FelixKrueger/TrimGalore

Validation fails when FASTA files used as input

vkkodali opened this issue · 4 comments

vkkodali commented

I am running trim_galore on paired-end FASTA files. Everything works as expected except the last step of validation, which fails with the error:

Input file doesn't seem to be in FastQ format at sequence 1

Can I explicitly tell trim_galore that the input files are in FASTA format and the validation step should not expect them to be FASTQ files?

FelixKrueger commented

I am afraid Trim Galore is designed for FastQ files only, if you want to trim FastA files you could probably use Cutadapt directly.

vkkodali commented

Would it be possible to add an option to disable validation?

FelixKrueger commented

You probably could find this line in trim_galore and comment it out...:

TrimGalore/trim_galore

Line 1546 in 4edff97

my ($val_1,$val_2,$un_1,$un_2) = validate_paired_end_files($file_1,$file_2);

Alternatively, you could also fake qualities and do a FastA > FastQ conversion? Just found this link...
https://bioinformatics.stackexchange.com/questions/11192/convert-fasta-to-fastq-with-dummy-quality-scores#:~:text=The%20first%20tool%2C%20to_fake_qual%20%2C%20creates,these%20into%20a%20fastq%20file.

vkkodali commented

You probably could find this line in trim_galore and comment it out...:

Thanks, I will give that a try.