switch to cleaner file and variable names, remove fastqscreen .csv as…

… main workflow input
nf-core · Dec 5, 2024 · a31a392 · a31a392
1 parent 5aeb8d1
commit a31a392
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Showing 7 changed files with 13 additions and 16 deletions.
diff --git a/assets/databasesheet.csv → assets/example_fastq_screen_references.csv b/assets/databasesheet.csv → assets/example_fastq_screen_references.csv
diff --git a/assets/schema_database.json → assets/schema_fastq_screen_references.json b/assets/schema_database.json → assets/schema_fastq_screen_references.json
@@ -1,8 +1,8 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/assets/schema_database.json",
-    "title": "nf-core/seqinspector pipeline - params.fastqscreen_databasesheet schema",
-    "description": "Schema for the file provided with params.fastq_screen_databasesheet",
+    "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/assets/schema_fastq_screen_references.json",
+    "title": "nf-core/seqinspector pipeline - params.fastq_screen_references schema",
+    "description": "Schema for the file provided with params.fastq_screen_references",
     "type": "array",
     "items": {
         "type": "object",

diff --git a/conf/test.config b/conf/test.config
@@ -26,7 +26,7 @@ params {
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
-    fastqscreen_database_sheet = "${projectDir}/assets/databasesheet.csv"
+    fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
 
     // Genome references
     genome = 'R64-1-1'

diff --git a/main.nf b/main.nf
@@ -44,16 +44,14 @@ workflow NFCORE_SEQINSPECTOR {
 
     take:
     samplesheet // channel: samplesheet read in from --input
-    database_sheet
 
     main:
 
     //
     // WORKFLOW: Run pipeline
     //
     SEQINSPECTOR (
-        samplesheet,
-        database_sheet,
+        samplesheet
     )
     emit:
     global_report   = SEQINSPECTOR.out.global_report    // channel: /path/to/multiqc_report.html
@@ -85,8 +83,7 @@ workflow {
     // WORKFLOW: Run main workflow
     //
     NFCORE_SEQINSPECTOR (
-        PIPELINE_INITIALISATION.out.samplesheet,
-        params.fastqscreen_database_sheet,
+        PIPELINE_INITIALISATION.out.samplesheet
     )
     //
     // SUBWORKFLOW: Run completion tasks

diff --git a/nextflow.config b/nextflow.config
@@ -20,7 +20,7 @@ params {
     igenomes_ignore            = false
 
     // Fastqscreen options
-    fastqscreen_database_sheet = './assets/databasesheet.csv'
+    fastq_screen_references    = './assets/example_fastq_screen_references.csv'
 
     // MultiQC options
     multiqc_config             = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -87,11 +87,11 @@
                     "hidden": true,
                     "default": "s3://ngi-igenomes/igenomes/"
                 },
-                "fastqscreen_database_sheet": {
+                "fastq_screen_references": {
                     "type": "string",
-                    "default": "./assets/databasesheet.csv",
+                    "default": "./assets/example_fastq_screen_references.csv",
                     "fa_icon": "fas fa-search",
-                    "description": "list of reference genomes (databases) to be mapped against in fastqscreen"
+                    "description": "A .csv of reference genomes to be mapped against by FastQ Screen"
                 }
             }
         },

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
@@ -29,7 +29,6 @@ workflow SEQINSPECTOR {
 
     take:
     ch_samplesheet               // channel: samplesheet read in from --input
-    ch_fastqscreen_databasesheet // channel: database sheet read in from --fastqscreen_database_sheet
 
     main:
 
@@ -80,10 +79,11 @@ workflow SEQINSPECTOR {
 
     // Parse the reference info needed to create a FastQ Screen config file
     // and transpose it into a tuple containing lists for each property
+
     ch_fastqscreen_refs = Channel
         .fromList(samplesheetToList(
-            "${projectDir}/assets/databasesheet.csv",
-            "${projectDir}/assets/schema_database.json"
+            "${projectDir}/assets/example_fastq_screen_references.csv",
+            "${projectDir}/assets/schema_fastq_screen_references.json"
         ))
         .toList()
         .transpose()