Merge pull request #45 from genomic-medicine-sweden/gms_references

changing some references from nf-core to gms

.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

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`
 

CITATIONS.md

@@ -1,4 +1,4 @@
-# nf-core/tomte: Citations
+# genomic-medicine-sweden/tomte: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 

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
                     },
                     {

assets/email_template.txt

@@ -1,9 +1,10 @@
 ----------------------------------------------------
-                                        ,--./,-.
-        ___     __   __   __   ___     /,-._.--~\\
-  |\\ | |__  __ /  ` /  \\ |__) |__         }  {
-  | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
-                                        `._,._,'
+   _____ __  __  _____            _                  _
+  / ____|  \\/  |/ ____|          | |                | |
+ | |  __| \\  / | (___    ______  | |_ ___  _ __ ___ | |_ ___
+ | | |_ | |\\/| |\\___ \\  |______| | __/ _ \\| '_ ` _ \\| __/ _ \
+ | |__| | |  | |____) |          | || (_) | | | | | | ||  __/
+  \\_____|_|  |_|_____/            \\__\\___/|_| |_| |_|\\__\\___|
  tomte v${version}
 ----------------------------------------------------
 Run Name: $runName

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/tomte/releases/tag/dev" target="_blank">nf-core/tomte</a>
+  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/tomte/releases/tag/dev" target="_blank">genomic-medicine-sweden/tomte</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/tomte/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://github.com/genomic-medicine-sweden/tomte/blob/master/docs/output.md" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-tomte-methods-description":
     order: -1000

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": {

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": [

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()
+        )
+    }
+
 }

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

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)

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 \\

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'

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)