snakemake学习笔记001：使用fastp对原始数据过滤

参考

• 1 简书文章snakemake使用笔记 - 简书 (jianshu.com)

• 2 https://stackoverflow.com/questions/56271154/use-snakemake-pair-end-bwa-alignment

• 3 https://bioinformaticsonline.com/snippets/view/43590/rules-to-run-fastp-snakemake

• 4 https://xizhihui.github.io/2018/10/28/%E6%B5%81%E7%A8%8B%E6%9E%84%E5%BB%BA-Snakemake%E4%BD%BF%E7%94%A8%E5%88%9D%E6%AD%A5/

• 5 https://www.youtube.com/watch?v=_wUGzqEjg6A&t=996s

• 6 https://www.youtube.com/watch?v=Bdxh0fSBOSA

• 7 https://www.youtube.com/watch?v=aZ0QlqtR2KM&t=279s

import os
import glob

input_folder = "/home/myan/scratch/private/pome_WGS/huoyan_14_variety/"
output_folder = "/home/myan/scratch/private/practice_data/snakemake/20220412/fastp.results/"

SRA,FRR = glob_wildcards(input_folder+"{sra}_{frr}.fq.gz")

rule all:
    input:
        expand(output_folder+"{sra}.html",sra=SRA),
        expand(output_folder+"{sra}.json",sra=SRA)


rule fastp:
    input:
        read01 = input_folder + "{sra}_1.fq.gz",
        read02 = input_folder + "{sra}_2.fq.gz"
    output:
        read01 = output_folder + "{sra}_1.clean.fq.gz",
        read02 = output_folder + "{sra}_2.clean.fq.gz",
        html = output_folder + "{sra}.html",
        json = output_folder + "{sra}.json"
    threads:
        8
    shell:
        """
        fastp -i {input.read01} -I {input.read02} -o {output.read01} -O {output.read02} --thread {threads} --html {output.html} --json {output.json}
        """

这里rule all的作用还是没有搞明白，看有的文档说是最终保留的文件 ，我这里rule all 只写了了最终的html和json，但是最终的结果里是有过滤后的fastq文件的

还有好多基础知识需要看