Snakefile_step1

SAMPLES = []
import glob
for filename in glob.glob("data/*.*") :
    f= filename.split(".")
    f1= f[0].split("/")
    SAMPLES.append(f1[-1])

rule all:
    input:
        "result/config.yaml",
        'result/qc/2_fastqc_trim/',
        'result/qc/3_flagstat/',
        'result/qc/4_picard/',
        'result/1_trim/',
        'result/2_bam/',
        'result/3_bam_filter/',
        'result/4_count/',
        'result/5_combined/',
        expand("result/qc/1_fastqc_raw/{sample}_fastqc.html",sample= SAMPLES),
        expand("result/qc/1_fastqc_raw/{sample}_fastqc.zip",sample= SAMPLES)

rule configscript:
    input: "scripts/create_config.sh"
    output:
        "result/config.yaml",
        directory('result/qc/2_fastqc_trim'),
        directory('result/qc/3_flagstat'),
        directory('result/qc/4_picard'),
        directory('result/1_trim'),
        directory('result/2_bam'),
        directory('result/3_bam_filter'),
        directory('result/4_count'),
        directory('result/5_combined')
    shell:'''
    bash scripts/create_config.sh
    '''

rule fastqc_raw:
    input: "data/{sample}.fastq.gz"
    output:
        "result/qc/1_fastqc_raw/{sample}_fastqc.html",
        "result/qc/1_fastqc_raw/{sample}_fastqc.zip"
    threads: 1
    shell:'''
    fastqc -t {threads} -o result/qc/1_fastqc_raw {input} --quiet
    '''