diff --git a/02_demultiplex/test/02_flexbar/.gitkeep b/02_demultiplex/test/02_flexbar/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/02_demultiplex/test/test_demultiplex_flexbar.sh b/02_demultiplex/test/test_demultiplex_flexbar.sh new file mode 100644 index 0000000000000000000000000000000000000000..76e9c44d243366ce9553ca076686e8f9360a033d --- /dev/null +++ b/02_demultiplex/test/test_demultiplex_flexbar.sh @@ -0,0 +1,13 @@ +source 98_infos/config.sh +flexbar=${SINGULARITY_EXEC_CMD}" "${EDNATOOLS_SIMG}" flexbar" + +## Prefix for all generated files + +pref="grinder_teleo1" +## Path to the directory containing forward and reverse reads +R1_fastq="${DATA_PATH}"/"$pref"/"$pref"_R1.fastq +R2_fastq="${DATA_PATH}"/"$pref"/"$pref"_R2.fastq +## path to 'tags.fasta' +Tags=`pwd`"/02_demultiplex/Tags.fasta" + +$flexbar -r $R1_fastq -p $R2_fastq --barcodes $Tags --barcodes2 $Tags -bt 0 -t 02_demultiplex/test/02_flexbar/flex