From 30c3fe3141adcae381684423bb94c6d708b46fdd Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Mon, 7 Oct 2024 14:46:47 +0000 Subject: [PATCH] Generate new screengrabs with rich-codex --- .../creating_with_nf_core/git_log.svg | 18 +- .../creating_with_nf_core/nextflow_run_1.svg | 262 +++---- .../nextflow_run_help.svg | 198 +++--- .../nextflow_run_no_outdir.svg | 390 +++++------ .../nfcore_lint_failure.svg | 270 +++++--- .../nfcore_lint_warnings.svg | 453 +++++++----- .../creating_with_nf_core/nfcore_list.svg | 108 +-- .../modules/nf-core-modules-create.svg | 137 ++-- public/images/tools/nf-core-download.svg | 99 ++- public/images/tools/nf-core-lint.svg | 249 ++++--- public/images/tools/nf-core-list-rna.svg | 138 ++-- public/images/tools/nf-core-list-stars.svg | 104 +-- public/images/tools/nf-core-list.svg | 108 +-- .../tools/nf-core-modules-bump-version.svg | 115 +-- .../images/tools/nf-core-modules-create.svg | 134 ++-- public/images/tools/nf-core-modules-info.svg | 654 +++++++++++++++--- public/images/tools/nf-core-modules-lint.svg | 18 +- public/images/tools/nf-core-modules-patch.svg | 156 ++--- .../images/tools/nf-core-modules-update.svg | 82 +-- public/images/tools/nf-core-schema-build.svg | 83 ++- .../tools/nf-core-subworkflows-lint.svg | 318 +++++---- .../nf-core-subworkflows-list-remote.svg | 132 ++-- .../tools/nf-core-subworkflows-update.svg | 86 +-- public/images/tools/nf-core-sync.svg | 114 +-- 24 files changed, 2609 insertions(+), 1817 deletions(-) diff --git a/public/images/contributing/creating_with_nf_core/git_log.svg b/public/images/contributing/creating_with_nf_core/git_log.svg index 9b4e716f14..c1bdf713a7 100644 --- a/public/images/contributing/creating_with_nf_core/git_log.svg +++ b/public/images/contributing/creating_with_nf_core/git_log.svg @@ -19,27 +19,27 @@ font-weight: 700; } - .terminal-1718823819-matrix { + .terminal-1993354176-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1718823819-title { + .terminal-1993354176-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1718823819-r1 { fill: #c5c8c6 } + .terminal-1993354176-r1 { fill: #c5c8c6 } - + - + @@ -51,11 +51,11 @@ - + - - $ git log --oneline -3029a70 initial template build from nf-core/tools, version 2.14.1 + + $ git log --oneline +7b45b25 initial template build from nf-core/tools, version 2.14.1 diff --git a/public/images/contributing/creating_with_nf_core/nextflow_run_1.svg b/public/images/contributing/creating_with_nf_core/nextflow_run_1.svg index 23663a109d..e88dd89b2f 100644 --- a/public/images/contributing/creating_with_nf_core/nextflow_run_1.svg +++ b/public/images/contributing/creating_with_nf_core/nextflow_run_1.svg @@ -19,278 +19,278 @@ font-weight: 700; } - .terminal-3751378249-matrix { + .terminal-1050508944-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3751378249-title { + .terminal-1050508944-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3751378249-r1 { fill: #c5c8c6 } -.terminal-3751378249-r2 { fill: #868887 } -.terminal-3751378249-r3 { fill: #98a84b } -.terminal-3751378249-r4 { fill: #4b4e55 } -.terminal-3751378249-r5 { fill: #608ab1 } -.terminal-3751378249-r6 { fill: #d0b344 } -.terminal-3751378249-r7 { fill: #98729f } -.terminal-3751378249-r8 { fill: #c5c8c6;font-weight: bold } + .terminal-1050508944-r1 { fill: #c5c8c6 } +.terminal-1050508944-r2 { fill: #868887 } +.terminal-1050508944-r3 { fill: #98a84b } +.terminal-1050508944-r4 { fill: #4b4e55 } +.terminal-1050508944-r5 { fill: #608ab1 } +.terminal-1050508944-r6 { fill: #d0b344 } +.terminal-1050508944-r7 { fill: #98729f } +.terminal-1050508944-r8 { fill: #c5c8c6;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nextflow run + nextflow run - + - - $ nextflow run nf-core-demo/ -profile test,docker --outdir test_results -N E X T F L O W  ~  version 24.04.1 -Launching `nf-core-demo/main.nf` [wise_pasteur] DSL2 - revision: 9539a5d3d4 -Downloading plugin nf-validation@1.1.3 -WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value` - - ------------------------------------------------------- -,--./,-. -        ___     __   __   __   ___     /,-._.--~' -  |\ | |__  __ /  ` /  \ |__) |__         }  { -  | \| |       \__, \__/ |  \ |___     \`-._,-`-, -`._,._,' -  nf-core/demo v1.0dev ------------------------------------------------------- -Core Nextflow options -runName                   : wise_pasteur -containerEngine           : docker -launchDir                 : /home/runner/work/website/website -workDir                   : /home/runner/work/website/website/work -projectDir                : /home/runner/work/website/website/nf-core-demo -userName                  : runner -profile                   : test,docker -configFiles               :  - -Input/output options -input                     : https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv -outdir                    : test_results - -Reference genome options -genome                    : R64-1-1 -fasta                     : s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa - -Institutional config options -config_profile_name       : Test profile -config_profile_description: Minimal test dataset to check pipeline function - -Max job request options -max_cpus                  : 2 -max_memory                : 6.GB -max_time                  : 6.h - -!! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------- -If you use nf-core/demo for your analysis please cite: - -* The pipeline - -* The nf-core framework -  https://doi.org/10.1038/s41587-020-0439-x - -* Software dependencies -  https://github.com/nf-core/demo/blob/master/CITATIONS.md ------------------------------------------------------- -[db/57e950] Submitted process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE1_PE) -[78/a98708] Submitted process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE3_SE) -[ae/1f6353] Submitted process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE) -[cd/057d43] Submitted process > NFCORE_DEMO:DEMO:MULTIQC --[nf-core/demo] Pipeline completed successfully- + + $ nextflow run nf-core-demo/ -profile test,docker --outdir test_results +N E X T F L O W  ~  version 24.04.4 +Launching `nf-core-demo/main.nf` [high_thompson] DSL2 - revision: 9539a5d3d4 +Downloading plugin nf-validation@1.1.3 +WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value` + + +------------------------------------------------------ +,--./,-. +        ___     __   __   __   ___     /,-._.--~' +  |\ | |__  __ /  ` /  \ |__) |__         }  { +  | \| |       \__, \__/ |  \ |___     \`-._,-`-, +`._,._,' +  nf-core/demo v1.0dev +------------------------------------------------------ +Core Nextflow options +runName                   : high_thompson +containerEngine           : docker +launchDir                 : /home/runner/work/website/website +workDir                   : /home/runner/work/website/website/work +projectDir                : /home/runner/work/website/website/nf-core-demo +userName                  : runner +profile                   : test,docker +configFiles               :  + +Input/output options +input                     : https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv +outdir                    : test_results + +Reference genome options +genome                    : R64-1-1 +fasta                     : s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa + +Institutional config options +config_profile_name       : Test profile +config_profile_description: Minimal test dataset to check pipeline function + +Max job request options +max_cpus                  : 2 +max_memory                : 6.GB +max_time                  : 6.h + +!! Only displaying parameters that differ from the pipeline defaults !! +------------------------------------------------------ +If you use nf-core/demo for your analysis please cite: + +* The pipeline + +* The nf-core framework +  https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies +  https://github.com/nf-core/demo/blob/master/CITATIONS.md +------------------------------------------------------ +[b8/43305d] Submitted process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE) +[13/1d0b6f] Submitted process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE1_PE) +[39/0cad3e] Submitted process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE3_SE) +[1a/0afa0c] Submitted process > NFCORE_DEMO:DEMO:MULTIQC +-[nf-core/demo] Pipeline completed successfully- diff --git a/public/images/contributing/creating_with_nf_core/nextflow_run_help.svg b/public/images/contributing/creating_with_nf_core/nextflow_run_help.svg index fa77411c56..a3aff5e1f0 100644 --- a/public/images/contributing/creating_with_nf_core/nextflow_run_help.svg +++ b/public/images/contributing/creating_with_nf_core/nextflow_run_help.svg @@ -19,158 +19,158 @@ font-weight: 700; } - .terminal-1785758157-matrix { + .terminal-2966389272-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1785758157-title { + .terminal-2966389272-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1785758157-r1 { fill: #c5c8c6 } -.terminal-1785758157-r2 { fill: #868887 } -.terminal-1785758157-r3 { fill: #98a84b } -.terminal-1785758157-r4 { fill: #4b4e55 } -.terminal-1785758157-r5 { fill: #608ab1 } -.terminal-1785758157-r6 { fill: #d0b344 } -.terminal-1785758157-r7 { fill: #98729f } -.terminal-1785758157-r8 { fill: #68a0b3 } -.terminal-1785758157-r9 { fill: #c5c8c6;font-weight: bold;text-decoration: underline; } + .terminal-2966389272-r1 { fill: #c5c8c6 } +.terminal-2966389272-r2 { fill: #868887 } +.terminal-2966389272-r3 { fill: #98a84b } +.terminal-2966389272-r4 { fill: #4b4e55 } +.terminal-2966389272-r5 { fill: #608ab1 } +.terminal-2966389272-r6 { fill: #d0b344 } +.terminal-2966389272-r7 { fill: #98729f } +.terminal-2966389272-r8 { fill: #68a0b3 } +.terminal-2966389272-r9 { fill: #c5c8c6;font-weight: bold;text-decoration: underline; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -182,52 +182,52 @@ - + - - $ nextflow run nf-core-demo/ --help -N E X T F L O W  ~  version 24.04.1 -Launching `nf-core-demo/main.nf` [gloomy_cori] DSL2 - revision: 50393df5b8 - - ------------------------------------------------------- -,--./,-. -        ___     __   __   __   ___     /,-._.--~' -  |\ | |__  __ /  ` /  \ |__) |__         }  { -  | \| |       \__, \__/ |  \ |___     \`-._,-`-, -`._,._,' -  nf-core/demo v1.0dev ------------------------------------------------------- -Typical pipeline command: - -nextflow run nf-core/demo -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR> - -Input/output options -  --input                            [string]  Path to comma-separated file containing information about the samples in the experiment. -  --outdir                           [string]  The output directory where the results will be saved. You have to use absolute paths to storage on Cloud  -                                               infrastructure.  -  --email                            [string]  Email address for completion summary. -  --multiqc_title                    [string]  MultiQC report title. Printed as page header, used for filename if not otherwise specified. - -Reference genome options -  --genome                           [string]  Name of iGenomes reference. -  --fasta                            [string]  Path to FASTA genome file. - -Generic options -  --multiqc_methods_description      [string]  Custom MultiQC yaml file containing HTML including a methods description. - - !! Hiding 25 params, use --validationShowHiddenParams to show them !! ------------------------------------------------------- -If you use nf-core/demo for your analysis please cite: - -* The pipeline - -* The nf-core framework -  https://doi.org/10.1038/s41587-020-0439-x - -* Software dependencies -  https://github.com/nf-core/demo/blob/master/CITATIONS.md ------------------------------------------------------- + + $ nextflow run nf-core-demo/ --help +N E X T F L O W  ~  version 24.04.4 +Launching `nf-core-demo/main.nf` [adoring_pare] DSL2 - revision: 50393df5b8 + + +------------------------------------------------------ +,--./,-. +        ___     __   __   __   ___     /,-._.--~' +  |\ | |__  __ /  ` /  \ |__) |__         }  { +  | \| |       \__, \__/ |  \ |___     \`-._,-`-, +`._,._,' +  nf-core/demo v1.0dev +------------------------------------------------------ +Typical pipeline command: + +nextflow run nf-core/demo -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR> + +Input/output options +  --input                            [string]  Path to comma-separated file containing information about the samples in the experiment. +  --outdir                           [string]  The output directory where the results will be saved. You have to use absolute paths to storage on Cloud  +                                               infrastructure.  +  --email                            [string]  Email address for completion summary. +  --multiqc_title                    [string]  MultiQC report title. Printed as page header, used for filename if not otherwise specified. + +Reference genome options +  --genome                           [string]  Name of iGenomes reference. +  --fasta                            [string]  Path to FASTA genome file. + +Generic options +  --multiqc_methods_description      [string]  Custom MultiQC yaml file containing HTML including a methods description. + + !! Hiding 25 params, use --validationShowHiddenParams to show them !! +------------------------------------------------------ +If you use nf-core/demo for your analysis please cite: + +* The pipeline + +* The nf-core framework +  https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies +  https://github.com/nf-core/demo/blob/master/CITATIONS.md +------------------------------------------------------ diff --git a/public/images/contributing/creating_with_nf_core/nextflow_run_no_outdir.svg b/public/images/contributing/creating_with_nf_core/nextflow_run_no_outdir.svg index a83bb9b7f3..24c983c52b 100644 --- a/public/images/contributing/creating_with_nf_core/nextflow_run_no_outdir.svg +++ b/public/images/contributing/creating_with_nf_core/nextflow_run_no_outdir.svg @@ -1,4 +1,4 @@ - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - nextflow run + nextflow run - + - - $ nextflow run nf-core-demo/ -profile test,docker -N E X T F L O W  ~  version 24.04.1 -Launching `nf-core-demo/main.nf` [reverent_goldstine] DSL2 - revision: 50393df5b8 -WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value` - - ------------------------------------------------------- -,--./,-. -        ___     __   __   __   ___     /,-._.--~' -  |\ | |__  __ /  ` /  \ |__) |__         }  { -  | \| |       \__, \__/ |  \ |___     \`-._,-`-, -`._,._,' -  nf-core/demo v1.0dev ------------------------------------------------------- -Core Nextflow options -runName                   : reverent_goldstine -containerEngine           : docker -launchDir                 : /home/runner/work/website/website -workDir                   : /home/runner/work/website/website/work -projectDir                : /home/runner/work/website/website/nf-core-demo -userName                  : runner -profile                   : test,docker -configFiles               :  - -Input/output options -input                     : https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv - -Reference genome options -genome                    : R64-1-1 -fasta                     : s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa - -Institutional config options -config_profile_name       : Test profile -config_profile_description: Minimal test dataset to check pipeline function - -Max job request options -max_cpus                  : 2 -max_memory                : 6.GB -max_time                  : 6.h - -!! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------- -If you use nf-core/demo for your analysis please cite: - -* The pipeline - -* The nf-core framework -  https://doi.org/10.1038/s41587-020-0439-x - -* Software dependencies -  https://github.com/nf-core/demo/blob/master/CITATIONS.md ------------------------------------------------------- -ERROR ~ ERROR: Validation of pipeline parameters failed! - - -- Check '.nextflow.log' file for details -The following invalid input values have been detected: - -* Missing required parameter: --outdir - - -- Check script 'nf-core-demo/./workflows/../subworkflows/local/utils_nfcore_demo_pipeline/../../nf-core/utils_nfvalidation_plugin/main.nf' at line: 57 or see '.nextflow.log' file for more details + + $ nextflow run nf-core-demo/ -profile test,docker +N E X T F L O W  ~  version 24.04.4 +Launching `nf-core-demo/main.nf` [kickass_noyce] DSL2 - revision: 50393df5b8 +WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value` + + +------------------------------------------------------ +,--./,-. +        ___     __   __   __   ___     /,-._.--~' +  |\ | |__  __ /  ` /  \ |__) |__         }  { +  | \| |       \__, \__/ |  \ |___     \`-._,-`-, +`._,._,' +  nf-core/demo v1.0dev +------------------------------------------------------ +Core Nextflow options +runName                   : kickass_noyce +containerEngine           : docker +launchDir                 : /home/runner/work/website/website +workDir                   : /home/runner/work/website/website/work +projectDir                : /home/runner/work/website/website/nf-core-demo +userName                  : runner +profile                   : test,docker +configFiles               :  + +Input/output options +input                     : https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv + +Reference genome options +genome                    : R64-1-1 +fasta                     : s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa + +Institutional config options +config_profile_name       : Test profile +config_profile_description: Minimal test dataset to check pipeline function + +Max job request options +max_cpus                  : 2 +max_memory                : 6.GB +max_time                  : 6.h + +!! Only displaying parameters that differ from the pipeline defaults !! +------------------------------------------------------ +If you use nf-core/demo for your analysis please cite: + +* The pipeline + +* The nf-core framework +  https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies +  https://github.com/nf-core/demo/blob/master/CITATIONS.md +------------------------------------------------------ +ERROR ~ ERROR: Validation of pipeline parameters failed! + + -- Check '.nextflow.log' file for details +The following invalid input values have been detected: + +* Missing required parameter: --outdir + + -- Check script 'nf-core-demo/./subworkflows/local/utils_nfcore_demo_pipeline/../../nf-core/utils_nfvalidation_plugin/main.nf' at line: 57 or see '.nextflow.log' file for more details diff --git a/public/images/contributing/creating_with_nf_core/nfcore_lint_failure.svg b/public/images/contributing/creating_with_nf_core/nfcore_lint_failure.svg index 0ee2413bf7..e65c5a9b92 100644 --- a/public/images/contributing/creating_with_nf_core/nfcore_lint_failure.svg +++ b/public/images/contributing/creating_with_nf_core/nfcore_lint_failure.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ nf-core lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - - -INFO     Testing pipeline: . - - -╭─[!] 1 Pipeline Test Warning────────────────────────────────────────────────────────────────────╮ -││ -│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │ -│doi (after the first release).                                                                  │ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─[✗] 1 Pipeline Test Failed─────────────────────────────────────────────────────────────────────╮ -││ -│files_unchanged: CODE_OF_CONDUCT.md does not match the template                                 │ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - - -╭───────────────────────╮ -│LINT RESULTS SUMMARY │ -├───────────────────────┤ -│[✔] 194 Tests Passed│ -│[?]   0 Tests Ignored│ -│[!]   1 Test Warning│ -│[✗]   1 Test Failed│ -╰───────────────────────╯ - -Tip: Some of these linting errors can automatically be resolved with the following command: - -    nf-core lint   --fix files_unchanged - + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Testing pipeline: . + + +╭─[!] 1 Pipeline Test Warning────────────────────────────────────────────────────────────────────╮ +││ +│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │ +│doi (after the first release).                                                                  │ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─[✗] 1 Pipeline Test Failed─────────────────────────────────────────────────────────────────────╮ +││ +│files_unchanged: CODE_OF_CONDUCT.md does not match the template                                 │ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + +╭─[!] 2 Module Test Warnings─────────────────────────────────────────────────────────────────────╮ +│              ╷                         ╷                                                         │ +│Module name │File path              │Test message                                           │ +│╶─────────────┼─────────────────────────┼────────────────────────────────────────────────────────╴│ +│fastqc│modules/nf-core/fastqc│New version available                                  │ +│multiqc│modules/nf-core/multiqc│New version available                                  │ +│              ╵                         ╵                                                         │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + +╭─[!] 3 Subworkflow Test Warnings────────────────────────────────────────────────────────────────╮ +│                            ╷                                  ╷                                  │ +│Subworkflow name          │File path                       │Test message                    │ +│╶───────────────────────────┼──────────────────────────────────┼─────────────────────────────────╴│ +│utils_nextflow_pipeline│subworkflows/nf-core/utils_next…│New version available           │ +│utils_nfcore_pipeline│subworkflows/nf-core/utils_nfco…│New version available           │ +│utils_nfvalidation_plugin│subworkflows/nf-core/utils_nfva…│New version available           │ +│                            ╵                                  ╵                                  │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭───────────────────────╮ +│LINT RESULTS SUMMARY │ +├───────────────────────┤ +│[✔] 189 Tests Passed│ +│[?]   0 Tests Ignored│ +│[!]   6 Test Warnings│ +│[✗]   1 Test Failed│ +╰───────────────────────╯ + +Tip: Some of these linting errors can automatically be resolved with the following command: + +    nf-core lint   --fix files_unchanged + diff --git a/public/images/contributing/creating_with_nf_core/nfcore_lint_warnings.svg b/public/images/contributing/creating_with_nf_core/nfcore_lint_warnings.svg index 1f423481b3..1761a70f96 100644 --- a/public/images/contributing/creating_with_nf_core/nfcore_lint_warnings.svg +++ b/public/images/contributing/creating_with_nf_core/nfcore_lint_warnings.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - $ nf-core lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - - -INFO     Testing pipeline: . - - -╭─[!] 25 Pipeline Test Warnings──────────────────────────────────────────────────────────────────╮ -││ -│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │ -│doi (after the first release).                                                                  │ -│pipeline_todos: TODO string in README.md: TODO nf-core:│ -│pipeline_todos: TODO string in README.md: Include a figure that guides the user through the │ -│major workflow steps. Many nf-core│ -│pipeline_todos: TODO string in README.md: Fill in short bullet-pointed list of the default steps│ -│in the pipeline│ -│pipeline_todos: TODO string in README.md: Describe the minimum required steps to execute the │ -│pipeline, e.g. how to prepare samplesheets.│ -│pipeline_todos: TODO string in README.md: update the following command to include all required │ -│parameters for a minimal example│ -│pipeline_todos: TODO string in README.md: If applicable, make list of people who have also │ -│contributed│ -│pipeline_todos: TODO string in README.md: Add citation for pipeline after first release. │ -│Uncomment lines below and update Zenodo doi and badge at the top of this file.│ -│pipeline_todos: TODO string in README.md: Add bibliography of tools and data used in your │ -│pipeline│ -│pipeline_todos: TODO string in nextflow.config: Specify your pipeline's command line flags│ -│pipeline_todos: TODO string in main.nf: Remove this line if you don't need a FASTA file│ -│pipeline_todos: TODO string in usage.md: Add documentation about anything specific to running │ -│your pipeline. For general topics, please point to (and add to) the main nf-core website.│ -│pipeline_todos: TODO string in output.md: Write this documentation describing your workflow's │ -│output│ -│pipeline_todos: TODO string in main.nf: Optionally add in-text citation tools to this list.│ -│pipeline_todos: TODO string in main.nf: Optionally add bibliographic entries to this list.│ -│pipeline_todos: TODO string in main.nf: Only uncomment below if logic in │ -│toolCitationText/toolBibliographyText has been filled!│ -│pipeline_todos: TODO string in methods_description_template.yml: #Update the HTML below to your │ -│preferred methods description, e.g. add publication citation for this pipeline│ -│pipeline_todos: TODO string in ci.yml: You can customise CI pipeline run tests as required│ -│pipeline_todos: TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as │ -│required│ -│pipeline_todos: TODO string in test.config: Specify the paths to your test data on │ -│nf-core/test-datasets│ -│pipeline_todos: TODO string in test.config: Give any required params for the test so that │ -│command line flags are not needed│ -│pipeline_todos: TODO string in test_full.config: Specify the paths to your full test data ( on │ -│nf-core/test-datasets or directly in repositories, e.g. SRA)│ -│pipeline_todos: TODO string in test_full.config: Give any required params for the test so that │ -│command line flags are not needed│ -│pipeline_todos: TODO string in base.config: Check the defaults for all processes│ -│pipeline_todos: TODO string in base.config: Customise requirements for specific processes.│ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - - -╭───────────────────────╮ -│LINT RESULTS SUMMARY │ -├───────────────────────┤ -│[✔] 194 Tests Passed│ -│[?]   0 Tests Ignored│ -│[!]  25 Test Warnings│ -│[✗]   0 Tests Failed│ -╰───────────────────────╯ -./README.md -./docs/usage.md -./docs/output.md -./subworkflows/local/utils_nfcore_demo_pipeline/main.nf -./nextflow.config -./main.nf -./.gitpod.yml -./assets/methods_description_template.yml -./.github/workflows/ci.yml -./.github/workflows/awsfulltest.yml -./.github/workflows/release-announcements.yml -./conf/test.config -./conf/test_full.config -./conf/base.config -./.git/hooks/sendemail-validate.sample + + + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Testing pipeline: . + + +╭─[!] 25 Pipeline Test Warnings──────────────────────────────────────────────────────────────────╮ +││ +│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │ +│doi (after the first release).                                                                  │ +│pipeline_todos: TODO string in README.md: TODO nf-core:│ +│pipeline_todos: TODO string in README.md: Include a figure that guides the user through the │ +│major workflow steps. Many nf-core│ +│pipeline_todos: TODO string in README.md: Fill in short bullet-pointed list of the default steps│ +│in the pipeline│ +│pipeline_todos: TODO string in README.md: Describe the minimum required steps to execute the │ +│pipeline, e.g. how to prepare samplesheets.│ +│pipeline_todos: TODO string in README.md: update the following command to include all required │ +│parameters for a minimal example│ +│pipeline_todos: TODO string in README.md: If applicable, make list of people who have also │ +│contributed│ +│pipeline_todos: TODO string in README.md: Add citation for pipeline after first release. │ +│Uncomment lines below and update Zenodo doi and badge at the top of this file.│ +│pipeline_todos: TODO string in README.md: Add bibliography of tools and data used in your │ +│pipeline│ +│pipeline_todos: TODO string in nextflow.config: Specify your pipeline's command line flags│ +│pipeline_todos: TODO string in main.nf: Remove this line if you don't need a FASTA file│ +│pipeline_todos: TODO string in methods_description_template.yml: #Update the HTML below to your │ +│preferred methods description, e.g. add publication citation for this pipeline│ +│pipeline_todos: TODO string in test.config: Specify the paths to your test data on │ +│nf-core/test-datasets│ +│pipeline_todos: TODO string in test.config: Give any required params for the test so that │ +│command line flags are not needed│ +│pipeline_todos: TODO string in test_full.config: Specify the paths to your full test data ( on │ +│nf-core/test-datasets or directly in repositories, e.g. SRA)│ +│pipeline_todos: TODO string in test_full.config: Give any required params for the test so that │ +│command line flags are not needed│ +│pipeline_todos: TODO string in base.config: Check the defaults for all processes│ +│pipeline_todos: TODO string in base.config: Customise requirements for specific processes.│ +│pipeline_todos: TODO string in main.nf: Optionally add in-text citation tools to this list.│ +│pipeline_todos: TODO string in main.nf: Optionally add bibliographic entries to this list.│ +│pipeline_todos: TODO string in main.nf: Only uncomment below if logic in │ +│toolCitationText/toolBibliographyText has been filled!│ +│pipeline_todos: TODO string in ci.yml: You can customise CI pipeline run tests as required│ +│pipeline_todos: TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as │ +│required│ +│pipeline_todos: TODO string in output.md: Write this documentation describing your workflow's │ +│output│ +│pipeline_todos: TODO string in usage.md: Add documentation about anything specific to running │ +│your pipeline. For general topics, please point to (and add to) the main nf-core website.│ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + +╭─[!] 2 Module Test Warnings─────────────────────────────────────────────────────────────────────╮ +│              ╷                         ╷                                                         │ +│Module name │File path              │Test message                                           │ +│╶─────────────┼─────────────────────────┼────────────────────────────────────────────────────────╴│ +│fastqc│modules/nf-core/fastqc│New version available                                  │ +│multiqc│modules/nf-core/multiqc│New version available                                  │ +│              ╵                         ╵                                                         │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + +╭─[!] 3 Subworkflow Test Warnings────────────────────────────────────────────────────────────────╮ +│                            ╷                                  ╷                                  │ +│Subworkflow name          │File path                       │Test message                    │ +│╶───────────────────────────┼──────────────────────────────────┼─────────────────────────────────╴│ +│utils_nextflow_pipeline│subworkflows/nf-core/utils_next…│New version available           │ +│utils_nfcore_pipeline│subworkflows/nf-core/utils_nfco…│New version available           │ +│utils_nfvalidation_plugin│subworkflows/nf-core/utils_nfva…│New version available           │ +│                            ╵                                  ╵                                  │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭───────────────────────╮ +│LINT RESULTS SUMMARY │ +├───────────────────────┤ +│[✔] 189 Tests Passed│ +│[?]   0 Tests Ignored│ +│[!]  30 Test Warnings│ +│[✗]   0 Tests Failed│ +╰───────────────────────╯ +./assets/methods_description_template.yml +./conf/test.config +./conf/test_full.config +./conf/base.config +./subworkflows/local/utils_nfcore_demo_pipeline/main.nf +./.gitpod.yml +./.git/hooks/sendemail-validate.sample +./README.md +./nextflow.config +./.github/workflows/ci.yml +./.github/workflows/awsfulltest.yml +./.github/workflows/release-announcements.yml +./main.nf +./docs/output.md +./docs/usage.md diff --git a/public/images/contributing/creating_with_nf_core/nfcore_list.svg b/public/images/contributing/creating_with_nf_core/nfcore_list.svg index 6aecb344bf..08cfb32aae 100644 --- a/public/images/contributing/creating_with_nf_core/nfcore_list.svg +++ b/public/images/contributing/creating_with_nf_core/nfcore_list.svg @@ -19,91 +19,91 @@ font-weight: 700; } - .terminal-3002242082-matrix { + .terminal-4067787406-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3002242082-title { + .terminal-4067787406-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3002242082-r1 { fill: #c5c8c6 } -.terminal-3002242082-r2 { fill: #98a84b } -.terminal-3002242082-r3 { fill: #9a9b99 } -.terminal-3002242082-r4 { fill: #608ab1 } -.terminal-3002242082-r5 { fill: #d0b344 } -.terminal-3002242082-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3002242082-r7 { fill: #868887 } -.terminal-3002242082-r8 { fill: #868887;font-style: italic; } + .terminal-4067787406-r1 { fill: #c5c8c6 } +.terminal-4067787406-r2 { fill: #98a84b } +.terminal-4067787406-r3 { fill: #9a9b99 } +.terminal-4067787406-r4 { fill: #608ab1 } +.terminal-4067787406-r5 { fill: #d0b344 } +.terminal-4067787406-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-4067787406-r7 { fill: #868887 } +.terminal-4067787406-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +115,30 @@ - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ multiplesequenceal… │    11 │            dev │  22 hours ago │           - │ -                   │ -│ raredisease         │    72 │          2.0.1 │  2 months ago │           - │ -                   │ -│ oncoanalyser        │    15 │            dev │     yesterday │           - │ -                   │ -│ taxprofiler         │    93 │          1.1.7 │   3 weeks ago │           - │ -                   │ -│ fastquorum          │    11 │            dev │     yesterday │           - │ -                   │ -[..truncated..] + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name     ┃Stars┃Latest Release┃      Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ scnanoseq          │    13 │            dev │ 56 minutes ago │           - │ -                   │ +│ magmap             │     3 │            dev │    an hour ago │           - │ -                   │ +│ chipseq            │   188 │          2.0.0 │    2 years ago │           - │ -                   │ +│ demultiplex        │    43 │          1.5.1 │   2 months ago │           - │ -                   │ +│ crisprseq          │    25 │          2.2.1 │   3 months ago │           - │ -                   │ +[..truncated..] diff --git a/public/images/contributing/modules/nf-core-modules-create.svg b/public/images/contributing/modules/nf-core-modules-create.svg index 4524441515..65b67ce978 100644 --- a/public/images/contributing/modules/nf-core-modules-create.svg +++ b/public/images/contributing/modules/nf-core-modules-create.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - $ nf-core modules create fastqc --author @janedoe --label process_low --meta -Cloning into 'modules'... - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - - -INFO     Repository type: modules -INFO    Press enter to use default values (shown in brackets)or type your own responses.  -ctrl+click underlined text to open links. -CRITICAL module directory exists: 'modules/nf-core/fastqc'. Use '--force' to overwrite               + + + + $ nf-core modules create fastqc --author @janedoe --label process_low --meta +Cloning into 'modules'... + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Repository type: modules +INFO    Press enter to use default values (shown in brackets)or type your own responses.  +ctrl+click underlined text to open links. +INFO     Using Bioconda package: 'bioconda::fastqc=0.12.1' +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/public/images/tools/nf-core-download.svg b/public/images/tools/nf-core-download.svg index 8adf547319..916602ed37 100644 --- a/public/images/tools/nf-core-download.svg +++ b/public/images/tools/nf-core-download.svg @@ -19,86 +19,85 @@ font-weight: 700; } - .terminal-2020865193-matrix { + .terminal-2541483181-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2020865193-title { + .terminal-2541483181-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2020865193-r1 { fill: #c5c8c6 } -.terminal-2020865193-r2 { fill: #98a84b } -.terminal-2020865193-r3 { fill: #9a9b99 } -.terminal-2020865193-r4 { fill: #608ab1 } -.terminal-2020865193-r5 { fill: #d0b344 } -.terminal-2020865193-r6 { fill: #cc555a } + .terminal-2541483181-r1 { fill: #c5c8c6 } +.terminal-2541483181-r2 { fill: #98a84b } +.terminal-2541483181-r3 { fill: #9a9b99 } +.terminal-2541483181-r4 { fill: #608ab1 } +.terminal-2541483181-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -110,29 +109,29 @@ - + - - $ mkdir tmp && cd tmp && nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - -WARNING  Could not find GitHub authentication token. Some API requests may fail.                     -INFO     Saving 'nf-core/rnaseq' -          Pipeline revision: '3.8' -          Use containers: 'none' -          Container library: 'quay.io' -          Output directory: 'nf-core-rnaseq' -          Include default institutional configuration: 'True' -INFO     Downloading centralised configs from GitHub                                                 -INFO     Downloading workflow files from GitHub                                                      + + $ mkdir tmp && cd tmp && nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +WARNING  Could not find GitHub authentication token. Some API requests may fail.                     +INFO     Saving 'nf-core/rnaseq' +          Pipeline revision: '3.8' +          Use containers: 'none' +          Container library: 'quay.io' +          Output directory: 'nf-core-rnaseq' +          Include default institutional configuration: 'True' +INFO     Downloading centralised configs from GitHub                                                 +INFO     Downloading workflow files from GitHub                                                      diff --git a/public/images/tools/nf-core-lint.svg b/public/images/tools/nf-core-lint.svg index bb7b6b879e..4c006fd171 100644 --- a/public/images/tools/nf-core-lint.svg +++ b/public/images/tools/nf-core-lint.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ nf-core lint - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - - -INFO     Testing pipeline: . - - -╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ -││ -│pipeline_todos: pipeline_todos                                                                  │ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─[!] 1 Pipeline Test Warning────────────────────────────────────────────────────────────────────╮ -││ -│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │ -│doi (after the first release).                                                                  │ -││ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - - -╭──────────────────────╮ -│LINT RESULTS SUMMARY│ -├──────────────────────┤ -│[✔] 194 Tests Passed│ -│[?]   1 Test Ignored│ -│[!]   1 Test Warning│ -│[✗]   0 Tests Failed│ -╰──────────────────────╯ + + $ nf-core lint + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Testing pipeline: . + + +╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮ +││ +│pipeline_todos: pipeline_todos                                                                  │ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─[!] 1 Pipeline Test Warning────────────────────────────────────────────────────────────────────╮ +││ +│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │ +│doi (after the first release).                                                                  │ +││ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + +╭─[!] 2 Module Test Warnings─────────────────────────────────────────────────────────────────────╮ +│              ╷                         ╷                                                         │ +│Module name │File path              │Test message                                           │ +│╶─────────────┼─────────────────────────┼────────────────────────────────────────────────────────╴│ +│fastqc│modules/nf-core/fastqc│New version available                                  │ +│multiqc│modules/nf-core/multiqc│New version available                                  │ +│              ╵                         ╵                                                         │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + +╭─[!] 3 Subworkflow Test Warnings────────────────────────────────────────────────────────────────╮ +│                            ╷                                  ╷                                  │ +│Subworkflow name          │File path                       │Test message                    │ +│╶───────────────────────────┼──────────────────────────────────┼─────────────────────────────────╴│ +│utils_nextflow_pipeline│subworkflows/nf-core/utils_next…│New version available           │ +│utils_nfcore_pipeline│subworkflows/nf-core/utils_nfco…│New version available           │ +│utils_nfvalidation_plugin│subworkflows/nf-core/utils_nfva…│New version available           │ +│                            ╵                                  ╵                                  │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭───────────────────────╮ +│LINT RESULTS SUMMARY │ +├───────────────────────┤ +│[✔] 189 Tests Passed│ +│[?]   1 Test Ignored│ +│[!]   6 Test Warnings│ +│[✗]   0 Tests Failed│ +╰───────────────────────╯ diff --git a/public/images/tools/nf-core-list-rna.svg b/public/images/tools/nf-core-list-rna.svg index 07869eac20..beb247cd83 100644 --- a/public/images/tools/nf-core-list-rna.svg +++ b/public/images/tools/nf-core-list-rna.svg @@ -19,114 +19,114 @@ font-weight: 700; } - .terminal-903957491-matrix { + .terminal-1343444112-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-903957491-title { + .terminal-1343444112-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-903957491-r1 { fill: #c5c8c6 } -.terminal-903957491-r2 { fill: #98a84b } -.terminal-903957491-r3 { fill: #9a9b99 } -.terminal-903957491-r4 { fill: #608ab1 } -.terminal-903957491-r5 { fill: #d0b344 } -.terminal-903957491-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-903957491-r7 { fill: #868887 } + .terminal-1343444112-r1 { fill: #c5c8c6 } +.terminal-1343444112-r2 { fill: #98a84b } +.terminal-1343444112-r3 { fill: #9a9b99 } +.terminal-1343444112-r4 { fill: #608ab1 } +.terminal-1343444112-r5 { fill: #d0b344 } +.terminal-1343444112-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1343444112-r7 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -138,38 +138,38 @@ - + - - $ nf-core list rna rna-seq - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ spatialvi           │    39 │            dev │    2 days ago │           - │ -                   │ -│ scnanoseq           │     5 │            dev │    4 days ago │           - │ -                   │ -│ rnafusion           │   130 │          3.0.2 │  1 months ago │           - │ -                   │ -│ rnaseq              │   792 │         3.14.0 │  4 months ago │           - │ -                   │ -│ rnasplice           │    34 │          1.0.4 │   2 weeks ago │           - │ -                   │ -│ circrna             │    40 │            dev │   2 weeks ago │           - │ -                   │ -│ differentialabunda… │    46 │          1.5.0 │   2 weeks ago │           - │ -                   │ -│ smrnaseq            │    68 │          2.3.1 │  1 months ago │           - │ -                   │ -│ scrnaseq            │   169 │          2.6.0 │   2 weeks ago │           - │ -                   │ -│ dualrnaseq          │    16 │          1.0.0 │   3 years ago │           - │ -                   │ -│ marsseq             │     5 │          1.0.3 │ 10 months ago │           - │ -                   │ -│ lncpipe             │    30 │            dev │   2 years ago │           - │ -                   │ -│ scflow              │    24 │            dev │   3 years ago │           - │ -                   │ -└─────────────────────┴───────┴────────────────┴───────────────┴─────────────┴─────────────────────┘ + + $ nf-core list rna rna-seq + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name     ┃Stars┃Latest Release┃      Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ scnanoseq          │    13 │            dev │ 58 minutes ago │           - │ -                   │ +│ smrnaseq           │    73 │          2.3.1 │   6 months ago │           - │ -                   │ +│ rnaseq             │   879 │         3.16.0 │     4 days ago │           - │ -                   │ +│ circrna            │    44 │            dev │    2 weeks ago │           - │ -                   │ +│ scrnaseq           │   210 │          2.7.1 │   2 months ago │           - │ -                   │ +│ spatialvi          │    49 │            dev │   1 months ago │           - │ -                   │ +│ rnasplice          │    42 │          1.0.4 │   5 months ago │           - │ -                   │ +│ denovotranscript   │     3 │          1.0.0 │   2 months ago │           - │ -                   │ +│ rnafusion          │   138 │          3.0.2 │   6 months ago │           - │ -                   │ +│ differentialabund… │    57 │          1.5.0 │   5 months ago │           - │ -                   │ +│ dualrnaseq         │    18 │          1.0.0 │    4 years ago │           - │ -                   │ +│ marsseq            │     5 │          1.0.3 │    1 years ago │           - │ -                   │ +│ lncpipe            │    33 │            dev │    2 years ago │           - │ -                   │ +└────────────────────┴───────┴────────────────┴────────────────┴─────────────┴─────────────────────┘ diff --git a/public/images/tools/nf-core-list-stars.svg b/public/images/tools/nf-core-list-stars.svg index fef6b77c33..93572521f8 100644 --- a/public/images/tools/nf-core-list-stars.svg +++ b/public/images/tools/nf-core-list-stars.svg @@ -19,88 +19,88 @@ font-weight: 700; } - .terminal-2331965736-matrix { + .terminal-1180432830-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2331965736-title { + .terminal-1180432830-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2331965736-r1 { fill: #c5c8c6 } -.terminal-2331965736-r2 { fill: #98a84b } -.terminal-2331965736-r3 { fill: #9a9b99 } -.terminal-2331965736-r4 { fill: #608ab1 } -.terminal-2331965736-r5 { fill: #d0b344 } -.terminal-2331965736-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2331965736-r7 { fill: #868887 } -.terminal-2331965736-r8 { fill: #868887;font-style: italic; } + .terminal-1180432830-r1 { fill: #c5c8c6 } +.terminal-1180432830-r2 { fill: #98a84b } +.terminal-1180432830-r3 { fill: #9a9b99 } +.terminal-1180432830-r4 { fill: #608ab1 } +.terminal-1180432830-r5 { fill: #d0b344 } +.terminal-1180432830-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1180432830-r7 { fill: #868887 } +.terminal-1180432830-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -112,29 +112,29 @@ - + - - $ nf-core list -s stars - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ rnaseq              │   792 │         3.14.0 │  4 months ago │           - │ -                   │ -│ sarek               │   340 │          3.4.2 │   2 weeks ago │           - │ -                   │ -│ mag                 │   182 │          3.0.0 │   1 weeks ago │           - │ -                   │ -│ chipseq             │   172 │          2.0.0 │   2 years ago │           - │ -                   │ -[..truncated..] + + $ nf-core list -s stars + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name     ┃Stars┃Latest Release┃      Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ rnaseq             │   879 │         3.16.0 │     4 days ago │           - │ -                   │ +│ sarek              │   395 │          3.4.4 │   1 months ago │           - │ -                   │ +│ scrnaseq           │   210 │          2.7.1 │   2 months ago │           - │ -                   │ +│ mag                │   209 │          3.1.0 │     3 days ago │           - │ -                   │ +[..truncated..] diff --git a/public/images/tools/nf-core-list.svg b/public/images/tools/nf-core-list.svg index 6aecb344bf..08cfb32aae 100644 --- a/public/images/tools/nf-core-list.svg +++ b/public/images/tools/nf-core-list.svg @@ -19,91 +19,91 @@ font-weight: 700; } - .terminal-3002242082-matrix { + .terminal-4067787406-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3002242082-title { + .terminal-4067787406-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3002242082-r1 { fill: #c5c8c6 } -.terminal-3002242082-r2 { fill: #98a84b } -.terminal-3002242082-r3 { fill: #9a9b99 } -.terminal-3002242082-r4 { fill: #608ab1 } -.terminal-3002242082-r5 { fill: #d0b344 } -.terminal-3002242082-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-3002242082-r7 { fill: #868887 } -.terminal-3002242082-r8 { fill: #868887;font-style: italic; } + .terminal-4067787406-r1 { fill: #c5c8c6 } +.terminal-4067787406-r2 { fill: #98a84b } +.terminal-4067787406-r3 { fill: #9a9b99 } +.terminal-4067787406-r4 { fill: #608ab1 } +.terminal-4067787406-r5 { fill: #d0b344 } +.terminal-4067787406-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-4067787406-r7 { fill: #868887 } +.terminal-4067787406-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +115,30 @@ - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - -┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ -┃┃┃┃┃┃Have latest        ┃ -┃Pipeline Name      ┃Stars┃Latest Release┃     Released┃Last Pulled┃release?           ┃ -┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ -│ multiplesequenceal… │    11 │            dev │  22 hours ago │           - │ -                   │ -│ raredisease         │    72 │          2.0.1 │  2 months ago │           - │ -                   │ -│ oncoanalyser        │    15 │            dev │     yesterday │           - │ -                   │ -│ taxprofiler         │    93 │          1.1.7 │   3 weeks ago │           - │ -                   │ -│ fastquorum          │    11 │            dev │     yesterday │           - │ -                   │ -[..truncated..] + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +┏━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ +┃┃┃┃┃┃Have latest        ┃ +┃Pipeline Name     ┃Stars┃Latest Release┃      Released┃Last Pulled┃release?           ┃ +┡━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ +│ scnanoseq          │    13 │            dev │ 56 minutes ago │           - │ -                   │ +│ magmap             │     3 │            dev │    an hour ago │           - │ -                   │ +│ chipseq            │   188 │          2.0.0 │    2 years ago │           - │ -                   │ +│ demultiplex        │    43 │          1.5.1 │   2 months ago │           - │ -                   │ +│ crisprseq          │    25 │          2.2.1 │   3 months ago │           - │ -                   │ +[..truncated..] diff --git a/public/images/tools/nf-core-modules-bump-version.svg b/public/images/tools/nf-core-modules-bump-version.svg index e5d72cf8e9..c71a3091f8 100644 --- a/public/images/tools/nf-core-modules-bump-version.svg +++ b/public/images/tools/nf-core-modules-bump-version.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + - + - + - - $ nf-core modules bump-version fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - - -Usage:nf-core modules [OPTIONS] COMMAND [ARGS]...                                                  - -Try'nf-core modules -h'for help -╭─ Error ──────────────────────────────────────────────────────────────────────────────────────────╮ -│ No such command 'bump-version'.                                                                  │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - + + $ nf-core modules bump-versions fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + + +╭──────────────────────────────────────────────────────────────────────────────────────────────────╮ +│[!] 1 Module version up to date.│ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮ +│Module name                             │Update Message                                       │ +├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤ +│ fastqc                                   │ Module version up to date: fastqc                     │ +╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯ diff --git a/public/images/tools/nf-core-modules-create.svg b/public/images/tools/nf-core-modules-create.svg index 0117304827..e412affc1e 100644 --- a/public/images/tools/nf-core-modules-create.svg +++ b/public/images/tools/nf-core-modules-create.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force -Cloning into 'modules'... - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - - -INFO     Repository type: modules -INFO    Press enter to use default values (shown in brackets)or type your own responses.  -ctrl+click underlined text to open links. -INFO     Using Bioconda package: 'bioconda::fastqc=0.12.1' + + $ nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force +Cloning into 'modules'... + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Repository type: modules +INFO    Press enter to use default values (shown in brackets)or type your own responses.  +ctrl+click underlined text to open links. +INFO     Using Bioconda package: 'bioconda::fastqc=0.12.1' +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/public/images/tools/nf-core-modules-info.svg b/public/images/tools/nf-core-modules-info.svg index cc0cf02fdf..b5803c953b 100644 --- a/public/images/tools/nf-core-modules-info.svg +++ b/public/images/tools/nf-core-modules-info.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - $ nf-core modules info abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - - -╭─ Module: abacas  ────────────────────────────────────────────────────────────────────────────────╮ -│ 🌐 Repository: https://github.com/nf-core/modules.git                                            │ -│ 🔧 Tools: abacas                                                                                 │ -│ 📖 Description: contiguate draft genome assembly                                                 │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -                  ╷                                                                   ╷              -📥 Inputs        │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - scaffold  (file)│Fasta file containing scaffold                                     │*.{fasta,fa} -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - fasta  (file)   │FASTA reference file                                               │*.{fasta,fa} -                  ╵                                                                   ╵              -                  ╷                                                                   ╷              -📤 Outputs       │Description                                                        │     Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [ id:'test',         │ -                  │single_end:false ]                                                 │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - results  (file) │List containing abacas output files [ 'test.abacas.bin',           │ *.{abacas}* -                  │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab',   │ -                  │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta',   │ -                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',                    │ -                  │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ]    │ -╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴ - versions  (file)│File containing software versions                                  │versions.yml -                  ╵                                                                   ╵              - - 💻  Installation command: nf-core modules install abacas - + + + + $ nf-core modules info abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +╭───────────────────────────────Traceback (most recent call last)────────────────────────────────╮ +│/opt/hostedtoolcache/Python/3.12.6/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/3.12.6/x64/lib/python3.12/site-packages/nf_core/__main__.py:150 in   │ +│run_nf_core│ +││ +│ 147 │   │   │   log.debug(f"Could not check latest version: {e}")                             │ +│ 148 │   │   stderr.print("\n")                                                                │ +│ 149 │   # Launch the click cli│ +│❱  150 │   nf_core_cli(auto_envvar_prefix="NFCORE")│ +│ 151 │ +│ 152 │ +│ 153 @tui()                                                                                    │ +││ +│/opt/hostedtoolcache/Python/3.12.6/x64/lib/python3.12/site-packages/rich_click/rich_command.py:3│ +│67 in __call__│ +││ +│364 │   │   # Include this here because I run into a false warning│ +│365 │   │   # in the PyCharm IDE otherwise; for some reason PyCharm doesn't│ +│366 │   │   # seem to think RichGroups are callable. (No issues with Mypy, though.)│ +│❱ 367 │   │   returnsuper().__call__(*args, **kwargs)│ +│368 │ +│369 │ +│370 classRichCommandCollection(CommandCollection, RichGroup):                                 │ +││ +│/opt/hostedtoolcache/Python/3.12.6/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/3.12.6/x64/lib/python3.12/site-packages/rich_click/rich_command.py:1│ +│52 in main│ +││ +│149 │   │   try:                                                                               │ +│150 │   │   │   try:                                                                           │ +│151 │   │   │   │   withself.make_context(prog_name, args, **extra) as ctx:                   │ +│❱ 152 │   │   │   │   │   rv = self.invoke(ctx)                                                  │ +│153 │   │   │   │   │   ifnot standalone_mode:                                                │ +│154 │   │   │   │   │   │   return rv                                                          │ +│155 │   │   │   │   │   # it's not safe to `ctx.exit(rv)` here!│ +││ +│/opt/hostedtoolcache/Python/3.12.6/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/3.12.6/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/3.12.6/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 │   │   │   returnctx.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/3.12.6/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/3.12.6/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 │   │   returnf(get_current_context(), *args, **kwargs)│ +│ 34 │   │ +│ 35 │   return update_wrapper(new_func, f)                                                     │ +│ 36 │ +││ +│/opt/hostedtoolcache/Python/3.12.6/x64/lib/python3.12/site-packages/nf_core/__main__.py:1318 in  │ +│modules_info│ +││ +│1315 │   │   │   ctx.obj["modules_repo_branch"],                                               │ +│1316 │   │   │   ctx.obj["modules_repo_no_pull"],                                              │ +│1317 │   │   )                                                                                 │ +│❱ 1318 │   │   stdout.print(module_info.get_component_info())                                    │ +│1319 │   except (UserWarning, LookupError) as e:│ +│1320 │   │   log.error(e)│ +│1321 │   │   sys.exit(1)│ +││ +│/opt/hostedtoolcache/Python/3.12.6/x64/lib/python3.12/site-packages/nf_core/components/info.py:1│ +│63 in get_component_info│ +││ +│160 │   │   ifself.meta isFalse:                                                             │ +│161 │   │   │   raiseUserWarning(f"Could not find {self.component_type[:-1]}'{self.compone   │ +│162 │   │   │ +│❱ 163 │   │   returnself.generate_component_info_help()│ +│164 │   │ +│165 │   defget_local_yaml(self):                                                              │ +│166 │   │   """Attempt to get the meta.yml file from a locally installed module/subworkflow.│ +││ +│/opt/hostedtoolcache/Python/3.12.6/x64/lib/python3.12/site-packages/nf_core/components/info.py:2│ +│74 in generate_component_info_help│ +││ +│271 │   │   │   inputs_table.add_column("Description")                                         │ +│272 │   │   │   inputs_table.add_column("Pattern", justify="right", style="green")             │ +│273 │   │   │   forinputinself.meta["input"]:                                               │ +│❱ 274 │   │   │   │   for key, info ininput.items():                                            │ +│275 │   │   │   │   │   inputs_table.add_row(                                                  │ +│276 │   │   │   │   │   │   f"[orange1 on black] {key} [/][dim i] ({info['type']})",           │ +│277 │   │   │   │   │   │   Markdown(info["description"] if info["description"] else""),      │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +AttributeError: 'list' object has no attribute 'items' diff --git a/public/images/tools/nf-core-modules-lint.svg b/public/images/tools/nf-core-modules-lint.svg index c6609a74ec..468bc539d3 100644 --- a/public/images/tools/nf-core-modules-lint.svg +++ b/public/images/tools/nf-core-modules-lint.svg @@ -19,27 +19,27 @@ font-weight: 700; } - .terminal-1377187411-matrix { + .terminal-1131360812-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1377187411-title { + .terminal-1131360812-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1377187411-r1 { fill: #c5c8c6 } + .terminal-1131360812-r1 { fill: #c5c8c6 } - + - + @@ -51,11 +51,11 @@ - + - - $ nf-core modules lint multiqc -/bin/sh: 2: cannot create modules/multiqc/main.nf.tmp: Directory nonexistent + + $ nf-core modules lint multiqc +sed: can't read modules/multiqc/main.nf: No such file or directory diff --git a/public/images/tools/nf-core-modules-patch.svg b/public/images/tools/nf-core-modules-patch.svg index f1d6dd9e37..c311ab4e17 100644 --- a/public/images/tools/nf-core-modules-patch.svg +++ b/public/images/tools/nf-core-modules-patch.svg @@ -19,127 +19,127 @@ font-weight: 700; } - .terminal-1056123978-matrix { + .terminal-2877172810-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1056123978-title { + .terminal-2877172810-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1056123978-r1 { fill: #c5c8c6 } -.terminal-1056123978-r2 { fill: #98a84b } -.terminal-1056123978-r3 { fill: #9a9b99 } -.terminal-1056123978-r4 { fill: #608ab1 } -.terminal-1056123978-r5 { fill: #d0b344 } -.terminal-1056123978-r6 { fill: #ff2627 } -.terminal-1056123978-r7 { fill: #00823d } -.terminal-1056123978-r8 { fill: #ff2c7a;font-weight: bold } + .terminal-2877172810-r1 { fill: #c5c8c6 } +.terminal-2877172810-r2 { fill: #98a84b } +.terminal-2877172810-r3 { fill: #9a9b99 } +.terminal-2877172810-r4 { fill: #608ab1 } +.terminal-2877172810-r5 { fill: #d0b344 } +.terminal-2877172810-r6 { fill: #ff2627 } +.terminal-2877172810-r7 { fill: #00823d } +.terminal-2877172810-r8 { fill: #ff2c7a;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -151,42 +151,42 @@ - + - - $ nf-core modules patch fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - - -INFO     Changes in module 'nf-core/fastqc' -INFO     Changes in 'fastqc/main.nf':                                                                - ---- modules/nf-core/fastqc/main.nf -+++ modules/nf-core/fastqc/main.nf -@@ -1,6 +1,6 @@ -process FASTQC {                                                                                   -    tag "$meta.id"                                                                                 --    label 'process_medium' -+    label 'process_low' - -    conda "${moduleDir}/environment.yml"                                                           -    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_  - - -INFO    'modules/nf-core/fastqc/environment.yml' is unchanged                                       -INFO    'modules/nf-core/fastqc/meta.yml' is unchanged                                              -INFO    'modules/nf-core/fastqc/tests/tags.yml' is unchanged                                        -INFO    'modules/nf-core/fastqc/tests/main.nf.test.snap' is unchanged                               -INFO    'modules/nf-core/fastqc/tests/main.nf.test' is unchanged                                    -INFO     Patch file of 'modules/nf-core/fastqc' written to 'modules/nf-core/fastqc/fastqc.diff' + + $ nf-core modules patch fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Changes in module 'nf-core/fastqc' +INFO    'modules/nf-core/fastqc/environment.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/meta.yml' is unchanged                                              +INFO    'modules/nf-core/fastqc/tests/tags.yml' is unchanged                                        +INFO    'modules/nf-core/fastqc/tests/main.nf.test.snap' is unchanged                               +INFO    'modules/nf-core/fastqc/tests/main.nf.test' is unchanged                                    +INFO     Patch file of 'modules/nf-core/fastqc' written to 'modules/nf-core/fastqc/fastqc.diff' diff --git a/public/images/tools/nf-core-modules-update.svg b/public/images/tools/nf-core-modules-update.svg index c4800530ef..3c77bd4dc2 100644 --- a/public/images/tools/nf-core-modules-update.svg +++ b/public/images/tools/nf-core-modules-update.svg @@ -19,73 +19,73 @@ font-weight: 700; } - .terminal-3074160147-matrix { + .terminal-3933203507-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3074160147-title { + .terminal-3933203507-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3074160147-r1 { fill: #c5c8c6 } -.terminal-3074160147-r2 { fill: #98a84b } -.terminal-3074160147-r3 { fill: #9a9b99 } -.terminal-3074160147-r4 { fill: #608ab1 } -.terminal-3074160147-r5 { fill: #d0b344 } + .terminal-3933203507-r1 { fill: #c5c8c6 } +.terminal-3933203507-r2 { fill: #98a84b } +.terminal-3933203507-r3 { fill: #9a9b99 } +.terminal-3933203507-r4 { fill: #608ab1 } +.terminal-3933203507-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -97,25 +97,25 @@ - + - - $ nf-core modules update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - - -INFO    'modules/nf-core/abacas' is already up to date                                              -INFO    'modules/nf-core/fastqc' is already up to date                                              -INFO    'modules/nf-core/multiqc' is already up to date                                             -INFO     Updates complete ✨                                                                         + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO    'modules/nf-core/abacas' is already up to date                                              +INFO     Updating 'nf-core/fastqc' +INFO     Updating 'nf-core/multiqc' +INFO     Updates complete ✨                                                                         diff --git a/public/images/tools/nf-core-schema-build.svg b/public/images/tools/nf-core-schema-build.svg index cb46e6223e..646243917b 100644 --- a/public/images/tools/nf-core-schema-build.svg +++ b/public/images/tools/nf-core-schema-build.svg @@ -1,4 +1,4 @@ - + - - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ nf-core schema build --no-prompts -sed: can't read 25,30d: No such file or directory + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +INFO    [✓] Default parameters match schema validation +INFO    [✓] Pipeline schema looks valid(found 31 params) +INFO     Writing schema with 32 params: 'nextflow_schema.json' diff --git a/public/images/tools/nf-core-subworkflows-lint.svg b/public/images/tools/nf-core-subworkflows-lint.svg index 3607349e76..ec9a687c20 100644 --- a/public/images/tools/nf-core-subworkflows-lint.svg +++ b/public/images/tools/nf-core-subworkflows-lint.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - + - + - - $ nf-core subworkflows lint bam_stats_samtools - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - - -INFO     Linting modules repo: '.' -INFO     Linting subworkflow: 'bam_stats_samtools' - -╭─[!] 15 Subworkflow Test Warnings───────────────────────────────────────────────────────────────╮ -│                     ╷                                     ╷                                      │ -│Subworkflow name   │File path                          │Test message                        │ -│╶────────────────────┼─────────────────────────────────────┼─────────────────────────────────────╴│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: //Add │ -│││all required assertions to verify │ -│││the test output.│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Add │ -│││tags for all modules used within │ -│││this subworkflow. Example:│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Change │ -│││the test name preferably indicating │ -│││the test-data and file-format used│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: Once │ -│││you have added the required tests, │ -│││please run the following command to │ -│││build this file:│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf.test: define │ -│││inputs of the workflow here. │ -│││Example:│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: A │ -│││subworkflow SHOULD import at least │ -│││two modules│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: If in doubt │ -│││look at other nf-core/subworkflows │ -│││to see how we are doing things! :)│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit emitted│ -│││channels│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: edit input │ -│││(take) channels│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in main.nf: substitute │ -│││modules here for the modules of your│ -│││subworkflow│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a │ -│││description of the subworkflow and │ -│││list keywords│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #Add a list│ -│││of the modules and/or subworkflows │ -│││used in the subworkflow│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ -│││of the channels used as input with a│ -│││description and their structure│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│TODO string in meta.yml: #List all │ -│││of the channels used as output with │ -│││a descriptions and their structure│ -│bam_stats_samtools │subworkflows/nf-core/bam_stats_sam…│versions not found in snapshot file │ -│                     ╵                                     ╵                                      │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭───────────────────────╮ -│LINT RESULTS SUMMARY│ -├───────────────────────┤ -│[✔]  42 Tests Passed │ -│[!]  15 Test Warnings│ -│[✗]   0 Tests Failed │ -╰───────────────────────╯ + + $ nf-core subworkflows lint bam_stats_samtools + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Linting modules repo: '.' +INFO     Linting subworkflow: 'bam_stats_samtools' + +╭─[!] 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│ +├───────────────────────┤ +│[✔]  37 Tests Passed │ +│[!]  14 Test Warnings│ +│[✗]   0 Tests Failed │ +╰───────────────────────╯ diff --git a/public/images/tools/nf-core-subworkflows-list-remote.svg b/public/images/tools/nf-core-subworkflows-list-remote.svg index 8b7d4e803c..155ff44ba3 100644 --- a/public/images/tools/nf-core-subworkflows-list-remote.svg +++ b/public/images/tools/nf-core-subworkflows-list-remote.svg @@ -19,109 +19,109 @@ font-weight: 700; } - .terminal-1319064317-matrix { + .terminal-2951307911-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1319064317-title { + .terminal-2951307911-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1319064317-r1 { fill: #c5c8c6 } -.terminal-1319064317-r2 { fill: #98a84b } -.terminal-1319064317-r3 { fill: #9a9b99 } -.terminal-1319064317-r4 { fill: #608ab1 } -.terminal-1319064317-r5 { fill: #d0b344 } -.terminal-1319064317-r6 { fill: #1984e9;text-decoration: underline; } -.terminal-1319064317-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-1319064317-r8 { fill: #868887;font-style: italic; } + .terminal-2951307911-r1 { fill: #c5c8c6 } +.terminal-2951307911-r2 { fill: #98a84b } +.terminal-2951307911-r3 { fill: #9a9b99 } +.terminal-2951307911-r4 { fill: #608ab1 } +.terminal-2951307911-r5 { fill: #d0b344 } +.terminal-2951307911-r6 { fill: #1984e9;text-decoration: underline; } +.terminal-2951307911-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2951307911-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core subworkflows list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - - -INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -┃Subworkflow Name                             ┃ -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ bam_cnv_wisecondorx                           │ -│ bam_create_som_pon_gatk                       │ -│ bam_dedup_stats_samtools_umicollapse          │ -│ bam_dedup_stats_samtools_umitools             │ -│ bam_docounts_contamination_angsd              │ -│ bam_markduplicates_picard                     │ -│ bam_markduplicates_samtools                   │ -│ bam_ngscheckmate                              │ -│ bam_qc_picard                                 │ -[..truncated..] + + $ nf-core subworkflows list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO     Subworkflows available from https://github.com/nf-core/modules.git(master):                + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +┃Subworkflow Name                                ┃ +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ bam_cnv_wisecondorx                              │ +│ bam_create_som_pon_gatk                          │ +│ bam_dedup_stats_samtools_umicollapse             │ +│ bam_dedup_stats_samtools_umitools                │ +│ bam_docounts_contamination_angsd                 │ +│ bam_markduplicates_picard                        │ +│ bam_markduplicates_samtools                      │ +│ bam_ngscheckmate                                 │ +│ bam_qc_picard                                    │ +[..truncated..] diff --git a/public/images/tools/nf-core-subworkflows-update.svg b/public/images/tools/nf-core-subworkflows-update.svg index d407a9d2e9..261e3a0cd1 100644 --- a/public/images/tools/nf-core-subworkflows-update.svg +++ b/public/images/tools/nf-core-subworkflows-update.svg @@ -19,76 +19,76 @@ font-weight: 700; } - .terminal-2940036566-matrix { + .terminal-1655525929-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2940036566-title { + .terminal-1655525929-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2940036566-r1 { fill: #c5c8c6 } -.terminal-2940036566-r2 { fill: #98a84b } -.terminal-2940036566-r3 { fill: #9a9b99 } -.terminal-2940036566-r4 { fill: #608ab1 } -.terminal-2940036566-r5 { fill: #d0b344 } + .terminal-1655525929-r1 { fill: #c5c8c6 } +.terminal-1655525929-r2 { fill: #98a84b } +.terminal-1655525929-r3 { fill: #9a9b99 } +.terminal-1655525929-r4 { fill: #608ab1 } +.terminal-1655525929-r5 { fill: #d0b344 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -100,26 +100,26 @@ - + - - $ nf-core subworkflows update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - - -INFO    'subworkflows/nf-core/bam_rseqc' is already up to date                                      -INFO    'subworkflows/nf-core/utils_nextflow_pipeline' is already up to date                        -INFO    'subworkflows/nf-core/utils_nfcore_pipeline' is already up to date                          -INFO    'subworkflows/nf-core/utils_nfvalidation_plugin' is already up to date                      -INFO     Updates complete ✨                                                                         + + $ nf-core subworkflows update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + + +INFO    'subworkflows/nf-core/bam_rseqc' is already up to date                                      +INFO     Updating 'nf-core/utils_nextflow_pipeline' +INFO     Updating 'nf-core/utils_nfcore_pipeline' +INFO     Updating 'nf-core/utils_nfvalidation_plugin' +INFO     Updates complete ✨                                                                         diff --git a/public/images/tools/nf-core-sync.svg b/public/images/tools/nf-core-sync.svg index c25c06767f..7f14026163 100644 --- a/public/images/tools/nf-core-sync.svg +++ b/public/images/tools/nf-core-sync.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + - + - + - - $ nf-core sync -[master 42c1f0f] Bump version - 3 files changed, 4 insertions(+), 3 deletions(-) - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.14.1 - https://nf-co.re - - -WARNING  Could not find GitHub authentication token. Some API requests may fail.                     -INFO     Pipeline directory: /home/runner/work/website/website/tmp/nf-core-nextbigthing -INFO     Original pipeline repository branch is 'master' -ERROR    Uncommitted changes found in pipeline directory!                                            -         Please commit these before running nf-core sync                                             + + $ nf-core sync +[master 1612f42] Bump version + 2 files changed, 7 insertions(+), 7 deletions(-) + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.14.1 - https://nf-co.re + + +WARNING  Could not find GitHub authentication token. Some API requests may fail.                     +INFO     Pipeline directory: /home/runner/work/website/website/tmp/nf-core-nextbigthing +INFO     Original pipeline repository branch is 'master' +INFO     Deleting all files in 'TEMPLATE' branch                                                     +INFO     Making a new template pipeline using pipeline variables                                     +INFO     Template contains no changes - no new commit created                                        +INFO     Checking out original branch: 'master' +INFO     No changes made to TEMPLATE - sync complete