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nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline
https://nf-co.re/eager
MIT License
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Found unexpected parameters --qualitybase: 64 #938

Closed KeLi1018 closed 1 year ago

KeLi1018 commented 1 year ago

Hi EAGER team! I'm running eager v.2.4.6 on a single end sample but I've had some issues.

Here is the code: nextflow run nf-core/eager --single_end --input "*.fastq.gz" --qualitybase 64 --fasta "reference.fna" -profile singularity --outdir ./

And the Nextflow error:

WARN: Found unexpected parameters: --qualitybase: 64

Command error: Error reading FASTQ record at line 1; aborting: Phred+33 encoded quality score is greater than the expected maximum of 41 (J). Please verify the format of these files. If the quality scores are actually Phred+64 encoded, then use the '--qualitybase 64' command-line option.

Sorry, I couldn't work out how to fix this. Thanks, its a very helpful pipeline.

jfy133 commented 1 year ago

Hi @KeLi1018 !

--qualitybase is a AdapterRemoval parameter (the error is from AdapterRemoval itself).

If I remember correctly, to change this via the pipeline you need to use --qualitymax: https://nf-co.re/eager/2.4.6/parameters#qualitymax

Feel free to reopen if it doesn't work!