eukrhythmic-analysis-spike

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/busco-snake.smk"
include: "rules/salmon-snake.smk"
include: "rules/annotate-snake.smk"
include: "rules/hardclean-snake.smk"
include: "rules/spades-snake.smk"
include: "rules/spike-snake.smk"
include: "rules/eukulele-snake.smk"

ruleorder: merge_all > copies
ruleorder: salmon_rename > salmon_clustering_against_mega
ruleorder: salmon_rename > salmon_clustering

rule all:
    input:
        # BUSCO ASSESSMENT OF FINAL ASSEMBLY
        busco = expand(os.path.join("{base}", "busco", "{database}", "{folder}", "{assembly}"), base = OUTPUTDIR, 
                       database = "eukaryota", folder = "mega_merge", assembly = "merged"), # eukaryota, bacteria
        # HMMER ALIGNMENT OF FINAL ASSEMBLY BEFORE MEGA-MERGE
        hmmer = expand(os.path.join("{base}", "pfam", "{folder}", "{assembly}.tblout"), base = OUTPUTDIR, 
                       folder = "by_assembly_group", assembly = assemblygroups),
        # DIAMOND ALIGNMENT AND KEGG ANNOTATION 
        kegg = expand(os.path.join("{base}", "kegg", "{folder}", "{assembly}_kegg.csv"), base = OUTPUTDIR, 
                      folder = "by_assembly_group", assembly = assemblygroups),
        # QUANTIFICATION BASED ON SPIKE FILE
        copies = expand(os.path.join(OUTPUTDIR, "salmon_{folder}", "copiesperL.tab"), 
                        folder = "by_assembly_group",
                        base = OUTPUTDIR),
        # EUKULELE
        eukulele = expand(os.path.join(OUTPUTDIR, "eukulele_{folder}"), 
                        folder = "by_assembly_group",
                        base = OUTPUTDIR)