Allow .R[1,2] and _R[1,2] fastqs

CHANGELOG.md

@@ -6,9 +6,9 @@
 * Remove parsing restrictions for submitted stranded/spike/species (#105, #106)
 * Pass unidentified ends instead of overwriting it as unknown
 * Move fastqc process before trim to catch fastq errors (#107)
-* Only use fastq's that match *.R[1,2].fastq.gz naming convention (#107)
+* Only use fastq's that match *[_.]R[1-2].fastq.gz naming convention (#107)
 * Add error output for no fastq's
-* Update input bag export config to only fetch fastq's that match *.R[1,2].fastq.gz naming convention
+* Update input bag export config to only fetch fastq's that match *[_.]R[1-2].fastq.gz naming convention
 
 *Known Bugs*
 * Override params (inputBag, fastq, species) aren't checked for integrity

workflow/scripts/bdbag_fetch.sh

@@ -18,7 +18,7 @@ if [ "${validate}" != "is valid" ]
 then
     exit 1
 fi
-for i in $(find */ -name "*.R[1-2].fastq.gz")
+for i in $(find */ -name "*[_.]R[1-2].fastq.gz")
 do
     path=${2}.$(echo ${i##*/} | grep -o "R[1,2].fastq.gz")
     cp ${i} ./${path}