[LINT] fix

nextflow_schema.json

@@ -58,7 +58,7 @@
                     "type": "string",
                     "format": "file-path",
                     "mimetype": "text/plain",
-                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
+                    "pattern": "^\\S+\\.fn?s?a(sta)?(\\.gz)?$",
                     "description": "Path to FASTA genome file.",
                     "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                     "fa_icon": "far fa-file-code"

subworkflows/local/input_check.nf

@@ -13,6 +13,7 @@ workflow INPUT_CHECK {
     if (params.split_fastq){
 
       SAMPLESHEET_CHECK ( samplesheet )
+        .csv
         .splitCsv ( header:true, sep:',' )
 	.map { create_fastq_channels(it) }
 	.splitFastq( by: params.fastq_chunks_size, pe:true, file: true, compress:true)
@@ -25,6 +26,7 @@ workflow INPUT_CHECK {
 
     }else{
       SAMPLESHEET_CHECK ( samplesheet )
+      	.csv
         .splitCsv ( header:true, sep:',' )
         .map { create_fastq_channels(it) }
 	.map { it -> [it[0], [it[1], it[2]]]}