaseq           │    13 │          1.0.0 │  3 years ago │           - │ -                   │ +│ marsseq              │     4 │          1.0.3 │ 5 months ago │           - │ -                   │ +│ lncpipe              │    26 │            dev │  1 years ago │           - │ -                   │ +│ scflow               │    22 │            dev │  2 years ago │           - │ -                   │ +└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘ diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg index 0d741d48ba..01431bf102 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-2494560554-matrix { + .terminal-11073929-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2494560554-title { + .terminal-11073929-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2494560554-r1 { fill: #c5c8c6 } -.terminal-2494560554-r2 { fill: #98a84b } -.terminal-2494560554-r3 { fill: #9a9b99 } -.terminal-2494560554-r4 { fill: #608ab1 } -.terminal-2494560554-r5 { fill: #d0b344 } -.terminal-2494560554-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2494560554-r7 { fill: #868887 } -.terminal-2494560554-r8 { fill: #868887;font-style: italic; } + .terminal-11073929-r1 { fill: #c5c8c6 } +.terminal-11073929-r2 { fill: #98a84b } +.terminal-11073929-r3 { fill: #9a9b99 } +.terminal-11073929-r4 { fill: #608ab1 } +.terminal-11073929-r5 { fill: #d0b344 } +.terminal-11073929-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-11073929-r7 { fill: #868887 } +.terminal-11073929-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -112,29 +112,29 @@ - + - - $ nf-core list -s stars - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq              │   704 │         3.13.2 │   4 weeks ago │           - │ -                   │ -│ sarek               │   288 │          3.4.0 │  1 months ago │           - │ -                   │ -│ chipseq             │   157 │          2.0.0 │   1 years ago │           - │ -                   │ -│ mag                 │   156 │          2.5.1 │  1 months ago │           - │ -                   │ -[..truncated..] + + $ nf-core list -s stars + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq              │   704 │         3.13.2 │   4 weeks ago │           - │ -                   │ +│ sarek               │   288 │          3.4.0 │  1 months ago │           - │ -                   │ +│ chipseq             │   157 │          2.0.0 │   1 years ago │           - │ -                   │ +│ mag                 │   156 │          2.5.1 │  1 months ago │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg index 2d8873a082..d0b37306a3 100644 --- a/docs/images/nf-core-list.svg +++ b/docs/images/nf-core-list.svg @@ -19,91 +19,91 @@ font-weight: 700; } - .terminal-1618644398-matrix { + .terminal-691768826-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1618644398-title { + .terminal-691768826-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1618644398-r1 { fill: #c5c8c6 } -.terminal-1618644398-r2 { fill: #98a84b } -.terminal-1618644398-r3 { fill: #9a9b99 } -.terminal-1618644398-r4 { fill: #608ab1 } -.terminal-1618644398-r5 { fill: #d0b344 } -.terminal-1618644398-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1618644398-r7 { fill: #868887 } -.terminal-1618644398-r8 { fill: #868887;font-style: italic; } + .terminal-691768826-r1 { fill: #c5c8c6 } +.terminal-691768826-r2 { fill: #98a84b } +.terminal-691768826-r3 { fill: #9a9b99 } +.terminal-691768826-r4 { fill: #608ab1 } +.terminal-691768826-r5 { fill: #d0b344 } +.terminal-691768826-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-691768826-r7 { fill: #868887 } +.terminal-691768826-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +115,30 @@ - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ ampliseq            │   140 │          2.7.1 │  1 months ago │           - │ -                   │ -│ raredisease         │    63 │          1.1.1 │  5 months ago │           - │ -                   │ -│ epitopeprediction   │    27 │          2.2.1 │  9 months ago │           - │ -                   │ -│ metatdenovo         │     3 │            dev │   5 hours ago │           - │ -                   │ -│ metaboigniter       │    11 │          2.0.0 │   4 hours ago │           - │ -                   │ -[..truncated..] + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ callingcards        │     2 │            dev │  18 hours ago │           - │ -                   │ +│ ampliseq            │   140 │          2.7.1 │  1 months ago │           - │ -                   │ +│ raredisease         │    63 │          1.1.1 │  5 months ago │           - │ -                   │ +│ epitopeprediction   │    27 │          2.2.1 │  9 months ago │           - │ -                   │ +│ metatdenovo         │     3 │            dev │     yesterday │           - │ -                   │ +[..truncated..] diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index 8ac4ba322d..13be58189e 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-200931299-matrix { + .terminal-1176762434-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-200931299-title { + .terminal-1176762434-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-200931299-r1 { fill: #c5c8c6 } -.terminal-200931299-r2 { fill: #98a84b } -.terminal-200931299-r3 { fill: #9a9b99 } -.terminal-200931299-r4 { fill: #608ab1 } -.terminal-200931299-r5 { fill: #d0b344 } -.terminal-200931299-r6 { fill: #98a84b;font-weight: bold } -.terminal-200931299-r7 { fill: #c5c8c6;font-weight: bold } + .terminal-1176762434-r1 { fill: #c5c8c6 } +.terminal-1176762434-r2 { fill: #98a84b } +.terminal-1176762434-r3 { fill: #9a9b99 } +.terminal-1176762434-r4 { fill: #608ab1 } +.terminal-1176762434-r5 { fill: #d0b344 } +.terminal-1176762434-r6 { fill: #98a84b;font-weight: bold } +.terminal-1176762434-r7 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -114,30 +114,30 @@ - + - - $ nf-core modules bump-versions fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - - -╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ -│[!] 1 Module version up to date.│ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ -│Module name                             │Update Message                                       │ -├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ -│ fastqc                                   │ Module version up to date: fastqc                     │ -╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ + + $ nf-core modules bump-versions fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + + +╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ +│[!] 1 Module version up to date.│ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ +│Module name                             │Update Message                                       │ +├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ +│ fastqc                                   │ Module version up to date: fastqc                     │ +╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index 65d9c90131..7cf8b9ca99 100644 --- a/docs/images/nf-core-modules-create.svg +++ b/docs/images/nf-core-modules-create.svg @@ -19,104 +19,104 @@ font-weight: 700; } - .terminal-95821698-matrix { + .terminal-3904970721-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-95821698-title { + .terminal-3904970721-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-95821698-r1 { fill: #c5c8c6 } -.terminal-95821698-r2 { fill: #98a84b } -.terminal-95821698-r3 { fill: #9a9b99 } -.terminal-95821698-r4 { fill: #608ab1 } -.terminal-95821698-r5 { fill: #d0b344 } -.terminal-95821698-r6 { fill: #68a0b3;font-weight: bold } + .terminal-3904970721-r1 { fill: #c5c8c6 } +.terminal-3904970721-r2 { fill: #98a84b } +.terminal-3904970721-r3 { fill: #9a9b99 } +.terminal-3904970721-r4 { fill: #608ab1 } +.terminal-3904970721-r5 { fill: #d0b344 } +.terminal-3904970721-r6 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -128,35 +128,35 @@ - + - - $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     Repository type: modules -INFO    Press enter to use default values (shown in brackets)or type your own responses.  -ctrl+click underlined text to open links. -INFO     Using Bioconda package: 'bioconda::fastqc=0.12.1' -INFO     Using Docker container: 'biocontainers/fastqc:0.12.1--hdfd78af_0' -INFO     Using Singularity container:                                                                -'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' -INFO     Created component template: 'fastqc' -INFO     Created following files:                                                                    -           modules/nf-core/fastqc/main.nf                                                            -           modules/nf-core/fastqc/meta.yml                                                           -           modules/nf-core/fastqc/environment.yml                                                    -           modules/nf-core/fastqc/tests/tags.yml                                                     -           modules/nf-core/fastqc/tests/main.nf.test                                                 + + $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Repository type: modules +INFO    Press enter to use default values (shown in brackets)or type your own responses.  +ctrl+click underlined text to open links. +INFO     Using Bioconda package: 'bioconda::fastqc=0.12.1' +INFO     Using Docker container: 'biocontainers/fastqc:0.12.1--hdfd78af_0' +INFO     Using Singularity container:                                                                +'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' +INFO     Created component template: 'fastqc' +INFO     Created following files:                                                                    +           modules/nf-core/fastqc/main.nf                                                            +           modules/nf-core/fastqc/meta.yml                                                           +           modules/nf-core/fastqc/environment.yml                                                    +           modules/nf-core/fastqc/tests/tags.yml                                                     +           modules/nf-core/fastqc/tests/main.nf.test                                                 diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg index ea713ba23c..b604cb3f7b 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-1933046224-matrix { + .terminal-149484079-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1933046224-title { + .terminal-149484079-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1933046224-r1 { fill: #c5c8c6 } -.terminal-1933046224-r2 { fill: #98a84b } -.terminal-1933046224-r3 { fill: #9a9b99 } -.terminal-1933046224-r4 { fill: #608ab1 } -.terminal-1933046224-r5 { fill: #d0b344 } -.terminal-1933046224-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1933046224-r7 { fill: #98a84b;font-weight: bold } -.terminal-1933046224-r8 { fill: #868887 } -.terminal-1933046224-r9 { fill: #d08442 } -.terminal-1933046224-r10 { fill: #868887;font-style: italic; } -.terminal-1933046224-r11 { fill: #98729f } + .terminal-149484079-r1 { fill: #c5c8c6 } +.terminal-149484079-r2 { fill: #98a84b } +.terminal-149484079-r3 { fill: #9a9b99 } +.terminal-149484079-r4 { fill: #608ab1 } +.terminal-149484079-r5 { fill: #d0b344 } +.terminal-149484079-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-149484079-r7 { fill: #98a84b;font-weight: bold } +.terminal-149484079-r8 { fill: #868887 } +.terminal-149484079-r9 { fill: #d08442 } +.terminal-149484079-r10 { fill: #868887;font-style: italic; } +.terminal-149484079-r11 { fill: #98729f } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -187,53 +187,53 @@ - + - - $ nf-core modules info abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ -│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ -│ 🔧 Tools: abacas                                                                                 │ -│ 📖 Description: contiguate draft genome assembly                                                 │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -                  ╷                                                                   ╷              -📥 Inputs        │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} -                  ╵                                                                   ╵              -                  ╷                                                                   ╷              -📤 Outputs       │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - results  (file) │List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* -                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ -                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ -                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ -                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - versions  (file)│File containing software versions                                  │versions.yml -                  ╵                                                                   ╵              - - 💻  Installation command: nf-core modules install abacas - + + $ nf-core modules info abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ +│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ +│ 🔧 Tools: abacas                                                                                 │ +│ 📖 Description: contiguate draft genome assembly                                                 │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +                  ╷                                                                   ╷              +📥 Inputs        │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} +                  ╵                                                                   ╵              +                  ╷                                                                   ╷              +📤 Outputs       │Description                                                        │     Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ +                  │single_end:false ]                                                 │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + results  (file) │List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* +                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ +                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ +                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ +                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ +╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ + versions  (file)│File containing software versions                                  │versions.yml +                  ╵                                                                   ╵              + + 💻  Installation command: nf-core modules install abacas + diff --git a/docs/images/nf-core-modules-install.svg b/docs/images/nf-core-modules-install.svg index 9ebfbce6d7..f444190f32 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-2637794350-matrix { + .terminal-160730253-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2637794350-title { + .terminal-160730253-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2637794350-r1 { fill: #c5c8c6 } -.terminal-2637794350-r2 { fill: #98a84b } -.terminal-2637794350-r3 { fill: #9a9b99 } -.terminal-2637794350-r4 { fill: #608ab1 } -.terminal-2637794350-r5 { fill: #d0b344 } + .terminal-160730253-r1 { fill: #c5c8c6 } +.terminal-160730253-r2 { fill: #98a84b } +.terminal-160730253-r3 { fill: #9a9b99 } +.terminal-160730253-r4 { fill: #608ab1 } +.terminal-160730253-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core modules install abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     Installing 'abacas' -INFO     Use the following statement to include this module:                                         - - include { ABACAS } from '../modules/nf-core/abacas/main'                                            - + + $ nf-core modules install abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Installing 'abacas' +INFO     Use the following statement to include this module:                                         + + include { ABACAS } from '../modules/nf-core/abacas/main'                                            + diff --git a/docs/images/nf-core-modules-lint.svg b/docs/images/nf-core-modules-lint.svg index 9c364ea5b3..03edcaf551 100644 --- a/docs/images/nf-core-modules-lint.svg +++ b/docs/images/nf-core-modules-lint.svg @@ -19,125 +19,125 @@ font-weight: 700; } - .terminal-1959956913-matrix { + .terminal-3750531600-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1959956913-title { + .terminal-3750531600-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1959956913-r1 { fill: #c5c8c6 } -.terminal-1959956913-r2 { fill: #98a84b } -.terminal-1959956913-r3 { fill: #9a9b99 } -.terminal-1959956913-r4 { fill: #608ab1 } -.terminal-1959956913-r5 { fill: #d0b344 } -.terminal-1959956913-r6 { fill: #68a0b3;font-weight: bold } -.terminal-1959956913-r7 { fill: #d0b344;font-weight: bold } -.terminal-1959956913-r8 { fill: #8d7b39 } -.terminal-1959956913-r9 { fill: #fdfdc5 } -.terminal-1959956913-r10 { fill: #c5c8c6;font-weight: bold } -.terminal-1959956913-r11 { fill: #98a84b;font-weight: bold } -.terminal-1959956913-r12 { fill: #cc555a } + .terminal-3750531600-r1 { fill: #c5c8c6 } +.terminal-3750531600-r2 { fill: #98a84b } +.terminal-3750531600-r3 { fill: #9a9b99 } +.terminal-3750531600-r4 { fill: #608ab1 } +.terminal-3750531600-r5 { fill: #d0b344 } +.terminal-3750531600-r6 { fill: #68a0b3;font-weight: bold } +.terminal-3750531600-r7 { fill: #d0b344;font-weight: bold } +.terminal-3750531600-r8 { fill: #8d7b39 } +.terminal-3750531600-r9 { fill: #fdfdc5 } +.terminal-3750531600-r10 { fill: #c5c8c6;font-weight: bold } +.terminal-3750531600-r11 { fill: #98a84b;font-weight: bold } +.terminal-3750531600-r12 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -149,40 +149,40 @@ - + - - $ nf-core modules lint multiqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     Linting modules repo: '.' -INFO     Linting module: 'multiqc' -INFO     Found 4 inputs in modules/nf-core/multiqc/main.nf                                           -INFO     Found 4 outputs in modules/nf-core/multiqc/main.nf                                          - -╭─[!] 1 Module Test Warning──────────────────────────────────────────────────────────────────────╮ -│              ╷                                 ╷                                                 │ -│Module name │File path                      │Test message                                   │ -│╶─────────────┼─────────────────────────────────┼────────────────────────────────────────────────╴│ -│multiqc│modules/nf-core/multiqc/main.nf│Conda update: bioconda::multiqc 1.18 -> 1.19│ -│              ╵                                 ╵                                                 │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭──────────────────────╮ -│LINT RESULTS SUMMARY│ -├──────────────────────┤ -│[✔]  50 Tests Passed│ -│[!]   1 Test Warning│ -│[✗]   0 Tests Failed│ -╰──────────────────────╯ + + $ nf-core modules lint multiqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Linting modules repo: '.' +INFO     Linting module: 'multiqc' +INFO     Found 4 inputs in modules/nf-core/multiqc/main.nf                                           +INFO     Found 4 outputs in modules/nf-core/multiqc/main.nf                                          + +╭─[!] 1 Module Test Warning──────────────────────────────────────────────────────────────────────╮ +│              ╷                                 ╷                                                 │ +│Module name │File path                      │Test message                                   │ +│╶─────────────┼─────────────────────────────────┼────────────────────────────────────────────────╴│ +│multiqc│modules/nf-core/multiqc/main.nf│Conda update: bioconda::multiqc 1.18 -> 1.19│ +│              ╵                                 ╵                                                 │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────╮ +│LINT RESULTS SUMMARY│ +├──────────────────────┤ +│[✔]  50 Tests Passed│ +│[!]   1 Test Warning│ +│[✗]   0 Tests Failed│ +╰──────────────────────╯ diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index 5d592084ac..a1b2806467 100644 --- a/docs/images/nf-core-modules-list-local.svg +++ b/docs/images/nf-core-modules-list-local.svg @@ -19,108 +19,108 @@ font-weight: 700; } - .terminal-3570470079-matrix { + .terminal-1750863134-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3570470079-title { + .terminal-1750863134-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3570470079-r1 { fill: #c5c8c6 } -.terminal-3570470079-r2 { fill: #98a84b } -.terminal-3570470079-r3 { fill: #9a9b99 } -.terminal-3570470079-r4 { fill: #608ab1 } -.terminal-3570470079-r5 { fill: #d0b344 } -.terminal-3570470079-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3570470079-r7 { fill: #868887;font-style: italic; } + .terminal-1750863134-r1 { fill: #c5c8c6 } +.terminal-1750863134-r2 { fill: #98a84b } +.terminal-1750863134-r3 { fill: #9a9b99 } +.terminal-1750863134-r4 { fill: #608ab1 } +.terminal-1750863134-r5 { fill: #d0b344 } +.terminal-1750863134-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1750863134-r7 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -132,36 +132,36 @@ - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     Modules installed in '.':                                                                   - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -┃Module Name        ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ custom/dumpsoftwar… │ https://github.co… │ bba7e362e4afead706… │ add                │ 2023-11-14 │ -│                     │                    │                     │ environment-schem… │            │ -│                     │                    │                     │ rename yaml-schema │            │ -│                     │                    │                     │ to meta-schema     │            │ -│                     │                    │                     │ (#4323)            │            │ -│ fastqc              │ https://github.co… │ 65ad3e0b9a4099592e… │ Update version     │ 2023-12-08 │ -│                     │                    │                     │ strings (#4556)    │            │ -│ multiqc             │ https://github.co… │ 4ab13872435962dadc… │ Pull multiqc       │ 2023-12-05 │ -│                     │                    │                     │ static multiqc     │            │ -[..truncated..] + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Modules installed in '.':                                                                   + +┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +┃Module Name        ┃Repository        ┃Version SHA        ┃Message           ┃Date      ┃ +┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ custom/dumpsoftwar… │ https://github.co… │ bba7e362e4afead706… │ add                │ 2023-11-14 │ +│                     │                    │                     │ environment-schem… │            │ +│                     │                    │                     │ rename yaml-schema │            │ +│                     │                    │                     │ to meta-schema     │            │ +│                     │                    │                     │ (#4323)            │            │ +│ fastqc              │ https://github.co… │ 65ad3e0b9a4099592e… │ Update version     │ 2023-12-08 │ +│                     │                    │                     │ strings (#4556)    │            │ +│ multiqc             │ https://github.co… │ 4ab13872435962dadc… │ Pull multiqc       │ 2023-12-05 │ +│                     │                    │                     │ static multiqc     │            │ +[..truncated..] diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index 1bc0eb0ff1..28be0b24ee 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-2130205015-matrix { + .terminal-2091866550-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2130205015-title { + .terminal-2091866550-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2130205015-r1 { fill: #c5c8c6 } -.terminal-2130205015-r2 { fill: #98a84b } -.terminal-2130205015-r3 { fill: #9a9b99 } -.terminal-2130205015-r4 { fill: #608ab1 } -.terminal-2130205015-r5 { fill: #d0b344 } -.terminal-2130205015-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-2130205015-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-2130205015-r8 { fill: #868887;font-style: italic; } + .terminal-2091866550-r1 { fill: #c5c8c6 } +.terminal-2091866550-r2 { fill: #98a84b } +.terminal-2091866550-r3 { fill: #9a9b99 } +.terminal-2091866550-r4 { fill: #608ab1 } +.terminal-2091866550-r5 { fill: #d0b344 } +.terminal-2091866550-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-2091866550-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2091866550-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core modules list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     Modules available from https://github.com/nf-core/modules.git(master):                     - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Module Name                                          ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ abacas                                                │ -│ abricate/run                                          │ -│ abricate/summary                                      │ -│ abritamr/run                                          │ -│ adapterremoval                                        │ -│ adapterremovalfixprefix                               │ -│ admixture                                             │ -│ affy/justrma                                          │ -│ agat/convertspgff2gtf                                 │ -[..truncated..] + + $ nf-core modules list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Modules available from https://github.com/nf-core/modules.git(master):                     + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Module Name                                          ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ abacas                                                │ +│ abricate/run                                          │ +│ abricate/summary                                      │ +│ abritamr/run                                          │ +│ adapterremoval                                        │ +│ adapterremovalfixprefix                               │ +│ admixture                                             │ +│ affy/justrma                                          │ +│ agat/convertspgff2gtf                                 │ +[..truncated..] diff --git a/docs/images/nf-core-modules-patch.svg b/docs/images/nf-core-modules-patch.svg index 7c6973da2c..25033c107a 100644 --- a/docs/images/nf-core-modules-patch.svg +++ b/docs/images/nf-core-modules-patch.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ nf-core modules patch fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -ERROR    module 'modules/nf-core/fastqc' is unchanged. No patch to compute                           + + $ nf-core modules patch fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Changes in module 'nf-core/fastqc' +INFO    'modules/nf-core/fastqc/environment.yml' is unchanged                                       +INFO    'modules/nf-core/fastqc/meta.yml' is unchanged                                              +INFO     Changes in 'fastqc/main.nf':                                                                + +--- modules/nf-core/fastqc/main.nf ++++ modules/nf-core/fastqc/main.nf +@@ -1,6 +1,6 @@ +process FASTQC {                                                                                   +    tag "$meta.id"                                                                                 +-    label 'process_medium' ++    label 'process_low' + +    conda "${moduleDir}/environment.yml"                                                           +    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_  + + +INFO    'modules/nf-core/fastqc/tests/tags.yml' is unchanged                                        +INFO    'modules/nf-core/fastqc/tests/main.nf.test' is unchanged                                    +INFO    'modules/nf-core/fastqc/tests/main.nf.test.snap' is unchanged                               +INFO     Patch file of 'modules/nf-core/fastqc' written to 'modules/nf-core/fastqc/fastqc.diff' diff --git a/docs/images/nf-core-modules-remove.svg b/docs/images/nf-core-modules-remove.svg index c63303b6e8..b1dafc6753 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-3245682048-matrix { + .terminal-2029268447-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3245682048-title { + .terminal-2029268447-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3245682048-r1 { fill: #c5c8c6 } -.terminal-3245682048-r2 { fill: #98a84b } -.terminal-3245682048-r3 { fill: #9a9b99 } -.terminal-3245682048-r4 { fill: #608ab1 } -.terminal-3245682048-r5 { fill: #d0b344 } + .terminal-2029268447-r1 { fill: #c5c8c6 } +.terminal-2029268447-r2 { fill: #98a84b } +.terminal-2029268447-r3 { fill: #9a9b99 } +.terminal-2029268447-r4 { fill: #608ab1 } +.terminal-2029268447-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -88,22 +88,22 @@ - + - - $ nf-core modules remove abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     Removed files for 'abacas' and its dependencies 'abacas'.                                   + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Removed files for 'abacas' and its dependencies 'abacas'.                                   diff --git a/docs/images/nf-core-modules-test.svg b/docs/images/nf-core-modules-test.svg index 0c531cf929..3416c21bc0 100644 --- a/docs/images/nf-core-modules-test.svg +++ b/docs/images/nf-core-modules-test.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - $ nf-core modules test fastqc --no-prompts --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -Usage:nf-core modules test [OPTIONS] <tool> or <tool/subtool>                                      - -Try'nf-core modules test -h'for help -╭─ Error ──────────────────────────────────────────────────────────────────────────────────────────╮ -│ No such option: --force Did you mean --once?                                                     │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - + + + + $ nf-core modules test fastqc --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Generating nf-test snapshot                                                                 +╭───────────────────────────────────────── nf-test output ─────────────────────────────────────────╮ +│                                                                                                  │ +│ 🚀 nf-test 0.8.2                                                                                 │ +│ https://code.askimed.com/nf-test                                                                 │ +│ (c) 2021 - 2023 Lukas Forer and Sebastian Schoenherr                                             │ +│                                                                                                  │ +│ Found 1 files in test directory.                                                                 │ +│                                                                                                  │ +│ Test Process FASTQC                                                                              │ +│                                                                                                  │ +│   Test [9cf5f580] 'sarscov2 - bam' FAILED (5.818s)                                               │ +│                                                                                                  │ +│   Assertion failed:                                                                              │ +│                                                                                                  │ +│   2 of 2 assertions failed                                                                       │ +│                                                                                                  │ +│   Nextflow stdout:                                                                               │ +│                                                                                                  │ +│   Process `FASTQC` declares 1 input channel but 2 were specified                                 │ +│                                                                                                  │ +│    -- Check script 'meta/mock.nf' at line: 41 or see                                             │ +│ '/home/runner/work/tools/tools/tmp/modules/.nf-test/tests/9cf5f5804db49395806e612d2a2c23ca/meta/ │ +│ nextflow.log' file for more details                                                              │ +│   Nextflow stderr:                                                                               │ +│                                                                                                  │ +│                                                                                                  │ +│                                                                                                  │ +│   Test [a2de5162] 'sarscov2 - bam - stub' FAILED (4.637s)                                        │ +│                                                                                                  │ +│   Assertion failed:                                                                              │ +│                                                                                                  │ +│   2 of 2 assertions failed                                                                       │ +│                                                                                                  │ +│   Nextflow stdout:                                                                               │ +│                                                                                                  │ +│   Process `FASTQC` declares 1 input channel but 2 were specified                                 │ +│                                                                                                  │ +│    -- Check script 'meta/mock.nf' at line: 41 or see                                             │ +│ '/home/runner/work/tools/tools/tmp/modules/.nf-test/tests/a2de51628f1d36119180ba630b7026a2/meta/ │ +│ nextflow.log' file for more details                                                              │ +│   Nextflow stderr:                                                                               │ +│                                                                                                  │ +│                                                                                                  │ +│                                                                                                  │ +│                                                                                                  │ +│ Test Workflow FASTQ_FASTQC_UMITOOLS_FASTP                                                        │ +│                                                                                                  │ +│   Test [19e7efa0] 'sarscov2 paired-end [fastq]' FAILED (5.439s)                                  │ +│                                                                                                  │ +│   Assertion failed:                                                                              │ +│                                                                                                  │ +│   14 of 14 assertions failed                                                                     │ +│                                                                                                  │ +│   Nextflow stdout:                                                                               │ +│                                                                                                  │ +│   ERROR ~ No such variable: Exception evaluating property 'html' for nextflow.script.ChannelOut, │ +│ Reason: groovy.lang.MissingPropertyException: No such property: html for class:                  │ +│ groovyx.gpars.dataflow.DataflowBroadcast                                                         │ +│   Possible solutions: head                                                                       │ +│                                                                                                  │ +│    -- Check script                                                                               │ +│ '/home/runner/work/tools/tools/tmp/modules/./subworkflows/nf-core/fastq_fastqc_umitools_fastp/te │ +│ sts/../main.nf' at line: 115 or see                                                              │ +│ '/home/runner/work/tools/tools/tmp/modules/.nf-test/tests/19e7efa075a613f6b4da77288e1c9f33/meta/ │ +│ nextflow.log' file for more details                                                              │ +│   Nextflow stderr:                                                                               │ +│                                                                                                  │ +│                                                                                                  │ +│                                                                                                  │ +│                                                                                                  │ +│                                                                                                  │ +│ FAILURE: Executed 3 tests in 15.898s (3 failed)                                                  │ +│                                                                                                  │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭───────────────────────────────────────── nf-test error ──────────────────────────────────────────╮ +│ Assertion failed:                                                                                │ +│                                                                                                  │ +│ assert process.success                                                                           │ +│        |       |                                                                                 │ +│        FASTQC  false                                                                             │ +│                                                                                                  │ +│ java.lang.RuntimeException: Process has no output channels. process.out can not be used.         │ +│ Assertion failed:                                                                                │ +│                                                                                                  │ +│ assert process.success                                                                           │ +│        |       |                                                                                 │ +│        FASTQC  false                                                                             │ +│                                                                                                  │ +│ java.lang.RuntimeException: Process has no output channels. process.out can not be used.         │ +│ Assertion failed:                                                                                │ +│                                                                                                  │ +│ assert workflow.success                                                                          │ +│        |        |                                                                                │ +│        workflow false                                                                            │ +│                                                                                                  │ +│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ +│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ +│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ +│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ +│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ +│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ +│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ +│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ +│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ +│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ +│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ +│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ +│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.       │ +│                                                                                                  │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +CRITICAL Ran, but found errors:                                                                      +          - nf-test failed                                                                           diff --git a/docs/images/nf-core-modules-update.svg b/docs/images/nf-core-modules-update.svg index 83def3a38b..6169857b74 100644 --- a/docs/images/nf-core-modules-update.svg +++ b/docs/images/nf-core-modules-update.svg @@ -19,76 +19,76 @@ font-weight: 700; } - .terminal-1647661905-matrix { + .terminal-2555794352-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1647661905-title { + .terminal-2555794352-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1647661905-r1 { fill: #c5c8c6 } -.terminal-1647661905-r2 { fill: #98a84b } -.terminal-1647661905-r3 { fill: #9a9b99 } -.terminal-1647661905-r4 { fill: #608ab1 } -.terminal-1647661905-r5 { fill: #d0b344 } + .terminal-2555794352-r1 { fill: #c5c8c6 } +.terminal-2555794352-r2 { fill: #98a84b } +.terminal-2555794352-r3 { fill: #9a9b99 } +.terminal-2555794352-r4 { fill: #608ab1 } +.terminal-2555794352-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core modules update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO    'modules/nf-core/abacas' is already up to date                                              -INFO    'modules/nf-core/custom/dumpsoftwareversions' is already up to date                         -INFO    'modules/nf-core/fastqc' is already up to date                                              -INFO    'modules/nf-core/multiqc' is already up to date                                             -INFO     Updates complete ✨                                                                         + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO    'modules/nf-core/abacas' is already up to date                                              +INFO    'modules/nf-core/custom/dumpsoftwareversions' is already up to date                         +INFO    'modules/nf-core/fastqc' is already up to date                                              +INFO    'modules/nf-core/multiqc' is already up to date                                             +INFO     Updates complete ✨                                                                         diff --git a/docs/images/nf-core-schema-build.svg b/docs/images/nf-core-schema-build.svg index 61249df24f..deb06cbf36 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-1899547324-matrix { + .terminal-343853851-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1899547324-title { + .terminal-343853851-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1899547324-r1 { fill: #c5c8c6 } -.terminal-1899547324-r2 { fill: #98a84b } -.terminal-1899547324-r3 { fill: #9a9b99 } -.terminal-1899547324-r4 { fill: #608ab1 } -.terminal-1899547324-r5 { fill: #d0b344 } -.terminal-1899547324-r6 { fill: #98a84b;font-weight: bold } -.terminal-1899547324-r7 { fill: #868887;font-weight: bold } -.terminal-1899547324-r8 { fill: #868887 } -.terminal-1899547324-r9 { fill: #4e707b;font-weight: bold } -.terminal-1899547324-r10 { fill: #68a0b3;font-weight: bold } + .terminal-343853851-r1 { fill: #c5c8c6 } +.terminal-343853851-r2 { fill: #98a84b } +.terminal-343853851-r3 { fill: #9a9b99 } +.terminal-343853851-r4 { fill: #608ab1 } +.terminal-343853851-r5 { fill: #d0b344 } +.terminal-343853851-r6 { fill: #98a84b;font-weight: bold } +.terminal-343853851-r7 { fill: #868887;font-weight: bold } +.terminal-343853851-r8 { fill: #868887 } +.terminal-343853851-r9 { fill: #4e707b;font-weight: bold } +.terminal-343853851-r10 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,23 +96,23 @@ - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 30 params) -INFO     Writing schema with 31 params: './nextflow_schema.json' + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 30 params) +INFO     Writing schema with 31 params: './nextflow_schema.json' diff --git a/docs/images/nf-core-schema-lint.svg b/docs/images/nf-core-schema-lint.svg index 3d95deadf3..f8ca82b271 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-3296938790-matrix { + .terminal-3360246661-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3296938790-title { + .terminal-3360246661-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3296938790-r1 { fill: #c5c8c6 } -.terminal-3296938790-r2 { fill: #98a84b } -.terminal-3296938790-r3 { fill: #9a9b99 } -.terminal-3296938790-r4 { fill: #608ab1 } -.terminal-3296938790-r5 { fill: #d0b344 } -.terminal-3296938790-r6 { fill: #98a84b;font-weight: bold } -.terminal-3296938790-r7 { fill: #868887;font-weight: bold } -.terminal-3296938790-r8 { fill: #868887 } -.terminal-3296938790-r9 { fill: #4e707b;font-weight: bold } + .terminal-3360246661-r1 { fill: #c5c8c6 } +.terminal-3360246661-r2 { fill: #98a84b } +.terminal-3360246661-r3 { fill: #9a9b99 } +.terminal-3360246661-r4 { fill: #608ab1 } +.terminal-3360246661-r5 { fill: #d0b344 } +.terminal-3360246661-r6 { fill: #98a84b;font-weight: bold } +.terminal-3360246661-r7 { fill: #868887;font-weight: bold } +.terminal-3360246661-r8 { fill: #868887 } +.terminal-3360246661-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -92,22 +92,22 @@ - + - - $ nf-core schema lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 31 params) + + $ nf-core schema lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 31 params) diff --git a/docs/images/nf-core-schema-validate.svg b/docs/images/nf-core-schema-validate.svg index e3619757ff..2eb5093ede 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-2578316438-matrix { + .terminal-2178481397-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2578316438-title { + .terminal-2178481397-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2578316438-r1 { fill: #c5c8c6 } -.terminal-2578316438-r2 { fill: #98a84b } -.terminal-2578316438-r3 { fill: #9a9b99 } -.terminal-2578316438-r4 { fill: #608ab1 } -.terminal-2578316438-r5 { fill: #d0b344 } -.terminal-2578316438-r6 { fill: #98a84b;font-weight: bold } -.terminal-2578316438-r7 { fill: #868887;font-weight: bold } -.terminal-2578316438-r8 { fill: #868887 } -.terminal-2578316438-r9 { fill: #4e707b;font-weight: bold } + .terminal-2178481397-r1 { fill: #c5c8c6 } +.terminal-2178481397-r2 { fill: #98a84b } +.terminal-2178481397-r3 { fill: #9a9b99 } +.terminal-2178481397-r4 { fill: #608ab1 } +.terminal-2178481397-r5 { fill: #d0b344 } +.terminal-2178481397-r6 { fill: #98a84b;font-weight: bold } +.terminal-2178481397-r7 { fill: #868887;font-weight: bold } +.terminal-2178481397-r8 { fill: #868887 } +.terminal-2178481397-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -95,23 +95,23 @@ - + - - $ nf-core schema validate nf-core-rnaseq/3_8 nf-params.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - -INFO    [✓] Default parameters match schema validation -INFO    [✓] Pipeline schema looks valid(found 93 params) -INFO    [✓] Input parameters look valid + + $ nf-core schema validate nf-core-rnaseq/3_8 nf-params.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 93 params) +INFO    [✓] Input parameters look valid diff --git a/docs/images/nf-core-subworkflows-create.svg b/docs/images/nf-core-subworkflows-create.svg index be37e78473..21edf7370b 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-1319275835-matrix { + .terminal-344362394-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1319275835-title { + .terminal-344362394-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1319275835-r1 { fill: #c5c8c6 } -.terminal-1319275835-r2 { fill: #98a84b } -.terminal-1319275835-r3 { fill: #9a9b99 } -.terminal-1319275835-r4 { fill: #608ab1 } -.terminal-1319275835-r5 { fill: #d0b344 } -.terminal-1319275835-r6 { fill: #68a0b3;font-weight: bold } + .terminal-344362394-r1 { fill: #c5c8c6 } +.terminal-344362394-r2 { fill: #98a84b } +.terminal-344362394-r3 { fill: #9a9b99 } +.terminal-344362394-r4 { fill: #608ab1 } +.terminal-344362394-r5 { fill: #d0b344 } +.terminal-344362394-r6 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -113,30 +113,30 @@ - + - - $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     Repository type: modules -INFO    Press enter to use default values (shown in brackets)or type your own responses.  -ctrl+click underlined text to open links. -INFO     Created component template: 'bam_stats_samtools' -INFO     Created following files:                                                                    -           subworkflows/nf-core/bam_stats_samtools/main.nf                                           -           subworkflows/nf-core/bam_stats_samtools/meta.yml                                          -           subworkflows/nf-core/bam_stats_samtools/tests/tags.yml                                    -           subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test                                + + $ nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Repository type: modules +INFO    Press enter to use default values (shown in brackets)or type your own responses.  +ctrl+click underlined text to open links. +INFO     Created component template: 'bam_stats_samtools' +INFO     Created following files:                                                                    +           subworkflows/nf-core/bam_stats_samtools/main.nf                                           +           subworkflows/nf-core/bam_stats_samtools/meta.yml                                          +           subworkflows/nf-core/bam_stats_samtools/tests/tags.yml                                    +           subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test                                diff --git a/docs/images/nf-core-subworkflows-info.svg b/docs/images/nf-core-subworkflows-info.svg index f76ce03fe7..d21f2e2b51 100644 --- a/docs/images/nf-core-subworkflows-info.svg +++ b/docs/images/nf-core-subworkflows-info.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - $ nf-core subworkflows info bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -╭─ Subworkflow: bam_rseqc  ────────────────────────────────────────────────────────────────────────╮ -│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ -│ 📖 Description: Subworkflow to run multiple commands in the RSeqC package                        │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -                       ╷                                                                   ╷         -📥 Inputs             │Description                                                        │Pattern -╺━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━╸ - meta  (map)          │Groovy Map containing sample information e.g. [ id:'test',         │ -                       │single_end:false ]                                                 │ -╶──────────────────────┼───────────────────────────────────────────────────────────────────┼───────╴ - bam  (file)          │BAM file to calculate statistics                                   │*.{bam} -╶──────────────────────┼───────────────────────────────────────────────────────────────────┼───────╴ - bai  (file)          │Index for input BAM file                                           │*.{bai} -╶──────────────────────┼───────────────────────────────────────────────────────────────────┼───────╴ - bed  (file)          │BED file for the reference gene model                              │*.{bed} -╶──────────────────────┼───────────────────────────────────────────────────────────────────┼───────╴ - rseqc_modules  (list)│List of rseqc modules to run e.g. [ 'bam_stat', 'infer_experiment' │ -                       │]                                                                  │ -                       ╵                                                                   ╵         -                                    ╷                                    ╷                           -📤 Outputs                         │Description                         │                  Pattern -╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━╸ - ch_bamstat  (file)                │bam statistics report               │           *.bam_stat.txt -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_innerdistance  (file)          │All the output files from           │            *.{txt,pdf,R} -                                    │RSEQC_INNERDISTANCE                 │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_innerdistance_distance  (file) │the inner distances                 │     *.inner_distance.txt -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_innerdistance_freq  (file)     │frequencies of different insert     │*.inner_distance_freq.txt -                                    │sizes                               │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_innerdistance_mean  (file)     │mean/median values of inner         │*.inner_distance_mean.txt -                                    │distances                           │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_innerdistance_pdf  (file)      │distribution plot of inner distances│*.inner_distance_plot.pdf -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_innerdistance_rscript  (file)  │script to reproduce the plot        │  *.inner_distance_plot.R -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_inferexperiment  (file)        │infer_experiment results report     │   *.infer_experiment.txt -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_junctionannotation  (file)     │All the output files from           │    *.{bed,xls,pdf,R,log} -                                    │RSEQC_JUNCTIONANNOTATION            │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_junctionannotation_bed  (file) │bed file of annotated junctions     │           *.junction.bed -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_junctionannotation_interact_bed│Interact bed file                   │           *.Interact.bed -(file)                             │                                    │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_junctionannotation_xls  (file) │xls file with junction information  │                    *.xls -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_junctionannotation_pdf  (file) │junction plot                       │           *.junction.pdf -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_junctionannotation_events_pdf │events plot                         │             *.events.pdf -(file)                             │                                    │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_junctionannotation_rscript    │Rscript to reproduce the plots      │                      *.r -(file)                             │                                    │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_junctionannotation_log  (file) │Log file generated by tool          │                    *.log -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_junctionsaturation  (file)     │All the output files from           │                *.{pdf,R} -                                    │RSEQC_JUNCTIONSATURATION            │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_junctionsaturation_pdf  (file) │Junction saturation report          │                    *.pdf -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_junctionsaturation_rscript    │Junction saturation R-script        │                      *.r -(file)                             │                                    │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_readdistribution  (file)       │the read distribution report        │  *.read_distribution.txt -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_readduplication  (file)        │All the output files from           │            *.{xls,pdf,R} -                                    │RSEQC_READDUPLICATION               │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_readduplication_seq_xls  (file)│Read duplication rate determined    │         *seq.DupRate.xls -                                    │from mapping position of read       │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_readduplication_pos_xls  (file)│Read duplication rate determined    │         *pos.DupRate.xls -                                    │from sequence of read               │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_readduplication_pdf  (file)    │plot of duplication rate            │                    *.pdf -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_readduplication_rscript  (file)│script to reproduce the plot        │                      *.R -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - ch_tin  (file)                    │TXT file containing tin.py results  │                    *.txt -                                    │summary                             │ -╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ - versions  (file)                  │File containing software versions   │             versions.yml -                                    ╵                                    ╵                           - - 💻  Installation command: nf-core subworkflows install bam_rseqc - + + + + $ nf-core subworkflows info bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +╭─ Subworkflow: bam_rseqc  ────────────────────────────────────────────────────────────────────────╮ +│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ +│ 📖 Description: Subworkflow to run multiple commands in the RSeqC package                        │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +[..truncated..] + ch_readduplication_rscript  (file)│script to reproduce the plot        │                      *.R +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + ch_tin  (file)                    │TXT file containing tin.py results  │                    *.txt +                                    │summary                             │ +╶───────────────────────────────────┼────────────────────────────────────┼─────────────────────────╴ + versions  (file)                  │File containing software versions   │             versions.yml +                                    ╵                                    ╵                           + + 💻  Installation command: nf-core subworkflows install bam_rseqc + diff --git a/docs/images/nf-core-subworkflows-install.svg b/docs/images/nf-core-subworkflows-install.svg index 3b303f44a4..4e1c3d29a9 100644 --- a/docs/images/nf-core-subworkflows-install.svg +++ b/docs/images/nf-core-subworkflows-install.svg @@ -19,76 +19,76 @@ font-weight: 700; } - .terminal-3637679507-matrix { + .terminal-1280284146-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3637679507-title { + .terminal-1280284146-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3637679507-r1 { fill: #c5c8c6 } -.terminal-3637679507-r2 { fill: #98a84b } -.terminal-3637679507-r3 { fill: #9a9b99 } -.terminal-3637679507-r4 { fill: #608ab1 } -.terminal-3637679507-r5 { fill: #d0b344 } + .terminal-1280284146-r1 { fill: #c5c8c6 } +.terminal-1280284146-r2 { fill: #98a84b } +.terminal-1280284146-r3 { fill: #9a9b99 } +.terminal-1280284146-r4 { fill: #608ab1 } +.terminal-1280284146-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core subworkflows install bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     Installing 'bam_rseqc' -INFO     Use the following statement to include this subworkflow:                                    - - include { BAM_RSEQC } from '../subworkflows/nf-core/bam_rseqc/main'                                 - + + $ nf-core subworkflows install bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Installing 'bam_rseqc' +INFO     Use the following statement to include this subworkflow:                                    + + include { BAM_RSEQC } from '../subworkflows/nf-core/bam_rseqc/main'                                 + diff --git a/docs/images/nf-core-subworkflows-lint.svg b/docs/images/nf-core-subworkflows-lint.svg index 48c4837788..ce3299a21f 100644 --- a/docs/images/nf-core-subworkflows-lint.svg +++ b/docs/images/nf-core-subworkflows-lint.svg @@ -19,239 +19,239 @@ font-weight: 700; } - .terminal-3624954477-matrix { + .terminal-4099828428-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3624954477-title { + .terminal-4099828428-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3624954477-r1 { fill: #c5c8c6 } -.terminal-3624954477-r2 { fill: #98a84b } -.terminal-3624954477-r3 { fill: #9a9b99 } -.terminal-3624954477-r4 { fill: #608ab1 } -.terminal-3624954477-r5 { fill: #d0b344 } -.terminal-3624954477-r6 { fill: #d0b344;font-weight: bold } -.terminal-3624954477-r7 { fill: #8d7b39 } -.terminal-3624954477-r8 { fill: #fdfdc5 } -.terminal-3624954477-r9 { fill: #d0b344;font-style: italic; } -.terminal-3624954477-r10 { fill: #c5c8c6;font-weight: bold } -.terminal-3624954477-r11 { fill: #98a84b;font-weight: bold } -.terminal-3624954477-r12 { fill: #cc555a } + .terminal-4099828428-r1 { fill: #c5c8c6 } +.terminal-4099828428-r2 { fill: #98a84b } +.terminal-4099828428-r3 { fill: #9a9b99 } +.terminal-4099828428-r4 { fill: #608ab1 } +.terminal-4099828428-r5 { fill: #d0b344 } +.terminal-4099828428-r6 { fill: #d0b344;font-weight: bold } +.terminal-4099828428-r7 { fill: #8d7b39 } +.terminal-4099828428-r8 { fill: #fdfdc5 } +.terminal-4099828428-r9 { fill: #d0b344;font-style: italic; } +.terminal-4099828428-r10 { fill: #c5c8c6;font-weight: bold } +.terminal-4099828428-r11 { fill: #98a84b;font-weight: bold } +.terminal-4099828428-r12 { fill: #cc555a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -263,78 +263,78 @@ - + - - $ nf-core subworkflows lint bam_stats_samtools - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     Linting modules repo: '.' -INFO     Linting subworkflow: 'bam_stats_samtools' - -╭─[!] 14 Subworkflow Test Warnings───────────────────────────────────────────────────────────────╮ -│                     ╷                                     ╷                                      │ -│Subworkflow name   │File path                          │Test message                        │ -│╶────────────────────┼─────────────────────────────────────┼─────────────────────────────────────╴│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: //Add │ -│││all required assertions to verify │ -│││the test output.│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Add │ -│││tags for all modules used within │ -│││this subworkflow. Example:│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Change │ -│││the test name preferably indicating │ -│││the test-data and file-format used│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Once │ -│││you have added the required tests, │ -│││please run the following command to │ -│││build this file:│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: define │ -│││inputs of the workflow here. │ -│││Example:│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: A │ -│││subworkflow SHOULD import at least │ -│││two modules│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: If in doubt │ -│││look at other nf-core/subworkflows │ -│││to see how we are doing things! :)│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit emitted│ -│││channels│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit input │ -│││(take) channels│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: substitute │ -│││modules here for the modules of your│ -│││subworkflow│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a │ -│││description of the subworkflow and │ -│││list keywords│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a list│ -│││of the modules and/or subworkflows │ -│││used in the subworkflow│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ -│││of the channels used as input with a│ -│││description and their structure│ -│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ -│││of the channels used as output with │ -│││a descriptions and their structure│ -│                     ╵                                     ╵                                      │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────╮ -│LINT RESULTS SUMMARY│ -├───────────────────────┤ -│[✔]  42 Tests Passed │ -│[!]  14 Test Warnings│ -│[✗]   0 Tests Failed │ -╰───────────────────────╯ + + $ nf-core subworkflows lint bam_stats_samtools + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Linting modules repo: '.' +INFO     Linting subworkflow: 'bam_stats_samtools' + +╭─[!] 14 Subworkflow Test Warnings───────────────────────────────────────────────────────────────╮ +│                     ╷                                     ╷                                      │ +│Subworkflow name   │File path                          │Test message                        │ +│╶────────────────────┼─────────────────────────────────────┼─────────────────────────────────────╴│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: //Add │ +│││all required assertions to verify │ +│││the test output.│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Add │ +│││tags for all modules used within │ +│││this subworkflow. Example:│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Change │ +│││the test name preferably indicating │ +│││the test-data and file-format used│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Once │ +│││you have added the required tests, │ +│││please run the following command to │ +│││build this file:│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: define │ +│││inputs of the workflow here. │ +│││Example:│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: A │ +│││subworkflow SHOULD import at least │ +│││two modules│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: If in doubt │ +│││look at other nf-core/subworkflows │ +│││to see how we are doing things! :)│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit emitted│ +│││channels│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit input │ +│││(take) channels│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: substitute │ +│││modules here for the modules of your│ +│││subworkflow│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a │ +│││description of the subworkflow and │ +│││list keywords│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a list│ +│││of the modules and/or subworkflows │ +│││used in the subworkflow│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ +│││of the channels used as input with a│ +│││description and their structure│ +│bam_stats_samtools│subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ +│││of the channels used as output with │ +│││a descriptions and their structure│ +│                     ╵                                     ╵                                      │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭───────────────────────╮ +│LINT RESULTS SUMMARY│ +├───────────────────────┤ +│[✔]  42 Tests Passed │ +│[!]  14 Test Warnings│ +│[✗]   0 Tests Failed │ +╰───────────────────────╯ diff --git a/docs/images/nf-core-subworkflows-list-local.svg b/docs/images/nf-core-subworkflows-list-local.svg index 7d33c4a6c1..47871a6f4d 100644 --- a/docs/images/nf-core-subworkflows-list-local.svg +++ b/docs/images/nf-core-subworkflows-list-local.svg @@ -19,67 +19,67 @@ font-weight: 700; } - .terminal-372904993-matrix { + .terminal-3058242688-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-372904993-title { + .terminal-3058242688-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-372904993-r1 { fill: #c5c8c6 } -.terminal-372904993-r2 { fill: #98a84b } -.terminal-372904993-r3 { fill: #9a9b99 } -.terminal-372904993-r4 { fill: #608ab1 } -.terminal-372904993-r5 { fill: #d0b344 } + .terminal-3058242688-r1 { fill: #c5c8c6 } +.terminal-3058242688-r2 { fill: #98a84b } +.terminal-3058242688-r3 { fill: #9a9b99 } +.terminal-3058242688-r4 { fill: #608ab1 } +.terminal-3058242688-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -91,23 +91,23 @@ - + - - $ nf-core subworkflows list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     No nf-core subworkflows found in '.' - + + $ nf-core subworkflows list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     No nf-core subworkflows found in '.' + diff --git a/docs/images/nf-core-subworkflows-list-remote.svg b/docs/images/nf-core-subworkflows-list-remote.svg index 31d72d0d2d..bdc5e51c7c 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-2778221227-matrix { + .terminal-2018331402-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2778221227-title { + .terminal-2018331402-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2778221227-r1 { fill: #c5c8c6 } -.terminal-2778221227-r2 { fill: #98a84b } -.terminal-2778221227-r3 { fill: #9a9b99 } -.terminal-2778221227-r4 { fill: #608ab1 } -.terminal-2778221227-r5 { fill: #d0b344 } -.terminal-2778221227-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-2778221227-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-2778221227-r8 { fill: #868887;font-style: italic; } + .terminal-2018331402-r1 { fill: #c5c8c6 } +.terminal-2018331402-r2 { fill: #98a84b } +.terminal-2018331402-r3 { fill: #9a9b99 } +.terminal-2018331402-r4 { fill: #608ab1 } +.terminal-2018331402-r5 { fill: #d0b344 } +.terminal-2018331402-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-2018331402-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2018331402-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core subworkflows list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Subworkflow Name                             ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ bam_cnv_wisecondorx                           │ -│ bam_create_som_pon_gatk                       │ -│ bam_dedup_stats_samtools_umitools             │ -│ bam_docounts_contamination_angsd              │ -│ bam_markduplicates_picard                     │ -│ bam_markduplicates_samtools                   │ -│ bam_ngscheckmate                              │ -│ bam_qc_picard                                 │ -│ bam_rseqc                                     │ -[..truncated..] + + $ nf-core subworkflows list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Subworkflow Name                             ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ bam_cnv_wisecondorx                           │ +│ bam_create_som_pon_gatk                       │ +│ bam_dedup_stats_samtools_umitools             │ +│ bam_docounts_contamination_angsd              │ +│ bam_markduplicates_picard                     │ +│ bam_markduplicates_samtools                   │ +│ bam_ngscheckmate                              │ +│ bam_qc_picard                                 │ +│ bam_rseqc                                     │ +[..truncated..] diff --git a/docs/images/nf-core-subworkflows-remove.svg b/docs/images/nf-core-subworkflows-remove.svg index 481490d4ef..28527bc299 100644 --- a/docs/images/nf-core-subworkflows-remove.svg +++ b/docs/images/nf-core-subworkflows-remove.svg @@ -19,100 +19,100 @@ font-weight: 700; } - .terminal-3888835335-matrix { + .terminal-1022880614-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3888835335-title { + .terminal-1022880614-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3888835335-r1 { fill: #c5c8c6 } -.terminal-3888835335-r2 { fill: #98a84b } -.terminal-3888835335-r3 { fill: #9a9b99 } -.terminal-3888835335-r4 { fill: #608ab1 } -.terminal-3888835335-r5 { fill: #d0b344 } + .terminal-1022880614-r1 { fill: #c5c8c6 } +.terminal-1022880614-r2 { fill: #98a84b } +.terminal-1022880614-r3 { fill: #9a9b99 } +.terminal-1022880614-r4 { fill: #608ab1 } +.terminal-1022880614-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -124,34 +124,34 @@ - + - - $ nf-core subworkflows remove bam_rseqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     Removed files for 'rseqc/bamstat' and its dependencies 'rseqc/bamstat'.                     -INFO     Removed files for 'rseqc/inferexperiment' and its dependencies 'rseqc/inferexperiment'.     -INFO     Removed files for 'rseqc/innerdistance' and its dependencies 'rseqc/innerdistance'.         -INFO     Removed files for 'rseqc/junctionannotation' and its dependencies                           -'rseqc/junctionannotation'.                                                                 -INFO     Removed files for 'rseqc/junctionsaturation' and its dependencies                           -'rseqc/junctionsaturation'.                                                                 -INFO     Removed files for 'rseqc/readdistribution' and its dependencies 'rseqc/readdistribution'.   -INFO     Removed files for 'rseqc/readduplication' and its dependencies 'rseqc/readduplication'.     -INFO     Removed files for 'rseqc/tin' and its dependencies 'rseqc/tin'.                             -INFO     Removed files for 'bam_rseqc' and its dependencies 'bam_rseqc, rseqc_bamstat,  -rseqc_inferexperiment, rseqc_innerdistance, rseqc_junctionannotation,  -rseqc_junctionsaturation, rseqc_readdistribution, rseqc_readduplication, rseqc_tin'.        + + $ nf-core subworkflows remove bam_rseqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO     Removed files for 'rseqc/bamstat' and its dependencies 'rseqc/bamstat'.                     +INFO     Removed files for 'rseqc/inferexperiment' and its dependencies 'rseqc/inferexperiment'.     +INFO     Removed files for 'rseqc/innerdistance' and its dependencies 'rseqc/innerdistance'.         +INFO     Removed files for 'rseqc/junctionannotation' and its dependencies                           +'rseqc/junctionannotation'.                                                                 +INFO     Removed files for 'rseqc/junctionsaturation' and its dependencies                           +'rseqc/junctionsaturation'.                                                                 +INFO     Removed files for 'rseqc/readdistribution' and its dependencies 'rseqc/readdistribution'.   +INFO     Removed files for 'rseqc/readduplication' and its dependencies 'rseqc/readduplication'.     +INFO     Removed files for 'rseqc/tin' and its dependencies 'rseqc/tin'.                             +INFO     Removed files for 'bam_rseqc' and its dependencies 'bam_rseqc, rseqc_bamstat,  +rseqc_inferexperiment, rseqc_innerdistance, rseqc_junctionannotation,  +rseqc_junctionsaturation, rseqc_readdistribution, rseqc_readduplication, rseqc_tin'.        diff --git a/docs/images/nf-core-subworkflows-test.svg b/docs/images/nf-core-subworkflows-test.svg index 909b3c00d8..cbc724f546 100644 --- a/docs/images/nf-core-subworkflows-test.svg +++ b/docs/images/nf-core-subworkflows-test.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + - - $ nf-core subworkflows test bam_rseqc --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO     Generating nf-test snapshot                                                                 -╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/utils.py:315 in      │ -│run_cmd│ -││ -│ 312 │   full_cmd = f"{executable}{cmd}"│ -│ 313 │   log.debug(f"Running command: {full_cmd}")                                             │ -│ 314 │   try:                                                                                  │ -│❱  315 │   │   proc = subprocess.run(shlex.split(full_cmd), stdout=subprocess.PIPE, stderr=subp  │ -│ 316 │   │   return (proc.stdout, proc.stderr)                                                 │ -│ 317 │   exceptOSErroras e:                                                                  │ -│ 318 │   │   if e.errno == errno.ENOENT:                                                       │ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/subprocess.py:548 in run│ -││ -│ 545 │   │   kwargs['stdout'] = PIPE                                                           │ -│ 546 │   │   kwargs['stderr'] = PIPE                                                           │ -│ 547 │   │ -│❱  548 │   with Popen(*popenargs, **kwargs) as process:                                          │ -│ 549 │   │   try:                                                                              │ -│ 550 │   │   │   stdout, stderr = process.communicate(input, timeout=timeout)                  │ -│ 551 │   │   except TimeoutExpired as exc:                                                     │ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/subprocess.py:1026 in __init__│ -││ -│1023 │   │   │   │   │   self.stderr = io.TextIOWrapper(self.stderr,                           │ -│1024 │   │   │   │   │   │   │   encoding=encoding, errors=errors)                             │ -│1025 │   │   │   │ -│❱ 1026 │   │   │   self._execute_child(args, executable, preexec_fn, close_fds,                  │ -│1027 │   │   │   │   │   │   │   │   pass_fds, cwd, env,                                       │ -│1028 │   │   │   │   │   │   │   │   startupinfo, creationflags, shell,                        │ -│1029 │   │   │   │   │   │   │   │   p2cread, p2cwrite,                                        │ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/subprocess.py:1950 in _execute_child│ -││ -│1947 │   │   │   │   │   │   err_filename = orig_executable                                    │ -│1948 │   │   │   │   │   if errno_num != 0:                                                    │ -│1949 │   │   │   │   │   │   err_msg = os.strerror(errno_num)                                  │ -│❱ 1950 │   │   │   │   │   raise child_exception_type(errno_num, err_msg, err_filename)          │ -│1951 │   │   │   │   raise child_exception_type(err_msg)                                       │ -│1952 │ -│1953 │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -FileNotFoundError: [Errno 2] No such file or directory: 'nf-test' - -During handling of the above exception, another exception occurred: - -╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ -│/opt/hostedtoolcache/Python/3.12.1/x64/bin/nf-core:8 in <module>│ -││ -│5 fromnf_core.__main__import run_nf_core                                                     │ -│6 if__name__ == '__main__':                                                                   │ -│7 │   sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])                         │ -│❱ 8 │   sys.exit(run_nf_core())                                                                  │ -│9 │ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/__main__.py:111 in   │ -│run_nf_core│ -││ -│ 108 │   │   │   log.debug(f"Could not check latest version: {e}")                             │ -│ 109 │   │   stderr.print("\n")                                                                │ -│ 110 │   # Launch the click cli│ -│❱  111 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │ -│ 112 │ -│ 113 │ -│ 114 @click.group(context_settings=dict(help_option_names=["-h", "--help"]))                   │ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/click/core.py:1157 in        │ -│__call__│ -││ -│1154 │   │ -│1155 │   def__call__(self, *args: t.Any, **kwargs: t.Any) -> t.Any:                           │ -│1156 │   │   """Alias for :meth:`main`."""│ -│❱ 1157 │   │   returnself.main(*args, **kwargs)                                                 │ -│1158 │ -│1159 │ -│1160 classCommand(BaseCommand):                                                               │ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/rich_click/rich_command.py:1│ -│26 in main│ -││ -│123 │   │   try:                                                                               │ -│124 │   │   │   try:                                                                           │ -│125 │   │   │   │   withself.make_context(prog_name, args, **extra) as ctx:                   │ -│❱ 126 │   │   │   │   │   rv = self.invoke(ctx)                                                  │ -│127 │   │   │   │   │   ifnot standalone_mode:                                                │ -│128 │   │   │   │   │   │   return rv                                                          │ -│129 │   │   │   │   │   # it's not safe to `ctx.exit(rv)` here!│ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/click/core.py:1688 in invoke│ -││ -│1685 │   │   │   │   super().invoke(ctx)                                                       │ -│1686 │   │   │   │   sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)                    │ -│1687 │   │   │   │   with sub_ctx:                                                             │ -│❱ 1688 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │ -│1689 │   │   │ -│1690 │   │   # In chain mode we create the contexts step by step, but after the│ -│1691 │   │   # base command has been invoked.  Because at that point we do not│ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/click/core.py:1688 in invoke│ -││ -│1685 │   │   │   │   super().invoke(ctx)                                                       │ -│1686 │   │   │   │   sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)                    │ -│1687 │   │   │   │   with sub_ctx:                                                             │ -│❱ 1688 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │ -│1689 │   │   │ -│1690 │   │   # In chain mode we create the contexts step by step, but after the│ -│1691 │   │   # base command has been invoked.  Because at that point we do not│ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/click/core.py:1434 in invoke│ -││ -│1431 │   │   │   echo(style(message, fg="red"), err=True)                                      │ -│1432 │   │   │ -│1433 │   │   ifself.callback isnotNone:                                                     │ -│❱ 1434 │   │   │   return ctx.invoke(self.callback, **ctx.params)                                │ -│1435 │   │ -│1436 │   defshell_complete(self, ctx: Context, incomplete: str) -> t.List["CompletionItem"]:  │ -│1437 │   │   """Return a list of completions for the incomplete value. Looks│ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/click/core.py:783 in invoke│ -││ -│ 780 │   │   │ -│ 781 │   │   with augment_usage_errors(__self):                                                │ -│ 782 │   │   │   with ctx:                                                                     │ -│❱  783 │   │   │   │   return __callback(*args, **kwargs)                                        │ -│ 784 │   │ -│ 785 │   defforward(                                                                          │ -│ 786 │   │   __self, __cmd: "Command", *args: t.Any, **kwargs: t.Any  # noqa: B902│ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/click/decorators.py:33 in    │ -│new_func│ -││ -│ 30 │   """│ -│ 31 │   │ -│ 32 │   defnew_func(*args: "P.args", **kwargs: "P.kwargs") -> "R":                            │ -│❱  33 │   │   return f(get_current_context(), *args, **kwargs)                                   │ -│ 34 │   │ -│ 35 │   return update_wrapper(new_func, f)                                                     │ -│ 36 │ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/__main__.py:1101 in  │ -│test_subworkflow│ -││ -│1098 │   │   │   branch=ctx.obj["modules_repo_branch"],                                        │ -│1099 │   │   │   verbose=ctx.obj["verbose"],                                                   │ -│1100 │   │   )                                                                                 │ -│❱ 1101 │   │   sw_tester.run()                                                                   │ -│1102 │   except (UserWarning, LookupError) as e:                                               │ -│1103 │   │   log.critical(e)                                                                   │ -│1104 │   │   sys.exit(1)                                                                       │ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/components/component│ -│s_test.py:94 in run│ -││ -│ 91 │   │   │   "NFT_DIFF_ARGS"│ -│ 92 │   │   ] = "--line-numbers --expand-tabs=2"# taken from https://code.askimed.com/nf-t│ -│ 93 │   │   with nf_core.utils.set_wd(Path(self.dir)):                                         │ -│❱  94 │   │   │   self.check_snapshot_stability()                                                │ -│ 95 │   │   iflen(self.errors) > 0:                                                           │ -│ 96 │   │   │   errors = "\n - ".join(self.errors)                                             │ -│ 97 │   │   │   raiseUserWarning(f"Ran, but found errors:\n - {errors}")                      │ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/components/component│ -│s_test.py:226 in check_snapshot_stability│ -││ -│223 │   defcheck_snapshot_stability(self) -> bool:                                            │ -│224 │   │   """Run the nf-test twice and check if the snapshot changes"""│ -│225 │   │   log.info("Generating nf-test snapshot")                                            │ -│❱ 226 │   │   ifnotself.generate_snapshot():                                                   │ -│227 │   │   │   returnFalse# stop here if the first run failed│ -│228 │   │   elifself.once:                                                                    │ -│229 │   │   │   returnTrue# stop here if the test should be run only once│ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/components/component│ -│s_test.py:194 in generate_snapshot│ -││ -│191 │   │   self.update = False# reset self.update to False to test if the new snapshot is│ -│192 │   │   tag = f"subworkflows/{self.component_name}"ifself.component_type == "subworkfl│ -│193 │   │   │ -│❱ 194 │   │   result = nf_core.utils.run_cmd(                                                    │ -│195 │   │   │   "nf-test",                                                                     │ -│196 │   │   │   f"test --tag {tag} --profile {os.environ['PROFILE']}{verbose}{update}",      │ -│197 │   │   )                                                                                  │ -││ -│/opt/hostedtoolcache/Python/3.12.1/x64/lib/python3.12/site-packages/nf_core/utils.py:319 in      │ -│run_cmd│ -││ -│ 316 │   │   return (proc.stdout, proc.stderr)                                                 │ -│ 317 │   exceptOSErroras e:                                                                  │ -│ 318 │   │   if e.errno == errno.ENOENT:                                                       │ -│❱  319 │   │   │   raiseRuntimeError(                                                           │ -│ 320 │   │   │   │   f"It looks like {executable} is not installed. Please ensure it is avail│ -│ 321 │   │   │   )                                                                             │ -│ 322 │   │   else:                                                                             │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -RuntimeError: It looks like nf-test is not installed. Please ensure it is available in your PATH. + + $ nf-core subworkflows test bam_rseqc --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - 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 2594a2fa65..0a9d9eceaf 100644 --- a/docs/images/nf-core-subworkflows-update.svg +++ b/docs/images/nf-core-subworkflows-update.svg @@ -19,67 +19,67 @@ font-weight: 700; } - .terminal-2684898182-matrix { + .terminal-2377731045-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2684898182-title { + .terminal-2377731045-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2684898182-r1 { fill: #c5c8c6 } -.terminal-2684898182-r2 { fill: #98a84b } -.terminal-2684898182-r3 { fill: #9a9b99 } -.terminal-2684898182-r4 { fill: #608ab1 } -.terminal-2684898182-r5 { fill: #d0b344 } + .terminal-2377731045-r1 { fill: #c5c8c6 } +.terminal-2377731045-r2 { fill: #98a84b } +.terminal-2377731045-r3 { fill: #9a9b99 } +.terminal-2377731045-r4 { fill: #608ab1 } +.terminal-2377731045-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -91,23 +91,23 @@ - + - - $ nf-core subworkflows update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - - -INFO    'subworkflows/nf-core/bam_rseqc' is already up to date                                      -INFO     Updates complete ✨                                                                         + + $ nf-core subworkflows update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + + +INFO    'subworkflows/nf-core/bam_rseqc' is already up to date                                      +INFO     Updates complete ✨                                                                         diff --git a/docs/images/nf-core-sync.svg b/docs/images/nf-core-sync.svg index 6b1e13eb56..18aa790e23 100644 --- a/docs/images/nf-core-sync.svg +++ b/docs/images/nf-core-sync.svg @@ -19,76 +19,76 @@ font-weight: 700; } - .terminal-3344648746-matrix { + .terminal-3646376585-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3344648746-title { + .terminal-3646376585-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3344648746-r1 { fill: #c5c8c6 } -.terminal-3344648746-r2 { fill: #98a84b } -.terminal-3344648746-r3 { fill: #9a9b99 } -.terminal-3344648746-r4 { fill: #608ab1 } -.terminal-3344648746-r5 { fill: #d0b344 } -.terminal-3344648746-r6 { fill: #cc555a } -.terminal-3344648746-r7 { fill: #98729f } -.terminal-3344648746-r8 { fill: #ff2c7a } + .terminal-3646376585-r1 { fill: #c5c8c6 } +.terminal-3646376585-r2 { fill: #98a84b } +.terminal-3646376585-r3 { fill: #9a9b99 } +.terminal-3646376585-r4 { fill: #608ab1 } +.terminal-3646376585-r5 { fill: #d0b344 } +.terminal-3646376585-r6 { fill: #cc555a } +.terminal-3646376585-r7 { fill: #98729f } +.terminal-3646376585-r8 { fill: #ff2c7a } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,25 +100,25 @@ - + - - $ nf-core sync - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.11 - https://nf-co.re - - -WARNING  Could not find GitHub authentication token. Some API requests may fail.                     -INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthing -INFO     Original pipeline repository branch is 'master' -INFO     Deleting all files in 'TEMPLATE' branch                                                     -INFO     Making a new template pipeline using pipeline variables                                     + + $ nf-core sync + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.11.1 - https://nf-co.re + + +WARNING  Could not find GitHub authentication token. Some API requests may fail.                     +INFO     Pipeline directory: /home/runner/work/tools/tools/tmp/nf-core-nextbigthing +INFO     Original pipeline repository branch is 'master' +INFO     Deleting all files in 'TEMPLATE' branch                                                     +INFO     Making a new template pipeline using pipeline variables                                     diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index ee912843b6..32eb8736d6 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -553,6 +553,7 @@ def check_up_to_date(self): Check that we have the "installed_by" value in 'modules.json', otherwise add it. Assume that the modules/subworkflows were installed by an nf-core command (don't track installed by subworkflows). """ + dump_modules_json = False try: self.load() if not self.has_git_url_and_modules(): @@ -566,9 +567,11 @@ def check_up_to_date(self): for _, component in install_dir_entry.items(): if "installed_by" in component and isinstance(component["installed_by"], str): log.debug(f"Updating {component} in modules.json") + dump_modules_json = True component["installed_by"] = [component["installed_by"]] except UserWarning: log.info("The 'modules.json' file is not up to date. Recreating the 'modules.json' file.") + dump_modules_json = True self.create() # Get unsynced components @@ -593,8 +596,10 @@ def check_up_to_date(self): # If some modules/subworkflows didn't have an entry in the 'modules.json' file # we try to determine the SHA from the commit log of the remote if len(modules_missing_from_modules_json) > 0: + dump_modules_json = True self.resolve_missing_from_modules_json(modules_missing_from_modules_json, "modules") if len(subworkflows_missing_from_modules_json) > 0: + dump_modules_json = True self.resolve_missing_from_modules_json(subworkflows_missing_from_modules_json, "subworkflows") # If the "installed_by" value is not present for modules/subworkflows, add it. @@ -603,6 +608,7 @@ def check_up_to_date(self): for install_dir, installed_components in dir_content.items(): for component, component_features in installed_components.items(): if "installed_by" not in component_features: + dump_modules_json = True self.modules_json["repos"][repo][component_type][install_dir][component]["installed_by"] = [ component_type ] @@ -612,12 +618,14 @@ def check_up_to_date(self): self.pipeline_components = None subworkflows_dict = self.get_all_components("subworkflows") if subworkflows_dict: + dump_modules_json = True for repo, subworkflows in subworkflows_dict.items(): for org, subworkflow in subworkflows: self.recreate_dependencies(repo, org, subworkflow) self.pipeline_components = original_pipeline_components - self.dump() + if dump_modules_json: + self.dump(run_prettier=True) def load(self): """ diff --git a/nf_core/pipeline-template/.github/workflows/release-announcments.yml b/nf_core/pipeline-template/.github/workflows/release-announcements.yml similarity index 100% rename from nf_core/pipeline-template/.github/workflows/release-announcments.yml rename to nf_core/pipeline-template/.github/workflows/release-announcements.yml diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index b4402c46a6..dec8051a17 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -120,10 +120,10 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - runOptions = '-u $(id -u):$(id -g)' + docker.runOptions = '-u $(id -u):$(id -g)' } arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { singularity.enabled = true diff --git a/setup.py b/setup.py index da6f0ffa61..84c6529dce 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import find_packages, setup -version = "2.11" +version = "2.11.1" with open("README.md") as f: readme = f.read()