Validation fails when FASTA files used as input

[vkkodali]

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]

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]

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

[FelixKrueger]

You probably could find this line in trim_galore and comment it out...: https://github.com/FelixKrueger/TrimGalore/blob/4edff97d22f3837d42a29e4afbfaeb6e07ffb11b/trim_galore#L1546

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]

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

Thanks, I will give that a try.