Snakefile_gt_ase

import os
#from collections import OrderedDict
import glob2, re, math
import pandas as pd
from helper_py_scripts import update_logs
from snakemake.utils import validate
from itertools import repeat
from snakemake.utils import min_version


min_version("6.4.0")


configfile: "new_config.yaml"

NUM, ID1, DONORS = glob_wildcards(f"{config['split_bams_pipeline']['split_bams_dir']}{config['fold_struct_bam_split2']}{{donors}}.bam")

include: "rules/resources.snkmk"
include: "rules/snv_aware_align.snkmk"

rule all:
    input:
        expand(f"{config['STARsolo_snv_aware']['bams_dir']}{config['fold_struct_snv_aware']}{{donors}}/{{donors}}{config['STARsolo_snv_aware']['bam']}", num=NUM, id1=ID1, donors=DONORS),
        expand(f"{config['STARsolo_snv_aware']['bams_dir']}{config['fold_struct_snv_aware']}{{donors}}/{{donors}}{config['STARsolo_snv_aware']['bai']}", num=NUM, id1=ID1, donors=DONORS)