diff --git a/.nf-core.yml b/.nf-core.yml index ded34340..52171fad 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -13,6 +13,13 @@ lint: - .github/ISSUE_TEMPLATE/bug_report.yml - .github/PULL_REQUEST_TEMPLATE.md - .github/workflows/linting.yml + - .github/workflows/branch.yml + - .github/ISSUE_TEMPLATE/feature_request.yml - assets/email_template.html - assets/email_template.txt + - lib/NfcoreTemplate.groovy - docs/README.md + nextflow_config: + - manifest.name + - manifest.homePage + multiqc_config: false diff --git a/CHANGELOG.md b/CHANGELOG.md index 7613c570..e077fc46 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,11 +1,11 @@ -# nf-core/tomte: Changelog +# genomic-medicine-seden/tomte: Changelog The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ## v1.0dev - [date] -Initial release of nf-core/tomte, created with the [nf-core](https://nf-co.re/) template. +Initial release of genomic-medicine-sweden/tomte, created with the [nf-core](https://nf-co.re/) template. ### `Added` diff --git a/CITATIONS.md b/CITATIONS.md index 4a7f9294..8869811f 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -1,4 +1,4 @@ -# nf-core/tomte: Citations +# genomic-medicine-sweden/tomte: Citations ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json index 3a8d70b7..eac9add4 100644 --- a/assets/adaptivecard.json +++ b/assets/adaptivecard.json @@ -17,7 +17,7 @@ "size": "Large", "weight": "Bolder", "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", - "text": "nf-core/tomte v${version} - ${runName}", + "text": "genomic-medicine-sweden/tomte v${version} - ${runName}", "wrap": true }, { diff --git a/assets/email_template.txt b/assets/email_template.txt index dad4784a..a0e702bb 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -1,9 +1,10 @@ ---------------------------------------------------- - ,--./,-. - ___ __ __ __ ___ /,-._.--~\\ - |\\ | |__ __ / ` / \\ |__) |__ } { - | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-, - `._,._,' + _____ __ __ _____ _ _ + / ____| \\/ |/ ____| | | | | + | | __| \\ / | (___ ______ | |_ ___ _ __ ___ | |_ ___ + | | |_ | |\\/| |\\___ \\ |______| | __/ _ \\| '_ ` _ \\| __/ _ \ + | |__| | | | |____) | | || (_) | | | | | | || __/ + \\_____|_| |_|_____/ \\__\\___/|_| |_| |_|\\__\\___| tomte v${version} ---------------------------------------------------- Run Name: $runName diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d5c64086..b66e8e95 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/tomte + This report has been generated by the genomic-medicine-sweden/tomte analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-tomte-methods-description": order: -1000 diff --git a/assets/schema_input.json b/assets/schema_input.json index f3338baa..0d5ea9b5 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,7 +1,7 @@ { "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/nf-core/tomte/master/assets/schema_input.json", - "title": "nf-core/tomte pipeline - params.input schema", + "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/tomte/master/assets/schema_input.json", + "title": "genomic-medicine-sweden/tomte pipeline - params.input schema", "description": "Schema for the file provided with params.input", "type": "array", "items": { diff --git a/assets/slackreport.json b/assets/slackreport.json index ca28efa7..9b869412 100644 --- a/assets/slackreport.json +++ b/assets/slackreport.json @@ -3,7 +3,7 @@ { "fallback": "Plain-text summary of the attachment.", "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "nf-core/tomte v${version} - ${runName}", + "author_name": "genomic-medicine-sweden/tomte v${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 01b8653d..86119c9e 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -349,4 +349,27 @@ class NfcoreTemplate { """.stripIndent() ) } + + // + // GMS tomte logo (WIP) + // + public static String gmsLogo(workflow, monochrome_logs) { + Map colors = logColours(monochrome_logs) + String workflow_version = NfcoreTemplate.version(workflow) + String.format( + """\n + ${dashedLine(monochrome_logs)} + ${colors.blue} _____ __ __ _____ _ _${colors.reset} + ${colors.blue} / ____| \\/ |/ ____| | | | |${colors.reset} + ${colors.blue} | | __| \\ / | (___ ______ | |_ ___ _ __ ___ | |_ ___${colors.reset} + ${colors.blue} | | |_ | |\\/| |\\___ \\ |______| | __/ _ \\| '_ ` _ \\| __/ _ \\${colors.reset} + ${colors.blue} | |__| | | | |____) | | || (_) | | | | | | || __/${colors.reset} + ${colors.blue} \\_____|_| |_|_____/ \\__\\___/|_| |_| |_|\\__\\___|${colors.reset} + + ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset} + ${dashedLine(monochrome_logs)} + """.stripIndent() + ) + } + } diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 098199fb..f437aa3c 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -1,5 +1,5 @@ // -// This file holds several functions specific to the main.nf workflow in the nf-core/tomte pipeline +// This file holds several functions specific to the main.nf workflow in the genomic-medicine-sweden/tomte pipeline // import nextflow.Nextflow diff --git a/main.nf b/main.nf index aa64214c..0ee71456 100644 --- a/main.nf +++ b/main.nf @@ -48,7 +48,7 @@ include { validateParameters; paramsHelp } from 'plugin/nf-validation' // Print help message if needed if (params.help) { - def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) + def logo = NfcoreTemplate.gmsLogo(workflow, params.monochrome_logs) def citation = '\n' + WorkflowMain.citation(workflow) + '\n' def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 8f3bb768..3e9ead06 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -17,7 +17,7 @@ process SAMPLESHEET_CHECK { when: task.ext.when == null || task.ext.when - script: // This script is bundled with the pipeline, in nf-core/tomte/bin/ + script: // This script is bundled with the pipeline, originally from nf-core """ check_samplesheet.py \\ $samplesheet \\ diff --git a/nextflow.config b/nextflow.config index 02f9e422..4cd43aed 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - nf-core/tomte Nextflow config file + genomic-medicine-sweden/tomte Nextflow config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Default config options for all compute environments ---------------------------------------------------------------------------------------- @@ -9,7 +9,6 @@ // Global default params, used in configs params { - // TODO nf-core: Specify your pipeline's command line flags // Input options input = null // References @@ -247,9 +246,9 @@ dag { } manifest { - name = 'nf-core/tomte' + name = 'genomic-medicine-sweden/tomte' author = """Clinical Genomics Stockholm""" - homePage = 'https://github.com/nf-core/tomte' + homePage = 'https://github.com/genomic-medicine-sweden/tomte' description = """Pipeline to analyse RNAseq from raredisease patients""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' diff --git a/workflows/tomte.nf b/workflows/tomte.nf index b0efea15..13cc1e9d 100644 --- a/workflows/tomte.nf +++ b/workflows/tomte.nf @@ -6,7 +6,7 @@ include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' -def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) +def logo = NfcoreTemplate.gmsLogo(workflow, params.monochrome_logs) def citation = '\n' + WorkflowMain.citation(workflow) + '\n' def summary_params = paramsSummaryMap(workflow)