updated test_glosed.config to use the scaled-down glosed database hosted at nf-core/test-datasets

Author: tom-brekke

conf/test_glosed.config

@@ -1,33 +1,24 @@
-/*
-========================================================================================
-    Nextflow config file for running minimal tests with GloSED database
-========================================================================================
-    Defines input files and everything required to run a fast and simple pipeline test
-    using the GloSED (Global Standardised Soil Eukaryome Dataset) reference database.
-
-    Use as follows:
-        nextflow run nf-core/ampliseq -profile test_glosed,<docker/singularity> --outdir <OUTDIR>
-
-----------------------------------------------------------------------------------------
-*/
-
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '256.GB',
-        time: '2.h'
-    ]
-}
-
 params {
     config_profile_name = 'Test profile for GloSED database'
     config_profile_description = 'Minimal test dataset to verify pipeline function with GloSED reference database'
 
-    // Input data
     FW_primer = "GTGYCAGCMGCCGCGGTAA"
     RV_primer = "GGACTACNVGGGTWTCTAAT"
     input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet.tsv"
     dada_ref_taxonomy = "glosed"
-
     skip_qiime = true
+
+    // IMPORTANT: override the actual database map used by the workflow
+    dada_ref_databases.glosed = [
+        title:"GloSED - Global standardised Soil Eukaryome Dataset",
+        file:[
+            "https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/GloSED__OTU_sequences_first1k.fasta.zip",
+            "https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/GloSED_Taxonomy_first1k.tsv.zip"
+        ],
+        citation:"Sundh J, Larsson E, Nilsson RH, et al. GloSED fungal ITS database. Zenodo. https://zenodo.org/records/17827890",
+        fmtscript:"taxref_reformat_glosed.sh",
+        dbversion:"GloSED test subset (first1k)"
+    ]
 }
+
+