Replace single string/option with comma separated list to support mul…

…tiple pipelines samplesheet generation

nextflow_schema.json

@@ -179,7 +179,7 @@
                 "generate_pipeline_samplesheets": {
                     "type": "string",
                     "default": "taxprofiler",
-                    "description": "Specify which pipeline to generate a samplesheet for.",
+                    "description": "Specify a comma separated string in quotes to specify which pipeline to generate a samplesheet for. Currently supported pipeline(s): taxprofiler",
                     "fa_icon": "fas fa-toolbox"
                 },
                 "generate_samplesheet_dbtype": {

subworkflows/local/utils_nfcore_createtaxdb_pipeline/main.nf

@@ -136,10 +136,16 @@ def validateInputParameters() {
         error('[nf-core/createtaxdb] Supplied --build_diamond, but missing at least one of: --prot2taxid, --nodesdmp, or --namesdmp (all are mandatory for DIAMOND).')
     }
 
+    // Validate samplesheet generation parameters
     if (params.generate_downstream_samplesheets && !params.generate_pipeline_samplesheets) {
         error('[nf-core/createtaxdb] If supplying `--generate_downsteam_samplesheets`, you must also specify which pipeline to generate for with `--generate_pipeline_samplesheets! Check input.')
     }
 
+    def supported_samplesheets = ['taxprofiler']
+    if (params.generate_downstream_samplesheets && !params.generate_pipeline_samplesheets.split(",").every { it in supported_samplesheets }) {
+        error("[nf-core/createtaxdb] Unrecognised or unsupported pipeline selection for samplesheet generation. Options: ${supported_samplesheets.join(", ")}. Specified: --generate_pipeline_samplesheets ${params.generate_pipeline_samplesheets}")
+    }
+
     if (params.generate_downstream_samplesheets && !params.generate_tar_archive && params.generate_samplesheet_dbtype == 'tar') {
         error('[nf-core/createtaxdb] Supplied --generate_downstream_samplesheets with --generate_samplesheet_dbtype tar, but missing --generate_tar_archive (mandatory for tar archive output).')
     }