add new test profile with small genome/data

conf/small_genome.config

@@ -0,0 +1,22 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/pathogensurveillance -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    sample_data = 'test/data/metadata/small_genome.csv'
+    outdir = 'test/output/small_genome'
+    n_ref_strains = 1
+    n_ref_species = 1
+    n_ref_genera = 1
+}

nextflow.config

@@ -217,7 +217,8 @@ profiles {
     complex_minimal             { includeConfig 'conf/complex_minimal.config' }
     complex                     { includeConfig 'conf/complex.config' }
     cqls                        { includeConfig 'conf/cqls.config' }
-    testserratia_38		{ includeConfig 'conf/testserratia_38.config' }
+    testserratia_38             { includeConfig 'conf/testserratia_38.config' }
+    small_genome                { includeConfig 'conf/small_genome.config' }
 }
 
 // Load nf-core custom profiles from different Institutions

test/data/metadata/small_genome.csv

@@ -0,0 +1,7 @@
+ncbi_accession,taxon,enabled,ref_ncbi_accession,ref_primary_usage,ref_contextual_usage
+SRR18850314,Limosilactobacillus fermentum,TRUE,,,
+SRR18850310,Limosilactobacillus fermentum,TRUE,,,
+ERR13427439,Limosilactobacillus fermentum,TRUE,,,
+SRR29695256,Plasmodium falciparum,FALSE,GCF_000002765.6,exclusive,exclusive
+SRR29397006,Plasmodium falciparum,FALSE,GCF_000002765.6,exclusive,exclusive
+SRR27942447,Plasmodium falciparum,FALSE,GCF_000002765.6,exclusive,exclusive