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fastp-wdl's Introduction

fastp-wdl

Partial WDLization of fastp that focuses on ease-of-use. Outputs fastp's HTML and JSON reports, and optionally parses those reports for specific information. Optionally outputs cleaned fastqs.

How does this WDL differ from fastp's defaults?

value WDL original justification
disable_adaptor_trimming true false This WDL assumes your reads have already been through Trimmomatic
disable_trim_poly_g true false Alignment with Trimmomatic
output_cleaned_fastqs true n/a fastp always generates cleaned fastqs; setting this to false allows a user who only cares about QC reports to save delocalization time by reducing the number of outputs

I want different features, has someone else WDLized this?

Check out Thiagen's version of fastp.

fastp reference

Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PMID: 30423086; PMCID: PMC6129281. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129281/

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