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fastp

note

All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).

https://github.com/OpenGene/fastp

Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

By default, the module generates the sample names based on the --report_title / -R option in the fastp command line (if present), or the input FastQ file names if not.

If you prefer, you can tell the module to use the filenames as sample names instead. To do so, use the following config option:

use_filename_as_sample_name:
    - fastp

See Using log filenames as sample names for more details.

File search patterns​

fastp:
  contents: '"before_filtering": {'
  fn: '*.json'
  num_lines: 50