# Pipeline


<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->

## Pipeline Configuration

------------------------------------------------------------------------

<a
href="https://github.com/mtinti/OligoSeeker/blob/main/OligoSeeker/pipeline.py#L22"
target="_blank" style="float:right; font-size:smaller">source</a>

### PipelineConfig

>  PipelineConfig (fastq_1:str='../test_files/test_1.fq.gz',
>                      fastq_2:str='../test_files/test_2.fq.gz',
>                      oligos_file:Optional[str]=None,
>                      oligos_string:Optional[str]=None,
>                      oligos_list:Optional[List[str]]=None,
>                      output_path:str='../test_files/test_outs',
>                      output_prefix:str='', offset_oligo:int=1,
>                      log_file:Optional[str]=None, log_level:int=20)

*Configuration settings for oligo codon counting pipeline.*

## Progress Reporting

------------------------------------------------------------------------

<a
href="https://github.com/mtinti/OligoSeeker/blob/main/OligoSeeker/pipeline.py#L82"
target="_blank" style="float:right; font-size:smaller">source</a>

### ProgressReporter

>  ProgressReporter (logger:Optional[logging.Logger]=None)

*Reports progress during long-running operations.*

## Oligo Codon Pipeline

------------------------------------------------------------------------

<a
href="https://github.com/mtinti/OligoSeeker/blob/main/OligoSeeker/pipeline.py#L120"
target="_blank" style="float:right; font-size:smaller">source</a>

### OligoCodonPipeline

>  OligoCodonPipeline (config:__main__.PipelineConfig)

*Complete pipeline for oligo codon counting.*