large_nt_refs = "data/ncbi_virus_dependoparvovirues_taxid10803.fa"
small_nt_refs = "data/caps.nt.fa"
small_aa_refs = "data/caps.fa"


rule all:
	input:
		"out/info.tsv",
		"out/diamond_fl.tsv",
		lambda wildcards: expand("out/minimap/{acc}.bam", acc=get_acc_list(wildcards)),
		lambda wildcards: expand("out/variants/{acc}.tsv", acc=get_acc_list(wildcards)),
		lambda wildcards: expand("out/bwa_paired_flagstat/{acc}.txt", acc=get_acc_list(wildcards)),
		lambda wildcards: expand("out/bwa_single_flagstat/{acc}.txt", acc=get_acc_list(wildcards)),


include: 'rules/fetch.smk'

include: 'rules/bwa_screen.smk'

include: 'rules/megahit_assembly.smk'

include: 'rules/analyse_megahit_assembly.smk'

include: 'rules/variant_calling_caps.smk'
