Fixed storeDir issue

Given a default, single accession run followed by a run
with all the accessions, the use of generic file output glob
in conjunction with storeDir directive caused an issue with read files
being incorrectly classed as present and reads for accession 1
output for every accession, causing pipeline to fail due tu duplicate
file names at multiqc step where the files are collected.

Author: rsuchecki

main.nf

@@ -64,14 +64,14 @@ process bgzip_chromosome_subregion {
 
 process extract_reads {
   tag { accession }
-  storeDir { "${params.outdir}/downloaded_reads" }  //use with care, caching will not work as normal so changes to input may not take effect
+  storeDir { "${workDir}/downloaded_reads" }  //use with care, caching will not work as normal so changes to input may not take effect
 
   input:
     val accession from accessionsChannel
     //e.g. ACBarrie
 
   output:
-    set val(accession), file('*.fastq.gz') into (extractedReadsChannelA, extractedReadsChannelB)
+    set val(accession), file("${accession}_R?.fastq.gz") into (extractedReadsChannelA, extractedReadsChannelB)
     //e.g. ACBarrie, [ACBarrie_R1.fastq.gz, ACBarrie_R2.fastq.gz]
 
   script: