Incorrect parsing of file sample names when long read files are present

[Daniel-VM]

ISSUE DESCRIPTION

When creating the samples_id.txt file I noticed that find ../RAW -name ".fastq.gz" | cut -d "/" -f 3 | cut -d "_" -f 1 | sort -u > samples_id.txtdoesn't correctly parse the file sample's name when long reads are present in the template's RAW/ directory. The following command might handle both long and short reads fastq.gz file names:

find ../RAW -name ".fastq.gz" | rev | cut -d "/" -f 1 | rev | cut -d "_" -f 1 | cut -d "." -f 1 | sort -u > samples_id.txt