Snakefile_IonTorrent

workdir: "."

(SAMPLES,) = glob_wildcards("/path/to/IonTorrent/bam-files/{sample}.bam") #enter path to IonTorrent bam-files

rule all:
    input: 
        expand("kraken_report_Ion/{sample}_kraken_report.txt", sample=SAMPLES)

rule samtools_sort:
    input:
        "/path/to/IonTorrent/bam-files/{sample}.bam" #enter path to IonTorrent bam-files
    output:
        "sorted_bam_Ion/{sample}_sorted.bam"
    shell:
        """
        samtools sort -o {output} {input.bam_file}
        """

rule extract_unmapped:
    input:
        "sorted_bam_Ion/{sample}_sorted.bam"
    output:
        "unmapped_Ion/{sample}_unmapped.bam"
    shell:
        "samtools view -f 4 {input} > {output}"

rule bam_to_fastq:
    input:
        "unmapped_Ion/{sample}_unmapped.bam"
    output:
        "fastq_Ion/{sample}_unmapped.fastq"
    shell:
        "samtools fastq {input} > {output}"

rule kraken:
    input:
        fastq="fastq_Ion/{sample}_unmapped.fastq",
        db="/path/to/kraken2_db" #enter path to db
    output:
        report = "kraken_report_Ion/{sample}_kraken_report.txt",
        out = "kraken_output_Ion/{sample}_kraken_output.txt"
    shell:
        """
        kraken2 --db {input.db} --output {output.out} \
        --report {output.report} --confidence 0.60 {input.fastq}
        """