Snakefile2

from read_accessions import read_txt_file
from snakemake.io import glob_wildcards

# Read sample names from the txt file
trimmed_accession_list = read_txt_file("trimmed_accessions.txt")



rule all:
    input:
        expand("trimmed_snakemake/{sample}/{sample}_trimmed_fastqc.html", sample=trimmed_accession_list),
        "trimmed_snakemake/trimmed_multiqc_report.html"
        

rule trim_fastq:
    input:
        "snakemake/{sample}/{sample}.fastq"
    output:
        "trimmed_snakemake/{sample}/{sample}_trimmed.fastq"
    shell:
        """
        echo 'Running trimming for {wildcards.sample}' &&
        trimmomatic SE -phred33 {input} trimmed_snakemake/{wildcards.sample}/{wildcards.sample}_trimmed_temp.fastq LEADING:20 TRAILING:20 SLIDINGWINDOW:10:20 HEADCROP:20 &&
        [ ! -e trimmed_snakemake/{wildcards.sample}/{wildcards.sample}_trimmed_temp.fastq ] || [ "{output}" -ef "trimmed_snakemake/{wildcards.sample}/{wildcards.sample}_trimmed_temp.fastq" ] || mv trimmed_snakemake/{wildcards.sample}/{wildcards.sample}_trimmed_temp.fastq "{output}" ||
        (echo 'Error in trimming' && exit 1)
        """

rule fastqc_trimmed:
    input:
        "trimmed_snakemake/{sample}/{sample}_trimmed.fastq"
    output:
        html="trimmed_snakemake/{sample}/{sample}_trimmed_fastqc.html",
        zip="trimmed_snakemake/{sample}/{sample}_trimmed_fastqc.zip"
    shell:
        """
        echo "Processing trimmed sample: {wildcards.sample}"
        fastqc {input}
        """

rule trimmed_multiqc:
    input:
        expand("trimmed_snakemake/{sample}/{sample}_trimmed_fastqc.zip", sample=trimmed_accession_list)
    output:
        "trimmed_snakemake/trimmed_multiqc_report.html"
    shell:
        "multiqc trimmed_snakemake/ --outdir trimmed_snakemake/ --filename trimmed_multiqc_report -f"