snakefile

import pandas as pd
configfile: "config/config.yaml"

samples = pd.read_table(config["samples"], index_col="sample")

rule all:
    input:
        "results/krakendb/db",
        expand("results/kraken/{sample}_report.txt", sample=samples.index)
        #expand("results/IVA/{sample}", sample=samples.index)

include: "rules/fastp.smk"
include: "rules/bowtie2.smk"
include: "rules/samtools.smk"
include: "rules/IVA.smk"
include: "rules/kraken.smk"