Read length not being included sometimes in mapping_illumina for viralrecon

[victor5lm]

As per the title, in some cases, the read length column in the mapping_illumina.tab file from viralrecon is not completed. Please check why this is happening.

[victor5lm]

This is solved by indicating that there could be an optional single quote between the sample name (this happens when the sample name is a number), by means of grep -E:

read_length=$(cat ${arr[1]}*/multiqc/multiqc_data/multiqc_fastqc.yaml | grep -A5 -E "'?${arr[0]}_1'?:$" | grep "Sequence length:" | tr "-" " " | rev | cut -d " " -f1 | rev)