Closed vkkodali closed 11 months ago
I am afraid Trim Galore is designed for FastQ files only, if you want to trim FastA files you could probably use Cutadapt directly.
Would it be possible to add an option to disable validation?
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.
You probably could find this line in
trim_galore
and comment it out...:
Thanks, I will give that a try.
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: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?