import os
import sys
import pandas as pd
from snakemake.utils import min_version

min_version("6.0")
SMKDIR = os.path.dirname(workflow.snakefile)
print(SMKDIR)
shell.prefix("which python; ")


configfile: "config/config.yaml"


um_score = config.get("um_score", 10)
df = pd.read_csv(config["tbl"], sep="\t")
df.asm = df.asm.map(os.path.abspath)


config["smkdir"] = SMKDIR

config["rb"] = os.path.abspath(f"{SMKDIR}/../target/release/rustybam")


###################################################
# START reference alignment
###################################################
module reference_alignment:
    snakefile:
        "reference_alignment.smk"
    config:
        config


use rule * from reference_alignment as ra_*


###################################################
# END reference alignment
###################################################


rule all:
    input:
        ra=rules.ra_reference_alignment.input,
