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FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
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Validation fails when FASTA files used as input #173

Closed vkkodali closed 11 months ago

vkkodali commented 11 months ago

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 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.

vkkodali commented 11 months ago

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

FelixKrueger commented 11 months ago

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 commented 11 months ago

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

Thanks, I will give that a try.