Look for uncompressed fastq as well

nextflow.config

@@ -5,7 +5,7 @@ manifest {
   description = 'Epi2me compatible Nextflow pipeline for processing ARTIC tiling amplicon Illumina sequencing reads from monkeypox virus (MPXV) samples.'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'
-  version = '1.0.8'
+  version = '1.0.9'
 }
 
 // Load base.config by default for all pipelines
@@ -26,7 +26,7 @@ def makeFastqSearchPath ( illuminaSuffixes, fastq_exts ) {
 params {
 
   illuminaSuffixes = ['*_R{1,2}_001', '*_R{1,2}', '*_{1,2}' ]
-  fastq_exts = ['.fastq.gz', '.fq.gz']
+  fastq_exts = ['.fastq.gz', '.fq.gz', '.fastq', '.fq']
   fastqSearchPath = makeFastqSearchPath( params.illuminaSuffixes, params.fastq_exts )
 
   max_memory                 = '32.GB'