eukrhythmic-setup

configfile: "config.yaml"

import io
import os
from os import listdir
from os.path import isfile, join
import sys
import pandas as pd
import numpy as np
import pathlib
from snakemake.exceptions import print_exception, WorkflowError  
sys.path.insert(1, 'scripts')

# Import relevant variable from config; exit if not supplied
import importworkspace
from importworkspace import *
os.system("python " + os.path.join("scripts", "importworkspace.py"))

# Contains function to check that variables are present and formatted correctly beyond provided values in config file
import checkrequirements
from checkrequirements import *

## CHECK THAT ALL REQUIREMENTS ARE SATISFIED BY EXECUTING checkrequirements() from `scripts/checkrequirements.py` ##
checkrequirementsfct()

include: "rules/fastqc-snake.smk"
include: "rules/bbmap-snake.smk
include: "rules/trimmomatic-snake.smk"
include: "rules/fastqc-trimmed-snake.smk"

ruleorder: trimmomatic > trimmomatic_SE

rule all:
    input:
        # FASTQC OUTPUTS
        fastqc1 = expand([os.path.join("{base}", "qc", "fastqc", "{sample}_{num}_fastqc.html"), 
                          os.path.join("{base}", "qc", "fastqc", "{sample}_{num}_fastqc.zip")], zip, 
                         base = OUTPUTDIR, sample = filenames, num = singleorpaired),
        # MULTIQC OUTPUTS
        multiqc1 = expand(os.path.join("{base}", "qc", "multiqc", "firstqcreport", "multiqc_report.html"), zip, 
                          base = OUTPUTDIR),
        # BBMAP OUTPUTS
        bbmap = expand(os.path.join("{base}", "bbmap", "{sample}_{num}.clean.fastq.gz"), zip, base = OUTPUTDIR, 
                       sample = filenames, num = singleorpaired),
        # TRIMMOMATIC OUTPUTS
        trimmed = expand([os.path.join("{base}", "firsttrim", "{sample}_1.trimmed.fastq.gz"), 
                          os.path.join("{base}", "firsttrim", "{sample}_2.trimmed.fastq.gz")], zip, 
                         base = OUTPUTDIR, sample = filenames),
        # FASTQC 2 OUTPUTS (trimmed)
        fastqc2 = expand([os.path.join("{base}", "qc", "fastqc_trimmed", "{sample}_{num}.trimmed_fastqc.html"), 
                          os.path.join("{base}", "qc", "fastqc_trimmed", "{sample}_{num}.trimmed_fastqc.zip")], 
                         zip, base = OUTPUTDIR, sample = filenames, num = singleorpaired),
        # MULTIQC 2 OUTPUTS
        multiqc2 = expand(os.path.join("{base}", "qc", "multiqc", "trimmedqcreport", "multiqc_report.html"), zip, 
                          base = OUTPUTDIR)