Making fastq_screen_references value to use baseDir

nkongenelly · nkongenelly · commit 3edc0ba1e85e · 2025-03-26T15:18:51.000+01:00
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,6 +1,9 @@
 lint:
   files_unchanged:
     - .github/CONTRIBUTING.md
+  nextflow_config:
+    - config_defaults:
+        - params.fastq_screen_references
 nf_core_version: 3.2.0
 repository_type: pipeline
 template:
diff --git a/nextflow.config b/nextflow.config
@@ -21,7 +21,7 @@ params {
     igenomes_ignore            = false
 
     // Fastqscreen options
-    fastq_screen_references    = './assets/example_fastq_screen_references.csv'
+    fastq_screen_references    = "${projectDir}/assets/example_fastq_screen_references.csv"
 
     // MultiQC options
     multiqc_config             = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -94,7 +94,7 @@
                 },
                 "fastq_screen_references": {
                     "type": "string",
-                    "default": "./assets/example_fastq_screen_references.csv",
+                    "default": "${projectDir}/assets/example_fastq_screen_references.csv",
                     "fa_icon": "fas fa-search",
                     "description": "A .csv of reference genomes to be mapped against by FastQ Screen"
                 }

Original file line number	Diff line number	Diff line change
`@@ -94,7 +94,7 @@`
`94`	`94`	`},`
`95`	`95`	`"fastq_screen_references": {`
`96`	`96`	`"type": "string",`
`97`		`- "default": "./assets/example_fastq_screen_references.csv",`
	`97`	`+ "default": "${projectDir}/assets/example_fastq_screen_references.csv",`
`98`	`98`	`"fa_icon": "fas fa-search",`
`99`	`99`	`"description": "A .csv of reference genomes to be mapped against by FastQ Screen"`
`100`	`100`	`}`