Snakefile-demux

from string import ascii_lowercase
import os
import subprocess
from pathlib import Path
import csv
import glob


# get current username for computer
home_dir = str(Path.home())

# read in the config file to get pathways/samples into variables

# determine if config file is in folder, if not, copy the config file from snakemake pipeline directory into working path
if Path('config_demux.yaml').is_file():
    config_fname = 'config_demux.yaml'
else:
    demux_config = f"{home_dir}/gbs/GBS_snakemake_pipeline/config/config_demux.yaml"

    with open('config_demux.yaml', 'w', newline='') as conf_out:
        with open(demux_config, 'r') as config:
            for line in config:
                conf_out.write(line)

    config_fname = 'config_demux.yaml'

configfile: config_fname

demux_dir = config["demux_dir"]
demux_parent = Path(demux_dir).name
demux_output = f"{demux_parent}.tar.gz"
reference_fai = config["reference"]

demux_files = glob.glob(f'{demux_dir}/*')

# generate a list of sorted bams and fastqc files that will be output at end of process
sample_outputs = [f'{Path(i).stem[:-2]}' for i in demux_files]  # get just name (no .1 or .2 on file name)

trim_input1 = demux_parent+'/{sample}.1.fastq'
print(trim_input1)
trim_input2 = demux_parent+'/{sample}.2.fastq'

# get the pathway from the read1 fastq file, this is where we want to run the pipeline (set working dir)
path_name, base_name = os.path.split(demux_dir)
file_handle = os.path.splitext(base_name)[0]
file_name = os.path.splitext(file_handle)[0]
lib_id = Path(demux_dir).parent.name  # for naming the am ID line - just get the name of the folder the demux lives in

workdir: path_name

#######################################  RULES ##################################################

rule all:
    input:
        expand("sorted_bams/{sort_out}.bam", sort_out=sample_outputs),
        "log/multiqc_report",
        demux_output

include: f"{home_dir}/gbs/GBS_snakemake_pipeline/workflow/rules/demux/trim-demux.smk"
include: f"{home_dir}/gbs/GBS_snakemake_pipeline/workflow/rules/demux/bwa_map-demux.smk"
include: f"{home_dir}/gbs/GBS_snakemake_pipeline/workflow/rules/demux/novosort-demux.smk"
include: f"{home_dir}/gbs/GBS_snakemake_pipeline/workflow/rules/demux/qc_stats.smk"
include:  f"{home_dir}/gbs/GBS_snakemake_pipeline/workflow/rules/demux/cleanup.smk"