fastp.smk

rule fastp:
    input:
        sample=["Data/SARS-Cov-2/{sample}_1.fastq.gz", "Data/SARS-Cov-2/{sample}_2.fastq.gz"]
    output:
        trimmed=["results/fastp/trimmed/{sample}.1.fastq", "results/fastp/trimmed/{sample}.2.fastq"],
        # Unpaired reads separately
        unpaired1="results/fastp/trimmed/{sample}.u1.fastq",
        unpaired2="results/fastp/trimmed/{sample}.u2.fastq",
        # or in a single file
        # unpaired="trimmed/{sample}.singletons.fastq",
        merged="results/fastp/trimmed/{sample}.merged.fastq",
        failed="results/fastp/trimmed/{sample}.failed.fastq",
        html="report/fastp/{sample}.html",
        json="report/fastp/{sample}.json"
    log:
        "workflow/report/fastp/{sample}.log"
    conda:
        "../envs/yourenv.yaml"
    params:
        # adapters="--adapter_sequence ACGGCTAGCTA --adapter_sequence_r2 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
        extra="--merge"
    threads: 4
    wrapper:
        "v1.3.2/bio/fastp"