# Mega Sequencing reads Preprocessing Subworkflows

## Specifications and Scope

The main aim of this subworkflow is to provide a common set of steps for processing high-throughput sequencing data, that can be installed across most nf-core pipelines analysing this type of data.
This will provide consistency and efficiency for developers across all pipelines.

The following points describe the scope:

- Should cover the most common steps of sequencing processing
- Each subworkflow should target a single sequencing platform
- Should provide maximum flexibility/choice for users (i.e. tool choice at each step)
- Each step should be skippable
- Final emitted output should be same regardless of the processing steps

Eventually these subworkflows could be aggregated into a single pipeline for the sole purpose of preprocessing data, that can be chained into downstream pipelines.

## (Illumina) Short Reads

graph LR;
    fastq[/fastq/]
    subgraph initial_stats
    fastq --> pre_fastqc
    fastq --> seqkit_sana --> pre_seqfu_check
    end

    pre_seqfu_check --> umitools_extract

    subgraph umicleandetection
        umitools_extract
    end

    umicleandetection --> adapterclip_merge

    subgraph adapterclip_merge
        direction LR
        fastp
        adapterremoval
        leehom
        cutadapt
        trimmomatic
        trimgalore
        fastp
        bbduk
        ngmerge
    end

    adapterclip_merge --> complexity_filtering

    subgraph complexity_filtering
        direction LR
        prinseqplusplus
        fastp_complexity
        bbmap_bbduk

    end

    complexity_filtering --> deduplication
    deduplication --> post_fastqc


    subgraph deduplication
        direction LR
        bbmap_clumpify
    end
    
    deduplication --> hostremoval 

    subgraph hostremoval
        direction LR
        deacon
        hostile
    end



    hostremoval --> run_merging --> final_qc

    subgraph run_merging
        cat_fastq
    end

    subgraph final_qc
    direction LR
    seqfu_stats
    post_seqfu_check
    end

    final_qc --> cleaned_fastq[/cleaned_fastq/]

## (Nanopore) Long Reads

TBD

## (PacBio) Long Reads

TBD