shell.executable("/bin/bash")
shell.prefix("source ~/.bashrc; ")

import os
configfile: "./config.json"

rule all:
	input:
		"report/multiqc_report.html",
		expand("report/reads_{sample}-krona.html", sample=config["SAMPLES"]),
		"report/quast_coassembly/report.html",
		expand("report/count-contigs-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
		"report/contigs_coassembly-taxNames.tsv",
		expand("report/count-contigs-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
		"report/genes_coassembly-taxNames.tsv",
		"report/diamond_nr_coassembly.tsv",
		"work/prokka/coassembly_prokka.tsv",
		"work/interproscan/coassembly.faa.tsv",
		"work/cdhit/catalogue.ffn",


include: "../workflow_metagenomics/quality.smk"
include: "../workflow_metagenomics/preprocess.smk"
include: "../workflow_metagenomics/kaiju.smk"
include: "../workflow_metagenomics/assembly.smk"
include: "../workflow_metagenomics/annotation.smk"
include: "../workflow_metagenomics/count.smk"
include: "../workflow_metagenomics/catalogue.smk"