RedDog.py

#!/bin/env python

'''
RedDog V1beta.11 ("StopBreakingIt") 260719 
====== 
Copyright (c) 2016 David Edwards, Bernie Pope, Kat Holt
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, 
are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, 
this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, 
this list of conditions and the following disclaimer in the documentation 
and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors 
may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, 
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Description: 

This program implements a worklow pipeline for short read length
sequencing analysis, including the read mapping task, through to variant
detection, followed by analyses (SNPs only).

It uses Rubra (https://github.com/bjpop/rubra) based on the
Ruffus package (v2.2).

It supports parallel evaluation of independent pipeline stages,
and can run stages on a cluster environment.

Note: for Illumina paired-end or single reads, or Ion Torrent single reads.
IMPORTANT: See config file/instructions for input options/requirements

Version History: See ReadMe.txt

'''
from ruffus import *
import os
import shutil
import sys
import glob
from rubra.utils import pipeline_options
from rubra.utils import (runStageCheck, splitPath)
from pipe_utils import (isGenbank, isFasta, chromInfoFasta, chromInfoGenbank, getValue, 
                        getCover, make_sequence_list, getSuccessCount, make_run_report, 
                        get_run_report_data, getFastaDetails, checkBases)

version = "V1beta.11"

modules = pipeline_options.stageDefaults['modules']

# determine the reference file,
# list of sequence files, and list of chromosmes.
try:
    reference = pipeline_options.reference
except:
    print "\nNo Reference supplied"
    print "Pipeline Stopped: please supply a reference in the config file\n"
    sys.exit()    

#check that a reference has been given in the options file
if reference == "":
    print "\nNo Reference supplied"
    print "Pipeline Stopped: please supply a reference in the config file\n"
    sys.exit()    

#check whether reference file exists
if not os.path.exists(reference):
    print "\nReference supplied does not exist"
    print "Pipeline Stopped: please check supplied reference\n"
    sys.exit()    

#check whether reference is in FASTA or GenBank format
if isFasta(reference):
    refGenbank = False
    checkBases(reference, 'fasta')
    replicons = chromInfoFasta(reference)

elif isGenbank(reference):
    refGenbank = True
    checkBases(reference, 'genbank')
    replicons = chromInfoGenbank(reference)
else:
    print "\nReference not in GenBank or FASTA format"
    print "Pipeline Stopped: please check your reference\n"
    sys.exit()

# check that reference name does not in contain "+"
if reference.find("+") != -1:
    print "\nReference has an illegal character in the name ('+') "
    print "Pipeline Stopped: please change the name of the reference\n"
    sys.exit()

# check that replicons in reference have non-unique names
if len(replicons)>1:
    for i in range(len(replicons)-1):
        for j in range (i+1, len(replicons)):
            if replicons[i][0] != replicons[j][0]:
                pass
            else:
                print "\nReference has replicons with non-unique names: " + replicons[i][0]
                print "Pipeline Stopped: please check your reference\n"
                sys.exit()

# check that replicon names in reference do not in contain '|', ':', '+', or '.'
# these all cause problems in third-party scripts
for i in range(len(replicons)):
    if replicons[i][0].find(":") != -1 or replicons[i][0].find("+") != -1 or replicons[i][0].find("|") != -1 or replicons[i][0].find(".") != -1:
        print "\nReference has replicon with an illegal character ('|', ':', '+', or '.'): " + replicons[i][0]
        print "Pipeline Stopped: please change the name of the replicon in the reference\n"
        sys.exit()

(refPrefix, refName, refExt) = splitPath(reference)

try:
    sequencePatterns = pipeline_options.sequences
except:
    print "\nNo Sequences option supplied"
    print "Pipeline Stopped: please include 'sequences' in the config file\n"
    sys.exit()    

try:
    runType = pipeline_options.runType
except:
    runType = ""

try:
    core_replicon = pipeline_options.core_replicon
except:
    core_replicon = ""

#check that a 'known' runType has been supplied
if runType != "":
    if runType == "pangenome" or runType == "phylogeny":
        pass
    else:
        print "\nUnrecognised run type"
        print "Pipeline Stopped: please check 'runType' in the config file\n"
        sys.exit()

# if no runType entered, work out default runType on number of replicons in reference
if runType == "":
    if len(replicons) > 100:
        runType = "pangenome"
    elif len(replicons) > 0:
        runType = "phylogeny"
if len(replicons) < 1:
    print "\nNo chromosomes found in reference"
    print "Pipeline Stopped: please check 'reference' in the config file\n"
    sys.exit()

repliconNames = []
longest_replicon_length = 0
for repliconName, repliconLength in replicons:
    repliconNames.append(repliconName)
    if int(repliconLength) > longest_replicon_length:
        longest_replicon_length = int(repliconLength)

core_replicons = []
if runType == "pangenome":
    if core_replicon == "":
        for repliconName, repliconLength in replicons:
            if int(repliconLength) == longest_replicon_length:
                core_replicon = repliconName
    core_replicons = core_replicon.split(', ')

sequences = []
if type(sequencePatterns) == list:
    for pattern in sequencePatterns:
        sequences += glob.glob(pattern)
else:
    sequences = glob.glob(sequencePatterns)

if sequences == []:
    if sequencePatterns == "":
        print "\nNo mapping - analysis only"
        print "Pipeline Stopped: Not Yet Available\n"
        sys.exit()
    else:
        print "\nNo matching sequences found"
        print "Pipeline Stopped: please check 'sequences' in the config file\n"
        sys.exit()

for sequence in sequences:
    if sequence.find(":") != -1 or sequence.find("+") != -1:
        print "\nA read set has an illegal character (':' or '+'): " + sequence
        print "Pipeline Stopped: please change the name of the read set\n"
        sys.exit()

try:
    readType = pipeline_options.readType
except:
    readType = 'PE'    

if readType == 'IT' or readType == 'PE' or readType == 'SE':
    pass
elif readType == '':
    readType = 'PE'
else:
    print "\nUnrecognised read type"
    print "Pipeline Stopped: please check 'readType' in the config file\n"
    sys.exit()

if readType == 'SE':
    readPattern = '.fastq.gz'
elif readType == 'IT':
    readPattern = '_in.iontor.fastq.gz'

mapping_out = ""
try:
    mapping = pipeline_options.mapping
except:
    mapping = 'bowtie'

if mapping == "":
    mapping = 'bowtie'

if mapping == 'bwa' and readType == 'SE':
    mapping_out = 'BWA V0.6.2 samse'
elif mapping == 'bwa' and readType == 'PE':
    mapping_out = 'BWA V0.6.2 sampe'
elif mapping == 'bowtie':
    mapping_out = 'Bowtie2 V2.2.9'
else:
    print "\nUnrecognised mapping option"
    print "Pipeline Stopped: please check 'mapping' in the config file\n"
    sys.exit()

try:
    SNPcaller = pipeline_options.SNPcaller
    if not(SNPcaller != 'c' or SNPcaller != 'm'):
        print "\nUnrecognised SNPcaller option"
        print "Pipeline Stopped: please check 'SNPcaller' in the config file\n"
    else:
        SNPcaller = '-' + SNPcaller
except:
    SNPcaller = '-c'

sequence_list = []
for sequence in sequences:
    (prefix, name, ext) = splitPath(sequence)
    if readType == "IT":
        sequence_list.append(name[:-16])
    elif readType == "PE":
        if name.find('_1.fastq') != -1 and name[:-8] not in sequence_list:
            sequence_list.append(name[:-8])
        if name.find('_2.fastq') != -1 and name[:-8] not in sequence_list:
            sequence_list.append(name[:-8])            
    else:
        sequence_list.append(name[:-6])

if readType == 'PE':
    missing_pairs = []
    for seqName in sequence_list:
        test_1 = False
        test_2 = False
        for sequence in sequences:
            if sequence.find(seqName+'_1.f') != -1:
                test_1 = True
            if sequence.find(seqName+'_2.f') != -1:
                test_2 = True
        if test_1 == False or test_2 == False:
            missing_pairs.append(seqName)
    if missing_pairs != []:
        print "\nNot all sequence sets have pairs:"
        for seq in missing_pairs:
            print seq
        print "Pipeline Stopped: please fix sequence pairs\n"
        sys.exit()

if mapping == 'bowtie':
    try:
        bowtie_map_type = pipeline_options.bowtie_map_type
    except:
        bowtie_map_type = '--sensitive-local'
    if bowtie_map_type == "":
        bowtie_map_type = '--sensitive-local'
    if (bowtie_map_type == "--very-fast" or
        bowtie_map_type == "--fast" or
        bowtie_map_type == "--sensitive" or
        bowtie_map_type == "--very-sensitive" or
        bowtie_map_type == "--very-fast-local" or
        bowtie_map_type == "--fast-local" or
        bowtie_map_type == "--sensitive-local" or
        bowtie_map_type == "--very-sensitive-local"):
        pass        
    else:
        print "\nUnrecognised Bowtie2 mapping option"
        print "Pipeline Stopped: please check 'bowtie_map_type' in the config file\n"
        sys.exit()
else:
    bowtie_map_type = "-"

try:
    bowtie_X_value = pipeline_options.bowtie_X_value
except:
    bowtie_X_value = 2000

try:
    minDepth = pipeline_options.minimum_depth
except:
    minDepth = 5

try:
    HetsVCF = pipeline_options.HetsVCF
    if HetsVCF != True and HetsVCF != False:
        print "\nUnrecognised HetsVCF option"
        print "Pipeline Stopped: please check 'HetsVCF' in the config file\n"
        sys.exit()
except:
    HetsVCF = True

try:
    coverFail = pipeline_options.cover_fail
except:
    coverFail = 50

try:
    depthFail = pipeline_options.depth_fail
except:
    depthFail = 10

try:
    mappedFail = pipeline_options.mapped_fail
except:
    mappedFail = 50

try:
    sdOutgroupMultiplier = pipeline_options.sd_out
except:
    sdOutgroupMultiplier = 2

try:
    strand_bias_cutoff = pipeline_options.strand_bias_cutoff
except:
    strand_bias_cutoff = 0.8

try:
    check_reads_mapped = pipeline_options.check_reads_mapped
except:
    check_reads_mapped = ""

if check_reads_mapped == "":
    for repliconName, repliconLength in replicons:
        if int(repliconLength) == longest_replicon_length:
            check_reads_mapped = repliconName
elif check_reads_mapped != 'off':
    if check_reads_mapped.find(',') == -1:
        if check_reads_mapped not in repliconNames:
            print "\nUnrecognised replicon used in 'check_reads_mapped': " + check_reads_mapped
            print "Pipeline Stopped: please check 'check_reads_mapped' in the config file\n"
            sys.exit()
    else:
        found_x = False
        final_ratio = 1.0
        list_of_replicons = []
        check_reps = check_reads_mapped.split(',')
        for item in check_reps:
            if item != 'x':
                if found_x != True:
                    list_of_replicons.append(item)
                else:
                    final_ratio -= float(item)
            else:
                found_x = True
        if final_ratio <= 0:
            print "\nFinal ratio in 'check_reads_mapped' less than or equal to zero"
            print "Pipeline Stopped: please check ratio(s) in 'check_reads_mapped' in the config file\n"
            sys.exit()
        list_of_replicons_done = []
        for replicon in list_of_replicons:
            if replicon not in repliconNames:
                print "\nUnrecognised replicon in 'check_reads_mapped': " + replicon
                print "Pipeline Stopped: please check 'check_reads_mapped' in the config file\n"
                sys.exit()
            elif replicon not in list_of_replicons_done:
                list_of_replicons_done.append(replicon)
            else:
                print "\nReplicon repeated in 'check_reads_mapped': " + replicon
                print "Pipeline Stopped: please check 'check_reads_mapped' in the config file\n"
                sys.exit()

try:
    outPrefix = pipeline_options.output
except:
    outPrefix = ""

if outPrefix == "":
    print "\nNo Output folder given"
    print "Pipeline Stopped: please check 'output' in the config file\n"
    sys.exit()

if outPrefix[-1] != '/':
    outPrefix += '/'

outTempPrefix = outPrefix + 'temp/'
outSuccessPrefix = outTempPrefix + 'success/'
outBamPrefix = outPrefix + 'bam/'
outVcfPrefix = outPrefix + 'vcf/'

if os.path.isdir(outPrefix) and not(os.path.exists(outSuccessPrefix + "dir.makeDir.Success")):
    print "\nOutput folder already exists"
    print "Pipeline Stopped: please change 'output' to a new folder\n"
    sys.exit()    

try:
    outMerge = pipeline_options.out_merge_target
except:
    print "\n'out_merge_target' not set"
    print "Pipeline Stopped: please set 'out_merge_target' in the config file\n"
    sys.exit()    

if outPrefix == outMerge:
    print "\nOutput folder and out_merge_target for run are the same"
    print "Pipeline Stopped: please check 'output' and 'out_merge_target' in the config file\n"
    sys.exit()

continuity_test = False
if outMerge != '':
    if outMerge[-1] != '/':
        outMerge += '/'
    outMergeBam = outMerge + 'bam/'
    outMergeVcf = outMerge + 'vcf/'
    if not(os.path.isdir(outMerge)):
        print "\nMerge target folder not found"
        print "Pipeline Stopped: please change 'out_merge_target' to previous output folder\n"
        sys.exit()
    else:
        if not(os.path.isdir(outMergeBam)):
            print "\nBAM folder not found"
            print "Pipeline Stopped: check 'out_merge_target' has BAM folder\n"
            sys.exit()    
        if not(os.path.isdir(outMergeVcf)):
            print "\nVCF folder not found"
            print "Pipeline Stopped: check 'out_merge_target' has VCF folder\n"
            sys.exit()    
    if os.path.exists(outMerge + 'finish.deleteDir.Success'):
        print "\n'out_merge_target' still has 'finish.deleteDir.Success' file"
        print "Pipeline Stopped: please delete this file before restarting\n"
        sys.exit()
    if os.path.exists(outMerge + refName +'_AllStats.txt') != True:
        print "\n'out_merge_target' has no '"+ refName+"_AllStats.txt' file"
        print "Pipeline Stopped: please check you have the correct 'reference' and/or "
        print "\t\t  'out_merge_target' before restarting\n"
        sys.exit()
    merge_run = True
    if os.path.exists(outMerge + refName + '_run_report.txt'):
        (read_history, 
        run_history, 
        old_ref_name, 
        old_ref_format, 
        old_replicon_count, 
        old_core_replicon_list, 
        old_run_type, 
        old_bowtie_preset, 
        old_bowtie_X, 
        old_user_failed_list, 
        old_min_depth, 
        old_cover_fail, 
        old_depth_fail, 
        old_mapped_fail, 
        old_replicon_test_list, 
        old_replicon_percent_list, 
        old_conservation,
        old_sd_out,
        old_replicon_list) = get_run_report_data(outMerge + refName + '_run_report.txt')
        continuity_test = True
        run_count = run_history.count('merge')
        if run_count == -1:
            run_count = 0
    else:
        print "\nMerge Run: No prior run report found"
        print "No continuity tests will be done...\n"
        run_history = '-'
        read_history = '_'
else:
    merge_run = False
    run_history = '-'
    read_history = '-'

try:
    if pipeline_options.replaceReads != "":
        replaceReads = pipeline_options.replaceReads
    else:
        replaceReads = "-"
except:
    replaceReads = "-"

try:
    conservation = float(pipeline_options.conservation)
except:
    conservation = 0.95

if conservation > 1.0 or conservation < 0.0:
    print "\n'conservation' set to value outside parameters"
    print "Pipeline Stopped: please change 'conservation' to a value between 0 and 1\n"
    sys.exit()

try:
    DifferenceMatrix = pipeline_options.DifferenceMatrix
    if DifferenceMatrix != True and DifferenceMatrix != False:
        print "\nUnrecognised DifferenceMatrix option"
        print "Pipeline Stopped: please check 'DifferenceMatrix' in the config file\n"
        sys.exit()
except:
    DifferenceMatrix = False

try:
    force_tree = pipeline_options.force_tree
    if force_tree != True and force_tree != False:
        print "\nUnrecognised force_tree option"
        print "Pipeline Stopped: please check 'force_tree' in the config file\n"
        sys.exit()
except:
    force_tree = False

try:
    force_no_tree = pipeline_options.force_no_tree
    if force_no_tree != True and force_no_tree != False:
        print "\nUnrecognised force_no_tree option"
        print "Pipeline Stopped: please check 'force_no_tree' in the config file\n"
        sys.exit()
except:
    force_no_tree = False

full_sequence_list = []
if outMerge == '':
    for item in sequence_list:
        full_sequence_list.append(item)
else:
    for item in sequence_list:
        full_sequence_list.append(item)
    try:
        sequence_list_file = open((outMerge + 'sequence_list.txt') , "r")
    except:
        print "\nNo sequence list found"
        print "Pipeline Stopped: please generate new 'sequence_list.txt' file\n"
        sys.exit()
    for line in sequence_list_file:
        full_sequence_list.append(line[:-1])
    sequence_list_file.close()

duplicate_isolate_name = []
for i in range(len(full_sequence_list)-1):
    for j in range(i+1, len(full_sequence_list)):
        if full_sequence_list[i] == full_sequence_list[j]:
            duplicate_isolate_name.append(i)

if duplicate_isolate_name != []:
    print "\nDuplicate reads (isolate) names found"
    print "Pipeline Stopped: please remove/rename duplicates"
    for i in duplicate_isolate_name:
        print full_sequence_list[i]
    print "\n" 
    sys.exit()

full_sequence_list_string = ""
for sequence in full_sequence_list:
    full_sequence_list_string += sequence + ","
full_sequence_list_string.rstrip()

sequence_list_string = ""
for sequence in sequence_list:
    sequence_list_string += sequence + ","
sequence_list_string.rstrip()

success_count = len(glob.glob(outSuccessPrefix+"*.Success"))

# test for continuity with prior run for merge runs
if continuity_test:
    if refName != old_ref_name:
        print "\nReference name is different from prior run(s)"
        print "Pipeline Stopped: please use correct reference\n"
        sys.exit()
    if refGenbank and old_ref_format != 'Genbank':
        print "\nExpected FASTA reference, not Genbank"
        print "Pipeline Stopped: please use correct reference\n"
        sys.exit()
    if not refGenbank and old_ref_format == 'Genbank':
        print "\nExpected Genbank reference, not FASTA"
        print "Pipeline Stopped: please use correct reference\n"
        sys.exit()
    if len(replicons) != int(old_replicon_count):
        print "\nDifferent number of replicons found in reference"
        print "Pipeline Stopped: please use correct reference\n"
        sys.exit()
    if runType != old_run_type:
        print "\nExpected " + old_run_type + " run; " + runType + " run specified"
        print "Pipeline Stopped: please specify same run type as previously used ("+old_run_type+")\n"
        sys.exit()
    replicon_fail = False
    if runType == 'pangenome':
        for replicon in old_core_replicon_list:
            if replicon not in core_replicons:
                replicon_fail = True
        for replicon in core_replicons:
            if replicon not in old_core_replicon_list:
                replicon_fail = True
        if replicion_fail:
            print "\nCore replicons have changed since last run"
            print "Pipeline Stopped: please specify reference with same replicons as previously used\n"
            sys.exit()
    else:
        replicon_names = []
        for replicon in replicons:
            replicon_names.append(replicon[0])
            if replicon[0] not in old_replicon_list:
                replicon_fail = True
        for replicon in old_replicon_list:
            if replicon not in replicon_names:
                replicon_fail = True
        if replicon_fail:
            print "\nReplicons have changed since last run"
            print "Pipeline Stopped: please specify reference with same replicons as previously\n"
            sys.exit()

    if old_mapped_fail != 'off':
        old_check_reads_mapped = ""
        for replicon in old_replicon_test_list:
            if len(old_replicon_test_list) > 1:
                old_check_reads_mapped += (replicon + ",")
            else:
                old_check_reads_mapped = replicon
        if len(old_replicon_test_list) > 1:
            old_check_reads_mapped += 'x,'
            for number in range(len(old_replicon_percent_list)-1):                
                if number < len(old_replicon_percent_list)-2:
                    old_check_reads_mapped += str(float(old_replicon_percent_list[number])/100) + ','
                else:
                    old_check_reads_mapped += str(float(old_replicon_percent_list[number])/100)

        if check_reads_mapped != 'off':
            check_test = True
            if len(old_replicon_test_list) == 1:
                if check_reads_mapped.find(',x,') != -1:
                    check_test = False
                else:
                    if old_replicon_test_list[0] != check_reads_mapped:
                        check_test = False

            if len(old_replicon_test_list) > 1:
                if check_reads_mapped.find(',x,') == -1:
                    check_test = False
                else:
                    all_values = check_reads_mapped.split(',x,')
                    names = all_values[0].split(',')
                    values = all_values[1].split(',')
                    if len(names) != len(old_replicon_test_list):
                        check_test = False
                    else:
                        for name in names:
                            if name not in old_replicon_test_list:
                                check_test = False
                        for name in old_replicon_test_list:
                            if name not in names:
                                check_test = False
                        replicon_value_test = []
                        for number in range(len(old_replicon_percent_list)-1):
                            replicon_value_test.append(float(old_replicon_percent_list[number])/100)
                        if len(values) != len(replicon_value_test):
                            check_test = False
                        else:
                            for number in range(len(values)):
                                if float(values[number]) != replicon_value_test[number]:
                                    check_test = False 

            if not check_test:
                print "\n'check_reads_mapped' has changed since last run"
                value_change = False
                attempts_count = 0
                while value_change == False:
                    keyboard_entry = raw_input("\nWhich 'check_reads_mapped' do you want to use: \n[1] the new value, or\n[2] the old value?\n")
                    if keyboard_entry == '1' or keyboard_entry == '2':
                        value_change = True
                    if keyboard_entry == '2':
                        print "\n'check_reads_mapped' restored to previously used setting:"
                        print old_check_reads_mapped + "\n\n"
                        check_reads_mapped = old_check_reads_mapped
                    elif keyboard_entry == '1':
                        print "\n'check_reads_mapped' using new setting:"
                        print check_reads_mapped + "\n"
                else:
                    attempts_count +=1
                    if attempts_count >= 3:
                        print "\nPipeline Stopped: too many tries\n"
                        sys.exit()
                    else:
                        print "Please enter either '1' for 'yes', or '2' for 'no'"

        else:
            print "\n'check_reads_mapped' has changed to 'off' since last run"    
            value_change = False
            attempts_count = 0
            while value_change == False:
                keyboard_entry = raw_input('\nAre you sure you want to turn off checking percentage of reads mapped: \n[1] yes, or\n[2] no?\n')
                if keyboard_entry == '1' or keyboard_entry == '2':
                    value_change = True
                    if keyboard_entry == '2':
                        print "\n'check_reads_mapped' restored to previously used setting:"
                        print old_check_reads_mapped + "\n"
                        check_reads_mapped = old_check_reads_mapped
                    elif keyboard_entry == '1':
                        print "\n'check_reads_mapped' set to 'off' confirmed\n"
                else:
                    attempts_count +=1
                    if attempts_count >= 3:
                        print "\nPipeline Stopped: too many tries\n"
                        sys.exit()
                    else:
                        print "Please enter either '1' for 'yes', or '2' for 'no'"

    else:
        if check_reads_mapped != "off":
            print "\n'check_reads_mapped' has changed from 'off' since last run"    
            value_change = False
            attempts_count = 0
            while value_change == False:
                keyboard_entry = raw_input('\nAre you sure you want to turn on checking percentage of reads mapped: \n[1] yes, or\n[2] no?\n')
                if keyboard_entry == '1' or keyboard_entry == '2':
                    value_change = True
                    if keyboard_entry == '2':
                        print "\n'check_reads_mapped' set to 'off' confirmed\n"
                        check_reads_mapped = 'off'
                    elif keyboard_entry == '1':
                        print "\n'check_reads_mapped' changed from 'off' and set to:"
                        print check_reads_mapped + "\n"
                else:
                    attempts_count +=1
                    if attempts_count >= 3:
                        print "\nPipeline Stopped: too many tries\n"
                        sys.exit()
                    else:
                        print "Please enter either '1' for 'yes', or '2' for 'no'"

    if old_bowtie_preset != '' and old_bowtie_preset != bowtie_map_type:
        print "\n'bowtie_map_type' has changed since last run"
        value_change = False
        attempts_count = 0
        while value_change == False:
            keyboard_entry = raw_input('\nDo you wish to use: \n[1] the new value ('+bowtie_map_type +'), or\n[2] the old value? ('+old_bowtie_preset+')\nNote: this only affects new read sets\n')
            if keyboard_entry == '1' or keyboard_entry == '2':
                value_change = True
                if keyboard_entry == '2':
                    bowtie_map_type = old_bowtie_preset 
                print "\n'bowtie_map_type' set to " + bowtie_map_type
            else:
                attempts_count +=1
                if attempts_count >= 3:
                    print "\nPipeline Stopped: too many tries\n"
                    sys.exit()
                else:
                    print "Please enter either '1' for new value, or '2' for old value"

    if old_bowtie_X != '' and int(old_bowtie_X) != bowtie_X_value:
        print "\n'bowtie_X_value' has changed since last run"
        value_change = False
        attempts_count = 0
        while value_change == False:
            keyboard_entry = raw_input('\nDo you wish to use: \n[1] the new value ('+str(bowtie_X_value) +'), or\n[2] the old value? ('+old_bowtie_X+')\nNote: this only affects new read sets\n')
            if keyboard_entry == '1' or keyboard_entry == '2':
                value_change = True
                if keyboard_entry == '2':
                    bowtie_X_value = int(old_bowtie_X)
                print "\n'bowtie_X_value' set to " + str(bowtie_X_value)
            else:
                attempts_count +=1
                if attempts_count >= 3:
                    print "\nPipeline Stopped: too many tries\n"
                    sys.exit()
                else:
                    print "Please enter either '1' for new value, or '2' for old value"

    if int(old_min_depth) != minDepth:
        print "\n'minimum_depth' for SNP calling has changed since last run"
        value_change = False
        attempts_count = 0
        while value_change == False:
            keyboard_entry = raw_input('\nDo you wish to use: \n[1] the new value ('+str(minDepth)+'), or\n[2] the old value? ('+old_min_depth+')\nNote: this only affects new read sets\n')
            if keyboard_entry == '1' or keyboard_entry == '2':
                value_change = True
                if keyboard_entry == '2':
                    minDepth = int(old_min_depth)
                print "\n'minimum_depth' set to " + str(minDepth)
            else:
                attempts_count +=1
                if attempts_count >= 3:
                    print "\nPipeline Stopped: too many tries\n"
                    sys.exit()
                else:
                    print "Please enter either '1' for new value, or '2' for old value"

    if int(old_cover_fail) != coverFail:
        print "\n'cover_fail' has changed since last run"
        value_change = False
        attempts_count = 0
        while value_change == False:
            keyboard_entry = raw_input('\nDo you wish to use: \n[1] the new value ('+str(coverFail)+'), or\n[2] the old value? ('+old_cover_fail+')\n')
            if keyboard_entry == '1' or keyboard_entry == '2':
                value_change = True
                if keyboard_entry == '2':
                    coverFail = int(old_cover_fail)
                print "\n'cover_fail' set to " + str(coverFail)
            else:
                attempts_count +=1
                if attempts_count >= 3:
                    print "\nPipeline Stopped: too many tries\n"
                    sys.exit()
                else:
                    print "Please enter either '1' for new value, or '2' for old value"

    if int(old_depth_fail) != depthFail:
        print "\n'depth_fail' has changed since last run"
        value_change = False
        attempts_count = 0
        while value_change == False:
            keyboard_entry = raw_input('\nDo you wish to use: \n[1] the new value ('+str(depthFail)+'), or\n[2] the old value? ('+old_depth_fail+')\n')
            if keyboard_entry == '1' or keyboard_entry == '2':
                value_change = True
                if keyboard_entry == '2':
                    depthFail = int(old_depth_fail)
                print "\n'depth_fail' set to " + str(depthFail)
            else:
                attempts_count +=1
                if attempts_count >= 3:
                    print "\nPipeline Stopped: too many tries\n"
                    sys.exit()
                else:
                    print "Please enter '1' for new value, or '2' for old value"

    if old_mapped_fail != 'off' and check_reads_mapped != 'off':
        if int(old_mapped_fail) != mappedFail:
            print "\n'mapped_fail' has changed since last run"
            value_change = False
            attempts_count = 0
            while value_change == False:
                keyboard_entry = raw_input('\nDo you wish to use: \n[1] the new value ('+str(mappedFail)+'), or\n[2] the old value? ('+old_mapped_fail+')\n')
                if keyboard_entry == '1' or keyboard_entry == '2':
                    value_change = True
                    if keyboard_entry == '2':
                        mappedFail = int(old_mapped_fail)
                    print "\n'mapped_fail' set to " + str(mappedFail)
                else:
                    attempts_count +=1
                    if attempts_count >= 3:
                        print "\nPipeline Stopped: too many tries\n"
                        sys.exit()
                    else:
                        print "Please enter either '1' for new value, or '2' for old value"

    if int(old_sd_out) != sdOutgroupMultiplier:
        print "\n'sd_out' has changed since last run"
        value_change = False
        attempts_count = 0
        while value_change == False:
            keyboard_entry = raw_input('\nDo you wish to use: \n[1] the new value ('+str(sdOutgroupMultiplier)+'), or\n[2] the old value? ('+old_sd_out+')\n')
            if keyboard_entry == '1' or keyboard_entry == '2':
                value_change = True
                if keyboard_entry == '2':
                    sdOutgroupMultiplier = old_sd_out
                print "\n'sd_out' set to " + str(sdOutgroupMultiplier)
            else:
                attempts_count +=1
                if attempts_count >= 3:
                    print "\nPipeline Stopped: too many tries\n"
                    sys.exit()
                else:
                    print "Please enter '1' for new value, or '2' for old value"

    if float(old_conservation) != conservation:
        print "\n'conservation' has changed since last run"
        value_change = False
        attempts_count = 0
        while value_change == False:
            keyboard_entry = raw_input('\nDo you wish to use: \n[1] the new value ('+str(conservation)+'), or\n[2] the old value? ('+old_conservation+')\n')
            if keyboard_entry == '1' or keyboard_entry == '2':
                value_change = True
                if keyboard_entry == '2':
                    conservation = int(old_conservation)
                print "\n'conservation' set to " + str(conservation)
            else:
                attempts_count +=1
                if attempts_count >= 3:
                    print "\nPipeline Stopped: too many tries\n"
                    sys.exit()
                else:
                    print "Please enter '1' for new value, or '2' for old value"



#Phew! Now that's all set up, we can begin...
#but first, output run conditions to user and get confirmation to run
print "\nRedDog " + version + " - " + runType + " run\n"
print "Copyright (c) 2016 David Edwards, Bernie Pope, Kat Holt"
print "All rights reserved. (see README.txt for more details)\n"

print "Mapping: " + mapping_out
if mapping == 'bowtie':
    print "Preset Option: " + bowtie_map_type
if refGenbank == False:
    ref_string = 'FASTA'
else:
    ref_string = 'GenBank'
print str(len(replicons)) + " replicon(s) in " + ref_string + " reference " + refName
if runType != '':
    if runType == 'phylogeny':
        number_string = str(len(replicons))
    else:
        number_string = str(len(core_replicons))
    print number_string + " replicon(s) to be reported"
number_string = str(len(sequence_list))
if readType == 'PE':
    print number_string + " sequence pair(s) to be mapped"
else:
    print number_string + " sequence(s) to be mapped"

print "\nOutput folder:"
print outPrefix
if outMerge != '':
    print "Remember: this output folder will be deleted at the end of the run\n"
    print "Merge new sets with the following folder ('out_merge_target'):"
    print outMerge

if pipeline_options.no_check:
    start_run = True
else:
    start_run = False
start_count = 0
while start_run == False:
    keyboard_entry = raw_input('\nStart Pipeline? (y/n) ')
    if keyboard_entry == 'y' or keyboard_entry == 'Y' or keyboard_entry == 'yes' or keyboard_entry == 'Yes' or keyboard_entry == 'YES':
        start_run = True
    elif keyboard_entry == 'n' or keyboard_entry == 'N' or keyboard_entry == 'no' or keyboard_entry == 'No' or keyboard_entry == 'NO':
        print "\nPipeline Stopped: user request\n"
        sys.exit()
    else:
        start_count +=1
        if start_count >= 3:
            print "\nPipeline Stopped: too many tries\n"
            sys.exit()
        else:
            print "Please enter 'y' (yes) or 'n' (no)"

print "\nStarting pipeline..."
stage_count = 0

# Create temp and other output subfolders
@files(input==None, outSuccessPrefix + "dir.makeDir.Success")
def makeDir(input, flagFile):
    runStageCheck('makeDir', flagFile, outPrefix, full_sequence_list_string)
stage_count += 1

if refGenbank == False:
    # Copy reference to outTemp
    newReference = outTempPrefix + refName + refExt
    @follows(makeDir)
    @files(reference, [newReference, outSuccessPrefix + refName + '.copyRef.Success'])
    def copyRef(reference, outputs):
        _output, flagFile = outputs
        runStageCheck('copyRef', flagFile, reference, outTempPrefix)
    reference = newReference
    stage_count += 1

    # Index copy of reference for SNP calling by samtools
    @follows(copyRef)
    @files(reference, [reference + '.fai', outSuccessPrefix + refName + '.indexRef.Success'])
    def indexRef(reference, outputs):
        _output, flagFile = outputs
        runStageCheck('indexRef', flagFile, reference)
    stage_count += 1

    if mapping == 'bowtie':
        # Index the reference file for bowtie2
        @follows(copyRef)
        @files(reference, [outTempPrefix + refName + '.1.bt2', outSuccessPrefix + refName + '.buildBowtieIndex.Success'])
        def buildBowtieIndex(reference, outputs):
            output, flagFile = outputs
            base = output[:-6]
            runStageCheck('buildBowtieIndex', flagFile, reference, base)
        stage_count += 1
    else:
        # Index the reference file for bwa
        @follows(copyRef)
        @files(reference, [reference + '.bwt', outSuccessPrefix + refName + '.buildBWAIndex.Success'])
        def buildBWAIndex(reference, outputs):
            _output, flagFile = outputs
            runStageCheck('buildBWAIndex', flagFile, reference)
        stage_count += 1

else:
    #make a fasta version of the reference for mapping
    genbank = reference
    reference = outTempPrefix + refName + ".fasta"
    @follows(makeDir)
    @files(genbank, [reference, outSuccessPrefix + refName + '.makeRef.Success'])
    def makeRef(genbank, outputs):        
        output, flagFile = outputs
        runStageCheck('makeRef', flagFile, genbank, output)
    stage_count += 1

    # Index constructed reference for SNP calling by samtools
    @follows(makeRef)
    @files(reference, [reference + '.fai', outSuccessPrefix + refName + '.indexRef.Success'])
    def indexRef(reference, outputs):
        _output, flagFile = outputs
        runStageCheck('indexRef', flagFile, reference)
    stage_count += 1

    if mapping == 'bowtie':
        # Index the reference file for bowtie2
        @follows(makeRef)
        @files(reference, [outTempPrefix + refName + '.1.bt2', outSuccessPrefix + refName + '.buildBowtieIndex.Success'])
        def buildBowtieIndex(reference, outputs):
            output, flagFile = outputs
            base = output[:-6]
            runStageCheck('buildBowtieIndex', flagFile, reference, base)
        stage_count += 1
    else:
        # Index the reference file for bwa
        @follows(makeRef)
        @files(reference, [reference + '.bwt', outSuccessPrefix + refName + '.buildBWAIndex.Success'])
        def buildBWAIndex(reference, outputs):
            _output, flagFile = outputs
            runStageCheck('buildBWAIndex', flagFile, reference)
        stage_count += 1

if mapping == 'bowtie':
    if readType == "PE":
        #align reads with Bowtie2 to sorted bam
        input = r'(.*)\/(.+)_1\.fastq.gz'
        extraInput = [r'\1/\2_2.fastq.gz']
        @follows(buildBowtieIndex)
        @transform(sequences, regex(input), add_inputs(extraInput), [outTempPrefix + r'\2/\2.bam', outSuccessPrefix + r'\2.alignBowtiePE.Success'])
        def alignBowtiePE(inputs, outputs):
            output, flagFile = outputs
#            (prefix, name, ext) = splitPath(output)
#            out = prefix + '/' + name
            seq1, [seq2] = inputs
            base = outTempPrefix + refName
            runStageCheck('alignBowtiePE', flagFile, bowtie_map_type, base, seq1, seq2, bowtie_X_value, output)
        stage_count += len(sequence_list)

        @transform(alignBowtiePE, regex(r"(.*)\/(.+).bam"), outSuccessPrefix + r'\2.checkBam.Success')
        def checkBam(inputs, flagFile):
            bamFile, _success = inputs
            (prefix, name, ext) = splitPath(bamFile)
            read_set = ""
            for seq in sequences:
                if seq.find(name+'_1.fastq') != -1:
                    read_set = seq
            runStageCheck('checkBam', flagFile, bamFile, readType, read_set)
        stage_count += len(sequence_list)        

        # Index sorted BAM alignments using samtools
        @follows(checkBam)
        @transform(alignBowtiePE, regex(r"(.*)\/(.+).bam"), [r'\1/\2.bam.bai', outSuccessPrefix + r'\2.indexBam.Success'])
        def indexBam(inputs, outputs):
            output, flagFile = outputs
            bamFile, _success = inputs
            runStageCheck('indexBam', flagFile, bamFile)
        stage_count += len(sequence_list) 

        #get bam stats by replicon
        @follows(indexBam)
        @transform(alignBowtiePE, regex(r"(.*)\/(.+).bam"), [r'\1/\2_samStats.txt', outSuccessPrefix + r'\2.getSamStats.Success'])
        def getSamStats(inputs, outputs):
            output, flagFile = outputs
            bamFile, _success = inputs
            runStageCheck('getSamStats', flagFile, bamFile, output)
        stage_count += len(sequence_list) 

# checkpoint_getSamStats
        @merge(getSamStats, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "getSamStats.checkpoint.Success"])
        def checkpoint_getSamStats(inputs,outputs):
            output, flagFile = outputs
            runStageCheck('checkpoint', flagFile, outTempPrefix, 'getSamStats')
        stage_count += 1

        #filter unmapped reads
        @follows(indexBam, checkpoint_getSamStats)
        @transform(alignBowtiePE, regex(r"(.*)\/(.+).bam"), [outBamPrefix + r'\2.bam', outSuccessPrefix + r'\2.filterUnmapped.Success'])
        def filterUnmapped(inputs, outputs):
            output, flagFile = outputs
            bamFile, _success = inputs
#            (prefix, name, ext) = splitPath(output)
#            out = prefix + '/' + name
            runStageCheck('filterUnmapped', flagFile, bamFile, output)
        stage_count += len(sequence_list) 

    else:
        if readType=="SE":
            #align reads with Bowtie2 to sorted bam
            @follows(buildBowtieIndex)
            @transform(sequences, regex(r"(.*)\/(.+).fastq.gz"), [outTempPrefix + r'\2/\2.bam', outSuccessPrefix + r'\2.alignBowtie.Success'])
            def alignBowtie(input, outputs):
                output, flagFile = outputs
#                (prefix, name, ext) = splitPath(output)
#                out = prefix + '/' + name
                base = outTempPrefix + refName
                runStageCheck('alignBowtie', flagFile, bowtie_map_type, base, input, output)
            stage_count += len(sequence_list) 
     
        else: #readType == "IT"
            #align reads with Bowtie2 to sorted bam
            @follows(buildBowtieIndex)
            @transform(sequences, regex(r"(.*)\/(.+)_in.iontor.fastq.gz"), [outTempPrefix + r'\2/\2.bam', outSuccessPrefix + r'\2.alignBowtie.Success'])
            def alignBowtie(input, outputs):
                output, flagFile = outputs
#                (prefix, name, ext) = splitPath(output)
#                out = prefix + '/' + name
                base = outTempPrefix + refName
                runStageCheck('alignBowtie', flagFile, bowtie_map_type, base, input, output)
            stage_count += len(sequence_list) 

        @transform(alignBowtie, regex(r"(.*)\/(.+).bam"), outSuccessPrefix + r'\2.checkBam.Success')
        def checkBam(inputs, flagFile):
            bamFile, _success = inputs
            (prefix, name, ext) = splitPath(bamFile)
            read_set = ""
            test = name+readPattern
            for seq in sequences:
                if seq.find(test) != -1:
                    read_set = seq
            runStageCheck('checkBam', flagFile, bamFile, readType, read_set)
        stage_count += len(sequence_list)        

        # Index sorted BAM alignments using samtools
        @follows(checkBam)
        @transform(alignBowtie, regex(r"(.*)\/(.+).bam"), [r'\1/\2.bam.bai', outSuccessPrefix + r'\2.indexBam.Success'])
        def indexBam(inputs, outputs):
            output, flagFile = outputs
            bamFile, _success = inputs
            runStageCheck('indexBam', flagFile, bamFile)
        stage_count += len(sequence_list) 

        #get bam stats by replicon
        @follows(indexBam)
        @transform(alignBowtie, regex(r"(.*)\/(.+).bam"), [r'\1/\2_samStats.txt', outSuccessPrefix + r'\2.getSamStats.Success'])
        def getSamStats(inputs, outputs):
            output, flagFile = outputs
            bamFile, _success = inputs
            runStageCheck('getSamStats', flagFile, bamFile, output)
        stage_count += len(sequence_list) 

# checkpoint_getSamStats
        @merge(getSamStats, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "getSamStats.checkpoint.Success"])
        def checkpoint_getSamStats(inputs,outputs):
            output, flagFile = outputs
            runStageCheck('checkpoint', flagFile, outTempPrefix, 'getSamStats')
        stage_count += 1

        #filter unmapped reads
        @follows(indexBam, checkpoint_getSamStats)
        @transform(alignBowtie, regex(r"(.*)\/(.+).bam"), [outBamPrefix + r'\2.bam', outSuccessPrefix + r'\2.filterUnmapped.Success'])
        def filterUnmapped(inputs, outputs):
            output, flagFile = outputs
            bamFile, _success = inputs
#            (prefix, name, ext) = splitPath(output)
#            out = prefix + '/' + name
            runStageCheck('filterUnmapped', flagFile, bamFile, output)
        stage_count += len(sequence_list) 

else: # mapping = 'BWA'
    if readType == "PE":
        # Align 'forward' sequences reads to the reference genome.
        @follows(buildBWAIndex)
        @transform(sequences, regex(r'(.*)\/(.+)_1\.fastq.gz'), [outTempPrefix + r'\2/\2_1.sai', outSuccessPrefix + r"\2.alignForward.Success"])
        def alignForward(sequence, outputs):
            output, flagFile = outputs
            runStageCheck('alignSequence', flagFile, reference, sequence, output)
        stage_count += len(sequences)/2 

        # Align 'reverse' sequences reads to the reference genome.
        @follows(buildBWAIndex)
        @transform(sequences, regex(r'(.*)\/(.+)_2\.fastq.gz'), [outTempPrefix + r'\2/\2_2.sai', outSuccessPrefix + r"\2.alignReverse.Success"])
        def alignReverse(sequence, outputs):
            output, flagFile = outputs
            runStageCheck('alignSequence', flagFile, reference, sequence, output)
        stage_count += len(sequences)/2

        #align reads with BWA to sorted bam
        input = r'(.*)\/(.+)_1\.sai'
        extraInput = [r'\1/\2_2.sai']
        @follows(alignReverse)
        @transform(alignForward, regex(input), add_inputs(extraInput), [r'\1/\2.bam', outSuccessPrefix + r'\2.alignBWAPE.Success'])
        def alignBWAPE(inputs, outputs):
            output, flagFile = outputs
            [align1, _success], [align2] = inputs
            (prefix, name, ext) = splitPath(align1)
            seqPrefix = ""
            for sequence in sequences:
                if sequence.find(name) != -1 and seqPrefix == "":
                    (seqPrefix, seqName, seqExt) = splitPath(sequence)
            name = seqPrefix + "/" + name[:-2]
            seq1 = name + '_1.fastq.gz'
            seq2 = name + '_2.fastq.gz'
#            (prefix, name, ext) = splitPath(output)
#            out = prefix + '/' + name
            runStageCheck('alignBWAPE', flagFile, reference, align1, align2, seq1, seq2, output)
        stage_count += len(sequence_list) 

        @transform(alignBWAPE, regex(r"(.*)\/(.+).bam"), outSuccessPrefix + r'\2.checkBam.Success')
        def checkBam(inputs, flagFile):
            bamFile, _success = inputs
            (prefix, name, ext) = splitPath(bamFile)
            read_set = ""
            for seq in sequences:
                if seq.find(name+'_1.fastq') != -1:
                    read_set = seq
            runStageCheck('checkBam', flagFile, bamFile, readType, read_set)
        stage_count += len(sequence_list)        

        # Index sorted BAM alignments using samtools
        @follows(checkBam)
        @transform(alignBWAPE, regex(r"(.*)\/(.+).bam"), [r'\1/\2.bam.bai', outSuccessPrefix + r'\2.indexBam.Success'])
        def indexBam(inputs, outputs):
            output, flagFile = outputs
            bamFile, _success = inputs
            runStageCheck('indexBam', flagFile, bamFile)
        stage_count += len(sequence_list) 

        #get bam stats by replicon
        @follows(indexBam)
        @transform(alignBWAPE, regex(r"(.*)\/(.+).bam"), [r'\1/\2_samStats.txt', outSuccessPrefix + r'\2.getSamStats.Success'])
        def getSamStats(inputs, outputs):
            output, flagFile = outputs
            bamFile, _success = inputs
            runStageCheck('getSamStats', flagFile, bamFile, output)
        stage_count += len(sequence_list) 

# checkpoint_getSamStats
        @merge(getSamStats, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "getSamStats.checkpoint.Success"])
        def checkpoint_getSamStats(inputs,outputs):
            output, flagFile = outputs
            runStageCheck('checkpoint', flagFile, outTempPrefix, 'getSamStats')
        stage_count += 1

        #filter unmapped reads
        @follows(indexBam, checkpoint_getSamStats)
        @transform(alignBWAPE, regex(r"(.*)\/(.+).bam"), [outBamPrefix + r'\2.bam', outSuccessPrefix + r'\2.filterUnmapped.Success'])
        def filterUnmapped(inputs, outputs):
            output, flagFile = outputs
            bamFile, _success = inputs
#            (prefix, name, ext) = splitPath(output)
#            out = prefix + '/' + name
            runStageCheck('filterUnmapped', flagFile, bamFile, output)
        stage_count += len(sequence_list) 

    else:
        # Align sequence reads to the reference genome.
        @follows(buildBWAIndex)
        @transform(sequences, regex(r"(.*)\/(.+).fastq.gz"), [outTempPrefix + r'\2/\2.sai', outSuccessPrefix + r"\2.alignSequence.Success"])
        def alignSequence(sequence, outputs):
            output, flagFile = outputs
            runStageCheck('alignSequence', flagFile, reference, sequence, output)
        stage_count += len(sequences)

        #align reads with BWA to sorted bam
        @follows(buildBWAIndex)
        @transform(alignSequence, regex(r"(.*)\/(.+).sai"), [r'\1/\2.bam', outSuccessPrefix + r'\2.alignBWASE.Success'])
        def alignBWASE(inputs, outputs):
            output, flagFile = outputs
            align, _success = inputs
            (prefix, name, ext) = splitPath(align)
            seqPrefix = ""
            for sequence in sequences:
                if sequence.find(name) != -1 and seqPrefix == "":
                    (seqPrefix, seqName, seqExt) = splitPath(sequence)
            seq = seqPrefix + "/" + name + '.fastq.gz'
#            (prefix, name, ext) = splitPath(output)
#            out = prefix + '/' + name
            runStageCheck('alignBWASE', flagFile, reference, align, seq, output)
        stage_count += len(sequence_list) 

        @transform(alignBWASE, regex(r"(.*)\/(.+).bam"), outSuccessPrefix + r'\2.checkBam.Success')
        def checkBam(inputs, flagFile):
            bamFile, _success = inputs
            (prefix, name, ext) = splitPath(bamFile)
            read_set = ""
            for seq in sequences:
                if seq.find(name+readPattern) != -1:
                    read_set = seq
            runStageCheck('checkBam', flagFile, bamFile, readType, read_set)
        stage_count += len(sequence_list)        

        # Index sorted BAM alignments using samtools
        @follows(checkBam)
        @transform(alignBWASE, regex(r"(.*)\/(.+).bam"), [r'\1/\2.bam.bai', outSuccessPrefix + r'\2.indexBam.Success'])
        def indexBam(inputs, outputs):
            output, flagFile = outputs
            bamFile, _success = inputs
            runStageCheck('indexBam', flagFile, bamFile)
        stage_count += len(sequence_list) 

        #get bam stats by replicon
        @follows(indexBam)
        @transform(alignBWASE, regex(r"(.*)\/(.+).bam"), [r'\1/\2_samStats.txt', outSuccessPrefix + r'\2.getSamStats.Success'])
        def getSamStats(inputs, outputs):
            output, flagFile = outputs
            bamFile, _success = inputs
            runStageCheck('getSamStats', flagFile, bamFile, output)
        stage_count += len(sequence_list) 

# checkpoint_getSamStats
        @merge(getSamStats, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "getSamStats.checkpoint.Success"])
        def checkpoint_getSamStats(inputs,outputs):
            output, flagFile = outputs
            runStageCheck('checkpoint', flagFile, outTempPrefix, 'getSamStats')
        stage_count += 1

        #filter unmapped reads
        @follows(indexBam, checkpoint_getSamStats)
        @transform(alignBWASE, regex(r"(.*)\/(.+).bam"), [outBamPrefix + r'\2.bam', outSuccessPrefix + r'\2.filterUnmapped.Success'])
        def filterUnmapped(inputs, outputs):
            output, flagFile = outputs
            bamFile, _success = inputs
#            (prefix, name, ext) = splitPath(output)
#            out = prefix + '/' + name
            runStageCheck('filterUnmapped', flagFile, bamFile, output)
        stage_count += len(sequence_list) 

# Index sorted BAM alignments using samtools
@transform(filterUnmapped, regex(r"(.*)\/(.+).bam"), [r'\1/\2.bam.bai', outSuccessPrefix + r'\2.indexFilteredBam.Success'])
def indexFilteredBam(inputs, outputs):
    output, flagFile = outputs
    bamFile, _success = inputs
    runStageCheck('indexBam', flagFile, bamFile)
stage_count += len(sequence_list) 

# get consensus sequence from bam
@follows(indexFilteredBam)
@follows(indexRef)
@transform(filterUnmapped, regex(r"(.*)\/(.+).bam"), [outTempPrefix + r"\2/\2_cns.fq", outSuccessPrefix + r"\2.getConsensus.Success"])
def getConsensus(inputs, outputs):
    output, flagFile = outputs
    bamFile, _success = inputs
    runStageCheck('getConsensus', flagFile, reference, bamFile, output)
stage_count += len(sequence_list) 

# checkpoint_getConsensus
@merge(getConsensus, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "getConsensus.checkpoint.Success"])
def checkpoint_getConsensus(inputs,outputs):
    output, flagFile = outputs
    runStageCheck('checkpoint', flagFile, outTempPrefix, 'getConsensus')
stage_count += 1

# Get coverage from BAM
@follows(indexFilteredBam)
@follows(indexRef)
@transform(filterUnmapped, regex(r"(.*)\/(.+).bam"), [outTempPrefix + r"\2/\2_coverage.txt", outSuccessPrefix + r"\2.getCoverage.Success"])
def getCoverage(inputs, outputs):
    output, flagFile = outputs
    bamFile, _success = inputs
    runStageCheck('getCoverage', flagFile, bamFile, output)
stage_count += len(sequence_list) 

# Get coverage by replicon
@transform(getCoverage, regex(r"(.*)\/(.+)_coverage.txt"), [r'\1/\2_rep_cover.txt', outSuccessPrefix + r'\2.getCoverByRep.Success'])
def getCoverByRep(inputs, outputs):
    output, flagFile = outputs
    coverageFile, _success = inputs
    runStageCheck('getCoverByRep', flagFile, reference, coverageFile, output)
stage_count += len(sequence_list) 

# Derive run statistics - first, the 'all statistics' data
@follows(checkpoint_getSamStats)
@transform(getCoverByRep, regex(r"(.*)\/(.+)_rep_cover.txt"), [r'\1/\2_AllStats.txt', outSuccessPrefix + r'\2.deriveAllStats.Success'])
def deriveAllStats(inputs, outputs):
    output, flagFile = outputs
    coverFile, _success = inputs
    runStageCheck('deriveAllStats', flagFile, coverFile)
stage_count += len(sequence_list)

# Collate run statistics into tab-delimited file
# and add header to the statistics file
# example rep cover file is to establish replicon order in the header (order from reference)
# also provides a user-friendly version of the all stats file with isolates as the header (for spreadsheets) 
@merge(deriveAllStats, [outPrefix + refName + "_AllStats.txt", outSuccessPrefix + refName + ".collateAllStats.Success"])
def collateAllStats(inputs, outputs):
    output, flagFile = outputs
    example_name = sequence_list[0]
    exampleRepCover = outTempPrefix + example_name + '/' + example_name + "_rep_cover.txt"
    runStageCheck('collateAllStats', flagFile, refName, exampleRepCover, outPrefix, sequence_list_string)
stage_count += 1

if runType == "pangenome":
    #create inputs for callRepSNPs
    def snpsByCoreReplicons():
        for repliconName in core_replicons:
            for seqName in sequence_list:
                sortedBam = outBamPrefix + seqName + '.bam'
                output = outTempPrefix + seqName + '/callRepSNPs/' + seqName + '_' + repliconName + '_raw.bcf'
                flagFile = outSuccessPrefix + seqName + '_' + repliconName + '.callRepSNPs.Success'
                yield([sortedBam, [output, flagFile], repliconName])

    # Call SNPs for core replicon(s)
    @follows(indexFilteredBam)
    @follows(indexRef)
    @files(snpsByCoreReplicons)
    def callRepSNPs(input, outputs, repliconName):
        output, flagFile  = outputs
        bcf_option = SNPcaller + 'v'
        runStageCheck('callRepSNPs', flagFile, reference, input, repliconName, bcf_option, output)
    stage_count += (len(sequence_list)*len(core_replicons)) 

# checkpoint_callRepSNPs
    @merge(callRepSNPs, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "callRepSNPs.checkpoint.Success"])
    def checkpoint_callRepSNPs(inputs,outputs):
        output, flagFile = outputs
        runStageCheck('checkpoint', flagFile, outTempPrefix, 'callRepSNPs')
    stage_count += 1

    #create inputs for filter variants on Q30
    def q30FilterByCoreReplicons():
        for repliconName in core_replicons:
            for seqName in sequence_list:
                rawBCF = outTempPrefix + seqName + '/callRepSNPs/' + seqName + '_' + repliconName + '_raw.bcf'
                coverFile = outTempPrefix + seqName + '/' + seqName + '_rep_cover.txt'                        
                output = outTempPrefix + seqName + '/q30VarFilter/' + seqName + '_' + repliconName + '_raw.vcf'
                flagFile = outSuccessPrefix + seqName + '_' + repliconName + '.q30VarFilter.Success'
                yield([rawBCF, [output, flagFile], coverFile, repliconName])
    
    # Filter variants on Q30
    @follows(getCoverByRep)
    @follows(checkpoint_callRepSNPs)
    @files(q30FilterByCoreReplicons)
    def q30VarFilter(rawBCF, outputs, coverFile, repliconName):
        output, flagFile = outputs
        cover = getCover(coverFile, repliconName)
        if runType == "PE":
            runStageCheck('q30VarFilterPE', flagFile, strand_bias_cutoff,rawBCF, minDepth, cover, output)
        else:
            runStageCheck('q30VarFilter', flagFile, rawBCF, minDepth, cover, output)

    stage_count += (len(sequence_list)*len(core_replicons)) 

    # Filter out simple hets
    @transform(q30VarFilter, regex(r"(.*)\/(.+)_raw.vcf"), [outVcfPrefix + r"\2_q30.vcf", outSuccessPrefix + r"\2.finalFilter.Success"])
    def finalFilter(inputs, outputs):
        vcfFile,_success = inputs
        output, flagFile = outputs
        (prefix, name, ext) = splitPath(vcfFile) 
        prefix += '/hets/'       
        runStageCheck('finalFilter', flagFile, vcfFile, output, prefix, HetsVCF)
    stage_count += (len(sequence_list)*len(core_replicons)) 

    # set up for getting vcf statistics
    def vcfStatsByCoreRep():
        for repliconName in core_replicons:
            for seqName in sequence_list:
                vcfFile = outVcfPrefix + seqName + '_' + repliconName + '_q30.vcf'
                output = outTempPrefix + seqName + '/getVCFStats/' + seqName + '_' + repliconName + '_vcf.txt'
                flagFile = outSuccessPrefix + seqName + '_' + repliconName + '.getVcfStats.Success'
                yield([vcfFile, [output, flagFile]])

    # Get the vcf statistics
    @follows(finalFilter)
    @files(vcfStatsByCoreRep)
    def getVcfStats(vcfFile, outputs):
        output, flagFile = outputs
        runStageCheck('getVcfStats', flagFile, vcfFile, output)
    stage_count += (len(sequence_list)*len(core_replicons))

    # Derive run statistics - second, the statistics for each replicon (largest or user-defined list)
    def statsByCoreRep():
        for repliconName in core_replicons:
            for seqName in sequence_list:
                coverFile = outTempPrefix + seqName + '/' + seqName + '_rep_cover.txt'
                output = outTempPrefix + seqName + '/deriveRepStats/' + seqName + '_' + repliconName + '_RepStats.txt'
                flagFile = outSuccessPrefix + seqName + '_' + repliconName + '.deriveRepStats.Success'
                yield([coverFile, [output, flagFile], repliconName, depthFail, coverFail])

    @follows(getVcfStats)
    @follows(checkpoint_getSamStats)
    @follows(getCoverByRep)
    @files(statsByCoreRep)
    def deriveRepStats(coverFile, outputs, repliconName, depthFail, coverFail):
        output, flagFile = outputs
        runStageCheck('deriveRepStats', flagFile, coverFile, repliconName, depthFail, coverFail, runType, mappedFail, check_reads_mapped)
    stage_count += (len(sequence_list)*len(core_replicons)) 

# checkpoint_deriveRepStats
    @merge(deriveRepStats, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "deriveRepStats.checkpoint.Success"])
    def checkpoint_deriveRepStats(inputs,outputs):
        output, flagFile = outputs
        runStageCheck('checkpoint', flagFile, outTempPrefix, 'deriveRepStats')
    stage_count += 1

    def inputByCoreRep():
        for repliconName in core_replicons:
            output = outPrefix + refName + '_' + repliconName + '_RepStats.txt'
            flagFile = outSuccessPrefix + refName + '_' + repliconName + '.collateRepStats.Success'
            yield([input==None, [output, flagFile], refName, repliconName])

    @follows(checkpoint_deriveRepStats)
    @files(inputByCoreRep)
    def collateRepStats(input, outputs, refName, repliconName):
        output, flagFile = outputs
        runStageCheck('collateRepStats', flagFile, refName, outPrefix, repliconName, sdOutgroupMultiplier, runType, sequence_list_string)
    stage_count += len(core_replicons) 

else: # runType == "phylogeny"
    #create inputs for callRepSNPs
    def snpsByReplicons():
        for repliconName in replicons:
            for seqName in sequence_list:
                sortedBam = outBamPrefix + seqName + '.bam'
                output = outTempPrefix + seqName + '/callRepSNPs/' + seqName + '_' + repliconName[0] + '_raw.bcf'
                flagFile = outSuccessPrefix + seqName + '_' + repliconName[0] + '.callRepSNPs.Success'
                replicon = repliconName[0]
                yield([sortedBam, [output, flagFile], replicon])

    # Call SNPs for all replicon(s)
    @follows(indexFilteredBam)
    @follows(indexRef)
    @files(snpsByReplicons)
    def callRepSNPs(input, outputs, replicon):
        output, flagFile  = outputs
        bcf_option = SNPcaller + 'v'
        runStageCheck('callRepSNPs', flagFile, reference, input, replicon, bcf_option, output)
    stage_count += (len(sequence_list)*len(replicons)) 

# checkpoint_callRepSNPs
    @merge(callRepSNPs, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "callRepSNPs.checkpoint.Success"])
    def checkpoint_callRepSNPs(inputs,outputs):
        output, flagFile = outputs
        runStageCheck('checkpoint', flagFile, outTempPrefix, 'callRepSNPs')
    stage_count += 1

    #create inputs for filter variants on Q30
    def q30FilterByReplicons():
        for repliconName in replicons:
            for seqName in sequence_list:
                rawBCF = outTempPrefix + seqName + '/callRepSNPs/' + seqName + '_' + repliconName[0] + '_raw.bcf'
                coverFile = outTempPrefix + seqName + '/' + seqName + '_rep_cover.txt'    
                output = outTempPrefix + seqName + '/q30VarFilter/' + seqName + '_' + repliconName[0] + '_raw.vcf'
                flagFile = outSuccessPrefix + seqName + '_' + repliconName[0] + '.q30VarFilter.Success'
                replicon = repliconName[0]
                yield([rawBCF, [output, flagFile], coverFile, replicon])
    
    # Filter variants on Q30
    @follows(getCoverByRep)
    @follows(checkpoint_callRepSNPs)
    @files(q30FilterByReplicons)
    def q30VarFilter(rawBCF, outputs, coverFile, replicon):
        output, flagFile = outputs
        cover = getCover(coverFile, replicon)
        if runType == "PE":
            runStageCheck('q30VarFilterPE', flagFile, strand_bias_cutoff,rawBCF, minDepth, cover, output)
        else:
            runStageCheck('q30VarFilter', flagFile, rawBCF, minDepth, cover, output)
    stage_count += (len(sequence_list)*len(replicons)) 

    # Filter out simple hets
    @transform(q30VarFilter, regex(r"(.*)\/(.+)_raw.vcf"), [outVcfPrefix + r"\2_q30.vcf", outSuccessPrefix + r"\2.finalFilter.Success"])
    def finalFilter(inputs, outputs):
        output, flagFile = outputs
        vcfFile, _Success = inputs
        (prefix, name, ext) = splitPath(vcfFile) 
        prefix += '/hets/'       
        runStageCheck('finalFilter', flagFile, vcfFile, output, prefix, HetsVCF)
    stage_count += (len(sequence_list)*len(replicons)) 

    # set up for getting vcf statistics
    def vcfStatsByRep():
        for repliconName in replicons:
            for seqName in sequence_list:
                vcfFile = outVcfPrefix + seqName + '_' + repliconName[0] + '_q30.vcf'
                output = outTempPrefix + seqName + '/getVCFStats/' + seqName + '_' + repliconName[0] + '_vcf.txt'
                flagFile = outSuccessPrefix + seqName + '_' + repliconName[0] + '.getVcfStats.Success'
                yield([vcfFile, [output, flagFile]])

    # Get the vcf statistics
    @follows(finalFilter)
    @files(vcfStatsByRep)
    def getVcfStats(vcfFile, outputs):
        output, flagFile = outputs
        runStageCheck('getVcfStats', flagFile, vcfFile, output)
    stage_count += (len(sequence_list)*len(replicons))

    # Derive run statistics - second, the statistics for each replicon (largest or user-defined list)
    def statsByRep():
        for repliconName in replicons:
            for seqName in sequence_list:
                coverFile = outTempPrefix + seqName + '/' + seqName + '_rep_cover.txt'
                output = outTempPrefix + seqName + '/deriveRepStats/' + seqName + '_' + repliconName[0] + '_RepStats.txt'
                flagFile = outSuccessPrefix + seqName + '_' + repliconName[0] + '.deriveRepStats.Success'
                replicon = repliconName[0]
                yield([coverFile, [output, flagFile], replicon, depthFail, coverFail])

    @follows(getVcfStats)
    @follows(checkpoint_getSamStats)
    @follows(getCoverByRep)
    @files(statsByRep)
    def deriveRepStats(coverFile, outputs, replicon, depthFail, coverFail):
        output, flagFile = outputs
        runStageCheck('deriveRepStats', flagFile, coverFile, replicon, depthFail, coverFail, runType, mappedFail, check_reads_mapped)
    stage_count += (len(sequence_list)*len(replicons)) 

# checkpoint_deriveRepStats
    @merge(deriveRepStats, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "deriveRepStats.checkpoint.Success"])
    def checkpoint_deriveRepStats(inputs,outputs):
        output, flagFile = outputs
        runStageCheck('checkpoint', flagFile, outTempPrefix, 'deriveRepStats')
    stage_count += 1

    def inputByRep():
        for repliconName in replicons:
            output = outPrefix + refName + '_' + repliconName[0] + '_RepStats.txt'
            flagFile = outSuccessPrefix + refName + '_' + repliconName[0] + '.collateRepStats.Success'
            replicon = repliconName[0]
            yield([input==None, [output, flagFile], refName, replicon])

    @follows(checkpoint_deriveRepStats)
    @files(inputByRep)
    def collateRepStats(input, outputs, refName, replicon):
        output, flagFile = outputs
        runStageCheck('collateRepStats', flagFile, refName, outPrefix, replicon, sdOutgroupMultiplier, runType, sequence_list_string)
    stage_count += len(replicons)

if outMerge != "":
    # Merge bams and vcfs to correct output merge directory
    @follows(collateAllStats)
    @follows(collateRepStats)
    @files(input==None, outSuccessPrefix + 'mergeOutputs.Success')
    def mergeOutputs(input, flagFile):
        inputBam = outBamPrefix + '*.bam'
        inputIndex = outBamPrefix + '*.bai'
        inputVcf = outVcfPrefix + '*.vcf' 
        runStageCheck('mergeOutputs', flagFile, inputBam, outMergeBam, inputIndex, outMergeBam, inputVcf, outMergeVcf)
    stage_count += 1
 
    # Merge AllStats.txt files <- need to add 'user' version when merging
    @follows(mergeOutputs)
    @transform(collateAllStats, regex(r"(.*)\/(.+)_AllStats.txt"), [outMerge + r"\2_AllStats.txt", outSuccessPrefix + r"\2.mergeAllStats.Success"])
    def mergeAllStats(inputs, outputs):
        input, _success = inputs
        output, flagFile = outputs
        runStageCheck('mergeAllStats', flagFile, input, outMerge)
    stage_count += 1

    # Merge RepStats.txt files
    @follows(mergeOutputs)
    @transform(collateRepStats, regex(r"(.*)\/(.+)_RepStats.txt"), [outMerge + r"\2_RepStats.txt", outSuccessPrefix + r"\2.mergeRepStats.Success"])
    def mergeRepStats(inputs, outputs):
        input, _success = inputs
        output, flagFile = outputs
        runStageCheck('mergeRepStats', flagFile, input, sdOutgroupMultiplier, replaceReads, outMerge, runType)
    if runType == "phylogeny":
        stage_count += len(replicons) 
    else:
        stage_count += len(core_replicons) 

    if runType == "phylogeny":
        # Start of phylogeny analysis
        def snpListByRep():
            for repliconName in replicons:
                input  = outMerge + refName + '_' + repliconName[0] + '_RepStats.txt'
                output = outTempPrefix + 'getRepSNPList/' + refName + '_' + repliconName[0] + '_SNPList.txt'
                flagFile = outSuccessPrefix + refName + '_' + repliconName[0] + '.getRepSNPList.Success'
                replicon = repliconName[0]
                yield([input, [output, flagFile], replicon])

        # Get unique SNP list for new set using stats file for each replicon
        @follows(mergeRepStats)
        @follows(mergeAllStats)
        @files(snpListByRep)
        def getRepSNPList(input, outputs, replicon):
            output, flagFile = outputs
            runStageCheck('getRepSNPList', flagFile, input, replicon, output)
        stage_count += len(replicons) 

    else: #runType == "pangenome":
        # Start of pangenome analysis
        def snpListByCoreRep():
            for repliconName in core_replicons:
                input  = outMerge + refName + '_' + repliconName + '_RepStats.txt'
                output = outTempPrefix + 'getRepSNPList/' + refName + '_' + repliconName + '_SNPList.txt'
                flagFile = outSuccessPrefix + refName + '_' + repliconName + '.getRepSNPList.Success'
                replicon = repliconName
                yield([input, [output, flagFile], replicon])

        # Get unique SNP list for new set using stats file for each replicon
        @follows(mergeRepStats)
        @follows(mergeAllStats)
        @files(snpListByCoreRep)
        def getRepSNPList(input, outputs, replicon):
            output, flagFile = outputs
            runStageCheck('getRepSNPList', flagFile, input, replicon, output)
        stage_count += len(core_replicons) 

else: #    if mergeReads == "":
    if runType == "phylogeny":
        # Start of new run phylogeny analysis
        def snpListByRep():
            for repliconName in replicons:
                input  = outPrefix + refName + '_' + repliconName[0] + '_RepStats.txt'
                output = outTempPrefix + 'getRepSNPList/' + refName + '_' + repliconName[0] + '_SNPList.txt'
                flagFile = outSuccessPrefix + refName + '_' + repliconName[0] + '.getRepSNPList.Success'
                replicon = repliconName[0]
                yield([input, [output, flagFile], replicon])

        # Get unique SNP list for new set using stats file for each replicon
        @follows(collateRepStats)
        @follows(collateAllStats)
        @files(snpListByRep)
        def getRepSNPList(input, outputs, replicon):
            output, flagFile = outputs
            runStageCheck('getRepSNPList', flagFile, input, replicon, output)
        stage_count += len(replicons) 

    else: #runType == "pangenome":
        # Start of new run pangenome analysis
        def snpListByCoreRep():
            for repliconName in core_replicons:
                input  = outPrefix + refName + '_' + repliconName + '_RepStats.txt'
                output = outTempPrefix + 'getRepSNPList/' + refName + '_' + repliconName + '_SNPList.txt'
                flagFile = outSuccessPrefix + refName + '_' + repliconName + '.getRepSNPList.Success'
                replicon = repliconName
                yield([input, [output, flagFile], replicon])

        # Get unique SNP list for new set using stats file for each replicon
        @follows(collateRepStats)
        @follows(collateAllStats)
        @files(snpListByCoreRep)
        def getRepSNPList(input, outputs, replicon):
            output, flagFile = outputs
            runStageCheck('getRepSNPList', flagFile, input, replicon, output)
        stage_count += len(core_replicons) 

# checkpoint_getRepSNPList
@merge(getRepSNPList, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "getRepSNPList.checkpoint.Success"])
def checkpoint_getRepSNPList(inputs,outputs):
    output, flagFile = outputs
    runStageCheck('checkpoint', flagFile, outTempPrefix, 'getRepSNPList')
stage_count += 1

if refGenbank == True:
    if outMerge != "":

        bams = []        
        for sequence in full_sequence_list:
            if sequence not in sequence_list:
                bams.append(outMergeBam + sequence + '.bam')

        # generate data for the gene cover and depth matrices
        @transform(getCoverage, regex(r"(.*)\/(.+)_coverage.txt"), [outTempPrefix + r'\2/\2_CoverDepthMatrix.txt', outSuccessPrefix + r'\2.deriveAllRepGeneCover.Success'])
        def deriveAllRepGeneCover(inputs, outputs):
            output, flagFile = outputs
            input, _success = inputs
            runStageCheck('deriveAllRepGeneCover', flagFile, outTempPrefix, genbank, input)
        stage_count += len(sequence_list)

        # merge the data with the 'old' gene cover and depth matrices
        @merge(deriveAllRepGeneCover, [outMerge + refName + "_CoverMatrix.csv", outSuccessPrefix + refName + "_CoverMatrix.mergeAllRepGeneCover.Success"])
        def mergeAllRepGeneCover(inputs, outputs):
            output, flagFile = outputs
            runStageCheck('mergeAllRepGeneCover', flagFile, outTempPrefix, outMerge, refName, sequence_list_string)
        stage_count += 1

        # parse gene cover (and depth - to come) matrices to summarise gene content
        @transform(mergeAllRepGeneCover, regex(r"(.*)\/(.+)_CoverMatrix.csv"), [outMerge + r"\2_GeneSummary.csv", outSuccessPrefix + r"\2_alleles.parseGeneContent.Success"])
        def parseGeneContent(inputs, outputs):
            output, flagFile = outputs
            input, _success = inputs
            (prefix, name, ext) = splitPath(output)
            (prefix2, name2, ext2) = splitPath(input)            
            output2 = prefix + "/" + name[:-11] + "PresenceAbsence.csv"
            input2 = prefix + "/" + name[:-11] + "DepthMatrix.csv"
            runStageCheck('parseGeneContent', flagFile, input, input2, output, output2)
        stage_count += 1

        # get consensus sequences for merged set
        @follows(checkpoint_getRepSNPList)
        @transform(bams, regex(r"(.*)\/(.+).bam"), [outTempPrefix + r"\2/\2_cns.fq", outSuccessPrefix + r"\2.getMergeConsensus.Success"])
        def getMergeConsensus(input, outputs):
            output, flagFile = outputs
            runStageCheck('getConsensus', flagFile, reference, input, output)
        stage_count += len(bams)

# checkpoint_getMergeConsensus
        @merge(getMergeConsensus, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "getMergeConsensus.checkpoint.Success"])
        def checkpoint_getMergeConsensus(inputs,outputs):
            output, flagFile = outputs
            runStageCheck('checkpoint', flagFile, outTempPrefix, 'getMergeConsensus')
        stage_count += 1
 
        if runType == 'pangenome':
            # generate the allele matrix entry for each isolate for each replicon
            def matrixEntryByCoreRep():
                for isolate in full_sequence_list:
                    for repliconName in core_replicons:
                        input = outTempPrefix + 'getRepSNPList/' + refName + '_' + repliconName + '_SNPList.txt'
                        output  = outTempPrefix + isolate + '/deriveRepAlleleMartix/' + refName + '_' + repliconName + '_' + isolate + '_alleles.txt'
                        flagFile = outSuccessPrefix + refName + '_' + repliconName + '_' + isolate + '.deriveRepAlleleMatrix.Success'
                        replicon = repliconName
                        consensus =  outTempPrefix + isolate + '/' + isolate + '_cns.fq'
                        repliconStats = outMerge + refName + '_' + repliconName + '_RepStats.txt'
                        merge_prefix = outMerge
                        yield([input, [output, flagFile], replicon, consensus,repliconStats, merge_prefix])

            @follows(checkpoint_getConsensus, checkpoint_getMergeConsensus)
            @follows(checkpoint_getRepSNPList)
            @files(matrixEntryByCoreRep)
            def deriveRepAlleleMatrix(input, outputs, replicon, consensus, repliconStats, merge_prefix):
                output, flagFile = outputs
                runStageCheck('deriveRepAlleleMatrix', flagFile, input, output, reference, replicon, consensus, repliconStats, merge_prefix)
            stage_count += (len(full_sequence_list)*len(core_replicons))

# checkpoint_deriveRepAlleleMatrix
            @merge(deriveRepAlleleMatrix, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "deriveRepAlleleMatrix.checkpoint.Success"])
            def checkpoint_deriveRepAlleleMatrix(inputs,outputs):
                output, flagFile = outputs
                runStageCheck('checkpoint', flagFile, outTempPrefix, 'deriveRepAlleleMatrix')
            stage_count += 1

            def matrixByCoreRep():
                for repliconName in core_replicons:
                    output  = outTempPrefix + refName + '_' + repliconName + '_alleles.csv'
                    flagFile = outSuccessPrefix + refName + '_' + repliconName + '.collateRepAlleleMatrix.Success'
                    rep_name = refName + '_' + repliconName
                    yield([input==None, [output, flagFile], rep_name])

            @follows(checkpoint_deriveRepAlleleMatrix)
            @files(matrixByCoreRep)
            def collateRepAlleleMatrix(input, outputs, rep_name):
                output, flagFile = outputs
                runStageCheck('collateRepAlleleMatrix', flagFile, outTempPrefix, output, full_sequence_list_string, rep_name)
            stage_count += len(core_replicons)

        else: #runType == 'phylogeny'
            # generate the allele matrix entry for each isolate for each replicon
            def matrixEntryByRep():
                for isolate in full_sequence_list:
                    for repliconName in replicons:
                        input = outTempPrefix + 'getRepSNPList/' + refName + '_' + repliconName[0] + '_SNPList.txt'
                        output  = outTempPrefix + isolate + '/deriveRepAlleleMartix/' + refName + '_' + repliconName[0] + '_' + isolate + '_alleles.txt'
                        flagFile = outSuccessPrefix + refName + '_' + repliconName[0] + '_' + isolate + '.deriveRepAlleleMatrix.Success'
                        replicon = repliconName[0]
                        consensus =  outTempPrefix + isolate + '/' + isolate + '_cns.fq'
                        repliconStats = outMerge + refName + '_' + repliconName[0] + '_RepStats.txt'
                        merge_prefix = outMerge
                        yield([input, [output, flagFile], replicon, consensus,repliconStats, merge_prefix])

            @follows(checkpoint_getConsensus, checkpoint_getMergeConsensus)
            @follows(checkpoint_getRepSNPList)
            @files(matrixEntryByRep)
            def deriveRepAlleleMatrix(input, outputs, replicon, consensus, repliconStats, merge_prefix):
                output, flagFile = outputs
                runStageCheck('deriveRepAlleleMatrix', flagFile, input, output, reference, replicon, consensus, repliconStats, merge_prefix)
            stage_count += (len(full_sequence_list)*len(replicons))

# checkpoint_deriveRepAlleleMatrix
            @merge(deriveRepAlleleMatrix, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "deriveRepAlleleMatrix.checkpoint.Success"])
            def checkpoint_deriveRepAlleleMatrix(inputs,outputs):
                output, flagFile = outputs
                runStageCheck('checkpoint', flagFile, outTempPrefix, 'deriveRepAlleleMatrix')
            stage_count += 1

            def matrixByRep():
                for repliconName in replicons:
                    output  = outTempPrefix + refName + '_' + repliconName[0] + '_alleles.csv'
                    flagFile = outSuccessPrefix + refName + '_' + repliconName[0] + '.collateRepAlleleMatrix.Success'
                    rep_name = refName + '_' + repliconName[0]
                    yield([input==None, [output, flagFile], rep_name])

            @follows(checkpoint_deriveRepAlleleMatrix)
            @files(matrixByRep)
            def collateRepAlleleMatrix(input, outputs, rep_name):
                output, flagFile = outputs
                runStageCheck('collateRepAlleleMatrix', flagFile, outTempPrefix, output, full_sequence_list_string, rep_name)
            stage_count += len(replicons)

        # parse SNP table to create alignment for tree and get coding consequences for snps
        @transform(collateRepAlleleMatrix, regex(r"(.*)\/(.+)_alleles.csv"), [outMerge + r"\2_alleles_var_cons"+str(conservation)+".csv", outSuccessPrefix + r"\2_alleles.parseSNPs.Success"])
        def parseSNPs(inputs, outputs):
            output, flagFile = outputs
            input,_success = inputs
            (prefix, name, ext) = splitPath(input)
            replicon = name[len(refName)+1:-8]
            runStageCheck('parseSNPs', flagFile, input, str(conservation), genbank, replicon, outMerge)
        if runType == "phylogeny":
            stage_count += len(replicons)
        else:
            stage_count += len(core_replicons)

        if conservation != 0.95:
            @transform(collateRepAlleleMatrix, regex(r"(.*)\/(.+)_alleles.csv"), [outMerge + r"\2_alleles_var_cons" + "0.95.csv", outSuccessPrefix + r"\2_alleles.parseSNPs_95.Success"])
            def parseSNPs_95(inputs, outputs):
                output, flagFile = outputs
                input,_success = inputs
                (prefix, name, ext) = splitPath(input)
                replicon = name[len(refName)+1:-8]
                conservation_temp = 0.95
                runStageCheck('parseSNPs', flagFile, input, str(conservation_temp), genbank, replicon, outMerge)
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)
            
            # create distance matrices based on pair-wise differences in SNPs
            if DifferenceMatrix:
                @follows(parseSNPs_95)
                @transform(parseSNPs, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outMerge + r"\2_SNP_diff.nxs", outSuccessPrefix + r"\2_alleles.getDifferenceMatrix.Success"])        
                def getDifferenceMatrix(inputs, outputs):
                    output, flagFile = outputs
                    input, _success = inputs
                    runStageCheck('getDifferenceMatrix', flagFile, input)
                if runType == "phylogeny":
                    stage_count += len(replicons)
                else:
                    stage_count += len(core_replicons)

        elif DifferenceMatrix:        
            # create distance matrices based on pair-wise differences in SNPs
            @transform(parseSNPs, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outMerge + r"\2_SNP_diff.nxs", outSuccessPrefix + r"\2_alleles.getDifferenceMatrix.Success"])        
            def getDifferenceMatrix(inputs, outputs):
                output, flagFile = outputs
                input, _success = inputs
                runStageCheck('getDifferenceMatrix', flagFile, input)        
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)

        # generate tree
        if conservation != 0.95:
            @follows(parseSNPs_95)
            @transform(parseSNPs, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outMerge + r"\2_alleles_var_cons"+str(conservation)+".tree", outSuccessPrefix + r"\2_alleles.makeTree.Success"])
            def makeTree(inputs, outputs):
                output, flagFile = outputs
                input, _success = inputs
                input = input[:-4] + ".mfasta"
                do_tree = False
                (isolate_count, snp_count) = getFastaDetails(input)
                if not force_no_tree:
                    if isolate_count <= 500:
                        do_tree = True
                    elif isolate_count > 500 and force_tree:
                        do_tree = True
                if do_tree:
                    runStageCheck('makeTree', flagFile, input, output)
                else:
                    runStageCheck('makeNoTree', flagFile, input, output)
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)
        else:
            @transform(parseSNPs, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outMerge + r"\2_alleles_var_cons"+str(conservation)+".tree", outSuccessPrefix + r"\2_alleles.makeTree.Success"])
            def makeTree(inputs, outputs):
                output, flagFile = outputs
                input, _success = inputs
                input = input[:-4] + ".mfasta"
                do_tree = False
                (isolate_count, snp_count) = getFastaDetails(input)
                if not force_no_tree:
                    if isolate_count <= 500:
                        do_tree = True
                    elif isolate_count > 500 and force_tree:
                        do_tree = True
                if do_tree:
                    runStageCheck('makeTree', flagFile, input, output)
                else:
                    runStageCheck('makeNoTree', flagFile, input, output)
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)

    else: #ie. mergeReads == "" and refGenbank == True
        # generate the gene cover and depth matrices
        @transform(getCoverage, regex(r"(.*)\/(.+)_coverage.txt"), [outTempPrefix + r'\2/\2_CoverDepthMatrix.txt', outSuccessPrefix + r'\2.deriveAllRepGeneCover.Success'])
        def deriveAllRepGeneCover(inputs, outputs):
            output, flagFile = outputs
            input, _success = inputs
            runStageCheck('deriveAllRepGeneCover', flagFile, outTempPrefix, genbank, input)
        stage_count += len(sequence_list)

        @merge(deriveAllRepGeneCover, [outPrefix + refName + "_CoverMatrix.csv", outSuccessPrefix + refName + "_CoverMatrix.collateAllRepGeneCover.Success"])
        def collateAllRepGeneCover(inputs, outputs):
            output, flagFile = outputs
            runStageCheck('collateAllRepGeneCover', flagFile, outTempPrefix, outPrefix, refName, sequence_list_string)
        stage_count += 1

        # parse gene cover (and depth - to come) matrices to summarise gene content
        @transform(collateAllRepGeneCover, regex(r"(.*)\/(.+)_CoverMatrix.csv"), [outPrefix + r"\2_GeneSummary.csv", outSuccessPrefix + r"\2_alleles.parseGeneContent.Success"])
        def parseGeneContent(inputs, outputs):
            output, flagFile = outputs
            input, _success = inputs
            (prefix, name, ext) = splitPath(output)
            (prefix2, name2, ext2) = splitPath(input)            
            output2 = prefix + "/" + name[:-11] + "PresenceAbsence.csv"
            input2 = prefix + "/" + name[:-11] + "DepthMatrix.csv"
            runStageCheck('parseGeneContent', flagFile, input, input2, output, output2)
        stage_count += 1

        if runType == 'pangenome':
            # generate the allele matrix entry for each isolate for each replicon
            def matrixEntryByCoreRep():
                for isolate in full_sequence_list:
                    for repliconName in core_replicons:
                        input = outTempPrefix + 'getRepSNPList/' + refName + '_' + repliconName + '_SNPList.txt'
                        output  = outTempPrefix + isolate + '/deriveRepAlleleMartix/' + refName + '_' + repliconName + '_' + isolate + '_alleles.txt'
                        flagFile = outSuccessPrefix + refName + '_' + repliconName + '_' + isolate + '.deriveRepAlleleMatrix.Success'
                        replicon = repliconName
                        consensus =  outTempPrefix + isolate + '/' + isolate + '_cns.fq'
                        repliconStats = outPrefix + refName + '_' + repliconName + '_RepStats.txt'
                        merge_prefix = '-'
                        yield([input, [output, flagFile], replicon, consensus,repliconStats, merge_prefix])

            @follows(checkpoint_getConsensus)
            @follows(checkpoint_getRepSNPList)
            @files(matrixEntryByCoreRep)
            def deriveRepAlleleMatrix(input, outputs, replicon, consensus, repliconStats, merge_prefix):
                output, flagFile = outputs
                runStageCheck('deriveRepAlleleMatrix', flagFile, input, output, reference, replicon, consensus, repliconStats, merge_prefix)
            stage_count += (len(full_sequence_list)*len(core_replicons))

# checkpoint_deriveRepAlleleMatrix
            @merge(deriveRepAlleleMatrix, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "deriveRepAlleleMatrix.checkpoint.Success"])
            def checkpoint_deriveRepAlleleMatrix(inputs,outputs):
                output, flagFile = outputs
                runStageCheck('checkpoint', flagFile, outTempPrefix, 'deriveRepAlleleMatrix')
            stage_count += 1

            def matrixByCoreRep():
                for repliconName in core_replicons:
                    output  = outTempPrefix + refName + '_' + repliconName + '_alleles.csv'
                    flagFile = outSuccessPrefix + refName + '_' + repliconName + '.collateRepAlleleMatrix.Success'
                    rep_name = refName + '_' + repliconName
                    yield([input==None, [output, flagFile], rep_name])

            @follows(checkpoint_deriveRepAlleleMatrix)
            @files(matrixByCoreRep)
            def collateRepAlleleMatrix(input, outputs, rep_name):
                output, flagFile = outputs
                runStageCheck('collateRepAlleleMatrix', flagFile, outTempPrefix, output, full_sequence_list_string, rep_name)
            stage_count += len(core_replicons)

        else: #runType == 'phylogeny'
            # generate the allele matrix entry for each isolate for each replicon
            def matrixEntryByRep():
                for isolate in full_sequence_list:
                    for repliconName in replicons:
                        input = outTempPrefix + 'getRepSNPList/' + refName + '_' + repliconName[0] + '_SNPList.txt'
                        output  = outTempPrefix + isolate + '/deriveRepAlleleMartix/' + refName + '_' + repliconName[0] + '_' + isolate + '_alleles.txt'
                        flagFile = outSuccessPrefix + refName + '_' + repliconName[0] + '_' + isolate + '.deriveRepAlleleMatrix.Success'
                        replicon = repliconName[0]
                        consensus =  outTempPrefix + isolate + '/' + isolate + '_cns.fq'
                        repliconStats = outPrefix + refName + '_' + repliconName[0] + '_RepStats.txt'
                        merge_prefix = '-'
                        yield([input, [output, flagFile], replicon, consensus,repliconStats, merge_prefix])

            @follows(checkpoint_getConsensus)
            @follows(checkpoint_getRepSNPList)
            @files(matrixEntryByRep)
            def deriveRepAlleleMatrix(input, outputs, replicon, consensus, repliconStats, merge_prefix):
                output, flagFile = outputs
                runStageCheck('deriveRepAlleleMatrix', flagFile, input, output, reference, replicon, consensus, repliconStats, merge_prefix)
            stage_count += (len(full_sequence_list)*len(replicons))

# checkpoint_deriveRepAlleleMatrix
            @merge(deriveRepAlleleMatrix, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "deriveRepAlleleMatrix.checkpoint.Success"])
            def checkpoint_deriveRepAlleleMatrix(inputs,outputs):
                output, flagFile = outputs
                runStageCheck('checkpoint', flagFile, outTempPrefix, 'deriveRepAlleleMatrix')
            stage_count += 1

            def matrixByRep():
                for repliconName in replicons:
                    output  = outTempPrefix + refName + '_' + repliconName[0] + '_alleles.csv'
                    flagFile = outSuccessPrefix + refName + '_' + repliconName[0] + '.collateRepAlleleMatrix.Success'
                    rep_name = refName + '_' + repliconName[0]
                    yield([input==None, [output, flagFile], rep_name])

            @follows(checkpoint_deriveRepAlleleMatrix)
            @files(matrixByRep)
            def collateRepAlleleMatrix(input, outputs, rep_name):
                output, flagFile = outputs
                runStageCheck('collateRepAlleleMatrix', flagFile, outTempPrefix, output, full_sequence_list_string, rep_name)
            stage_count += len(replicons)

        # parse SNP table to create alignment for tree and get coding consequences for snps
        @transform(collateRepAlleleMatrix, regex(r"(.*)\/(.+)_alleles.csv"), [outPrefix + r"\2_alleles_var_cons"+str(conservation)+".csv", outSuccessPrefix + r"\2_alleles.parseSNPs.Success"])
        def parseSNPs(inputs, outputs):
            output, flagFile = outputs
            input,_success = inputs
            (prefix, name, ext) = splitPath(input)
            replicon = name[len(refName)+1:-8]
            runStageCheck('parseSNPs', flagFile, input, str(conservation), genbank, replicon, outPrefix)
        if runType == "phylogeny":
            stage_count += len(replicons)
        else:
            stage_count += len(core_replicons)

        if conservation != 0.95:
            @transform(collateRepAlleleMatrix, regex(r"(.*)\/(.+)_alleles.csv"), [outPrefix + r"\2_alleles_var_cons0.95.csv", outSuccessPrefix + r"\2_alleles.parseSNPs_95.Success"])
            def parseSNPs_95(inputs, outputs):
                output, flagFile = outputs
                input,_success = inputs
                (prefix, name, ext) = splitPath(input)
                replicon = name[len(refName)+1:-8]
                conservation_temp = 0.95
                runStageCheck('parseSNPs', flagFile, input, str(conservation_temp), genbank, replicon, outPrefix)
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)
            
            # create distance matrices based on pair-wise differences in SNPs
            if DifferenceMatrix:
                @follows(parseSNPs_95)
                @transform(parseSNPs, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outPrefix + r"\2_SNP_diff.nxs", outSuccessPrefix + r"\2_alleles.getDifferenceMatrix.Success"])        
                def getDifferenceMatrix(inputs, outputs):
                    output, flagFile = outputs
                    input, _success = inputs
                    runStageCheck('getDifferenceMatrix', flagFile, input)
                if runType == "phylogeny":
                    stage_count += len(replicons)
                else:
                    stage_count += len(core_replicons)

        elif DifferenceMatrix:        
            # create distance matrices based on pair-wise differences in SNPs
            @transform(parseSNPs, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outPrefix + r"\2_SNP_diff.nxs", outSuccessPrefix + r"\2_alleles.getDifferenceMatrix.Success"])        
            def getDifferenceMatrix(inputs, outputs):
                output, flagFile = outputs
                input, _success = inputs
                runStageCheck('getDifferenceMatrix', flagFile, input)        
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)

        if conservation != 0.95:
        # generate tree
            @follows(parseSNPs_95)
            @transform(parseSNPs, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outPrefix + r"\2_alleles_var_cons"+str(conservation)+".tree", outSuccessPrefix + r"\2_alleles.makeTree.Success"])
            def makeTree(inputs, outputs):
                output, flagFile = outputs
                input, _success = inputs
                input = input[:-4] + ".mfasta"
                do_tree = False
                (isolate_count, snp_count) = getFastaDetails(input)
                if not force_no_tree:
                    if isolate_count <= 500:
                        do_tree = True
                    elif isolate_count > 500 and force_tree:
                        do_tree = True
                if do_tree:
                    runStageCheck('makeTree', flagFile, input, output)
                else:
                    runStageCheck('makeNoTree', flagFile, input, output)
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)
        else:
            @transform(parseSNPs, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outPrefix + r"\2_alleles_var_cons"+str(conservation)+".tree", outSuccessPrefix + r"\2_alleles.makeTree.Success"])
            def makeTree(inputs, outputs):
                output, flagFile = outputs
                input, _success = inputs
                input = input[:-4] + ".mfasta"
                do_tree = False
                (isolate_count, snp_count) = getFastaDetails(input)
                if not force_no_tree:
                    if isolate_count <= 500:
                        do_tree = True
                    elif isolate_count > 500 and force_tree:
                        do_tree = True
                if do_tree:
                    runStageCheck('makeTree', flagFile, input, output)
                else:
                    runStageCheck('makeNoTree', flagFile, input, output)
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)

else: # refGenbank == False
    if outMerge != "":
        # get consensus sequence for merged set
        bams = []
        for sequence in full_sequence_list:
            if sequence not in sequence_list:
                bams.append(outMergeBam + sequence + '.bam')

        @follows(checkpoint_getRepSNPList)
        @transform(bams, regex(r"(.*)\/(.+).bam"), [outTempPrefix + r"\2/\2_cns.fq", outSuccessPrefix + r"\2.getMergeConsensus.Success"])
        def getMergeConsensus(input, outputs):
            output, flagFile = outputs
            runStageCheck('getConsensus', flagFile, reference, input, output)
        stage_count += len(bams)

# checkpoint_getMergeConsensus
        @merge(getMergeConsensus, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "getMergeConsensus.checkpoint.Success"])
        def checkpoint_getMergeConsensus(inputs,outputs):
            output, flagFile = outputs
            runStageCheck('checkpoint', flagFile, outTempPrefix, 'getMergeConsensus')
        stage_count += 1

        if runType == 'pangenome':
            # generate the allele matrix entry for each isolate for each replicon
            def matrixEntryByCoreRep():
                for isolate in full_sequence_list:
                    for repliconName in core_replicons:
                        input = outTempPrefix + 'getRepSNPList/' + refName + '_' + repliconName + '_SNPList.txt'
                        output  = outTempPrefix + isolate + '/deriveRepAlleleMartix/' + refName + '_' + repliconName + '_' + isolate + '_alleles.txt'
                        flagFile = outSuccessPrefix + refName + '_' + repliconName + '_' + isolate + '.deriveRepAlleleMatrix.Success'
                        replicon = repliconName
                        consensus =  outTempPrefix + isolate + '/' + isolate + '_cns.fq'
                        repliconStats = outMerge + refName + '_' + repliconName + '_RepStats.txt'
                        merge_prefix = outMerge
                        yield([input, [output, flagFile], replicon, consensus,repliconStats, merge_prefix])

            @follows(checkpoint_getConsensus, checkpoint_getMergeConsensus)
            @follows(checkpoint_getRepSNPList)
            @files(matrixEntryByCoreRep)
            def deriveRepAlleleMatrix(input, outputs, replicon, consensus, repliconStats, merge_prefix):
                output, flagFile = outputs
                runStageCheck('deriveRepAlleleMatrix', flagFile, input, output, reference, replicon, consensus, repliconStats, merge_prefix)
            stage_count += (len(full_sequence_list)*len(core_replicons))

# checkpoint_deriveRepAlleleMatrix
            @merge(deriveRepAlleleMatrix, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "deriveRepAlleleMatrix.checkpoint.Success"])
            def checkpoint_deriveRepAlleleMatrix(inputs,outputs):
                output, flagFile = outputs
                runStageCheck('checkpoint', flagFile, outTempPrefix, 'deriveRepAlleleMatrix')
            stage_count += 1

            def matrixByCoreRep():
                for repliconName in core_replicons:
                    output  = outTempPrefix + refName + '_' + repliconName + '_alleles.csv'
                    flagFile = outSuccessPrefix + refName + '_' + repliconName + '.collateRepAlleleMatrix.Success'
                    rep_name = refName + '_' + repliconName
                    yield([input==None, [output, flagFile], rep_name])

            @follows(checkpoint_deriveRepAlleleMatrix)
            @files(matrixByCoreRep)
            def collateRepAlleleMatrix(input, outputs, rep_name):
                output, flagFile = outputs
                runStageCheck('collateRepAlleleMatrix', flagFile, outTempPrefix, output, full_sequence_list_string, rep_name)
            stage_count += len(core_replicons)

        else: #runType == 'phylogeny'
            # generate the allele matrix entry for each isolate for each replicon
            def matrixEntryByRep():
                for isolate in full_sequence_list:
                    for repliconName in replicons:
                        input = outTempPrefix + 'getRepSNPList/' + refName + '_' + repliconName[0] + '_SNPList.txt'
                        output  = outTempPrefix + isolate + '/deriveRepAlleleMartix/' + refName + '_' + repliconName[0] + '_' + isolate + '_alleles.txt'
                        flagFile = outSuccessPrefix + refName + '_' + repliconName[0] + '_' + isolate + '.deriveRepAlleleMatrix.Success'
                        replicon = repliconName[0]
                        consensus =  outTempPrefix + isolate + '/' + isolate + '_cns.fq'
                        repliconStats = outMerge + refName + '_' + repliconName[0] + '_RepStats.txt'
                        merge_prefix = outMerge
                        yield([input, [output, flagFile], replicon, consensus,repliconStats, merge_prefix])

            @follows(checkpoint_getConsensus, checkpoint_getMergeConsensus)
            @follows(checkpoint_getRepSNPList)
            @files(matrixEntryByRep)
            def deriveRepAlleleMatrix(input, outputs, replicon, consensus, repliconStats, merge_prefix):
                output, flagFile = outputs
                runStageCheck('deriveRepAlleleMatrix', flagFile, input, output, reference, replicon, consensus, repliconStats, merge_prefix)
            stage_count += (len(full_sequence_list)*len(replicons))

# checkpoint_deriveRepAlleleMatrix
            @merge(deriveRepAlleleMatrix, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "deriveRepAlleleMatrix.checkpoint.Success"])
            def checkpoint_deriveRepAlleleMatrix(inputs,outputs):
                output, flagFile = outputs
                runStageCheck('checkpoint', flagFile, outTempPrefix, 'deriveRepAlleleMatrix')
            stage_count += 1

            def matrixByRep():
                for repliconName in replicons:
                    output  = outTempPrefix + refName + '_' + repliconName[0] + '_alleles.csv'
                    flagFile = outSuccessPrefix + refName + '_' + repliconName[0] + '.collateRepAlleleMatrix.Success'
                    rep_name = refName + '_' + repliconName[0]
                    yield([input==None, [output, flagFile], rep_name])

            @follows(checkpoint_deriveRepAlleleMatrix)
            @files(matrixByRep)
            def collateRepAlleleMatrix(input, outputs, rep_name):
                output, flagFile = outputs
                runStageCheck('collateRepAlleleMatrix', flagFile, outTempPrefix, output, full_sequence_list_string, rep_name)
            stage_count += len(replicons)

        # parse SNP table to create alignment for tree
        @transform(collateRepAlleleMatrix, regex(r"(.*)\/(.+)_alleles.csv"), [outMerge + r"\2_alleles_var_cons"+str(conservation)+".csv", outSuccessPrefix + r"\2_alleles.parseSNPsNoGBK.Success"])
        def parseSNPsNoGBK(inputs, outputs):
            input,_success = inputs
            output, flagFile = outputs
            runStageCheck('parseSNPsNoGBK', flagFile, input, str(conservation), outMerge)
        if runType == "phylogeny":
            stage_count += len(replicons)
        else:
            stage_count += len(core_replicons)

        if conservation != 0.95:
            conservation_temp = 0.95
            @transform(collateRepAlleleMatrix, regex(r"(.*)\/(.+)_alleles.csv"), [outMerge + r"\2_alleles_var_cons" + "0.95.csv", outSuccessPrefix + r"\2_alleles.parseSNPsNoGBK_95.Success"])
            def parseSNPsNoGBK_95(inputs, outputs):
                input,_success = inputs
                output, flagFile = outputs
                runStageCheck('parseSNPsNoGBK', flagFile, input, str(conservation_temp), outMerge)
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)
            
            # create distance matrices based on pair-wise differences in SNPs
            if DifferenceMatrix:
                @follows(parseSNPsNoGBK_95)
                @transform(parseSNPsNoGBK, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outMerge + r"\2_SNP_diff.nxs", outSuccessPrefix + r"\2_alleles.getDifferenceMatrix.Success"])        
                def getDifferenceMatrix(inputs, outputs):
                    output, flagFile = outputs
                    input, _success = inputs
                    runStageCheck('getDifferenceMatrix', flagFile, input)
                if runType == "phylogeny":
                    stage_count += len(replicons)
                else:
                    stage_count += len(core_replicons)

        elif DifferenceMatrix:        
            # create distance matrices based on pair-wise differences in SNPs
            @transform(parseSNPsNoGBK, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outMerge + r"\2_SNP_diff.nxs", outSuccessPrefix + r"\2_alleles.getDifferenceMatrix.Success"])        
            def getDifferenceMatrix(inputs, outputs):
                output, flagFile = outputs
                input, _success = inputs
                runStageCheck('getDifferenceMatrix', flagFile, input)
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)

        # generate tree
        if conservation != 0.95:
            @follows(parseSNPsNoGBK_95)
            @transform(parseSNPsNoGBK, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outMerge + r"\2_alleles_var_cons"+str(conservation)+".tree", outSuccessPrefix + r"\2_alleles.makeTree.Success"])
            def makeTree(inputs, outputs):
                output, flagFile = outputs
                input, _success = inputs
                input = input[:-4] + ".mfasta"
                do_tree = False
                (isolate_count, snp_count) = getFastaDetails(input)
                if not force_no_tree:
                    if isolate_count <= 500:
                        do_tree = True
                    elif isolate_count > 500 and force_tree:
                        do_tree = True
                if do_tree:
                    runStageCheck('makeTree', flagFile, input, output)
                else:
                    runStageCheck('makeNoTree', flagFile, input, output)
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)
        else:
            @transform(parseSNPsNoGBK, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outMerge + r"\2_alleles_var_cons"+str(conservation)+".tree", outSuccessPrefix + r"\2_alleles.makeTree.Success"])
            def makeTree(inputs, outputs):
                output, flagFile = outputs
                input, _success = inputs
                input = input[:-4] + ".mfasta"
                do_tree = False
                (isolate_count, snp_count) = getFastaDetails(input)
                if not force_no_tree:
                    if isolate_count <= 500:
                        do_tree = True
                    elif isolate_count > 500 and force_tree:
                        do_tree = True
                if do_tree:
                    runStageCheck('makeTree', flagFile, input, output)
                else:
                    runStageCheck('makeNoTree', flagFile, input, output)
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)

    else: #refGenbank == False and outMerge == ''

        if runType == 'pangenome':
            # generate the allele matrix entry for each isolate for each replicon
            def matrixEntryByCoreRep():
                for isolate in full_sequence_list:
                    for repliconName in core_replicons:
                        input = outTempPrefix + 'getRepSNPList/' + refName + '_' + repliconName + '_SNPList.txt'
                        output  = outTempPrefix + isolate + '/deriveRepAlleleMartix/' + refName + '_' + repliconName + '_' + isolate + '_alleles.txt'
                        flagFile = outSuccessPrefix + refName + '_' + repliconName + '_' + isolate + '.deriveRepAlleleMatrix.Success'
                        replicon = repliconName
                        consensus =  outTempPrefix + isolate + '/' + isolate + '_cns.fq'
                        repliconStats = outPrefix + refName + '_' + repliconName + '_RepStats.txt'
                        merge_prefix = '-'
                        yield([input, [output, flagFile], replicon, consensus,repliconStats, merge_prefix])

            @follows(checkpoint_getConsensus)
            @follows(checkpoint_getRepSNPList)
            @files(matrixEntryByCoreRep)
            def deriveRepAlleleMatrix(input, outputs, replicon, consensus, repliconStats, merge_prefix):
                output, flagFile = outputs
                runStageCheck('deriveRepAlleleMatrix', flagFile, input, output, reference, replicon, consensus, repliconStats, merge_prefix)
            stage_count += (len(full_sequence_list)*len(core_replicons))

# checkpoint_deriveRepAlleleMatrix
            @merge(deriveRepAlleleMatrix, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "deriveRepAlleleMatrix.checkpoint.Success"])
            def checkpoint_deriveRepAlleleMatrix(inputs,outputs):
                output, flagFile = outputs
                runStageCheck('checkpoint', flagFile, outTempPrefix, 'deriveRepAlleleMatrix')
            stage_count += 1

            def matrixByCoreRep():
                for repliconName in core_replicons:
                    output  = outTempPrefix + refName + '_' + repliconName + '_alleles.csv'
                    flagFile = outSuccessPrefix + refName + '_' + repliconName + '.collateRepAlleleMatrix.Success'
                    rep_name = refName + '_' + repliconName
                    yield([input==None, [output, flagFile], rep_name])

            @follows(checkpoint_deriveRepAlleleMatrix)
            @files(matrixByCoreRep)
            def collateRepAlleleMatrix(input, outputs, rep_name):
                output, flagFile = outputs
                runStageCheck('collateRepAlleleMatrix', flagFile, outTempPrefix, output, full_sequence_list_string, rep_name)
            stage_count += len(core_replicons)

        else: #runType == 'phylogeny'
            # generate the allele matrix entry for each isolate for each replicon
            def matrixEntryByRep():
                for isolate in full_sequence_list:
                    for repliconName in replicons:
                        input = outTempPrefix + 'getRepSNPList/' + refName + '_' + repliconName[0] + '_SNPList.txt'
                        output  = outTempPrefix + isolate + '/deriveRepAlleleMartix/' + refName + '_' + repliconName[0] + '_' + isolate + '_alleles.txt'
                        flagFile = outSuccessPrefix + refName + '_' + repliconName[0] + '_' + isolate + '.deriveRepAlleleMatrix.Success'
                        replicon = repliconName[0]
                        consensus =  outTempPrefix + isolate + '/' + isolate + '_cns.fq'
                        repliconStats = outPrefix + refName + '_' + repliconName[0] + '_RepStats.txt'
                        merge_prefix = '-'
                        yield([input, [output, flagFile], replicon, consensus,repliconStats, merge_prefix])

            @follows(checkpoint_getConsensus)
            @follows(checkpoint_getRepSNPList)
            @files(matrixEntryByRep)
            def deriveRepAlleleMatrix(input, outputs, replicon, consensus, repliconStats, merge_prefix):
                output, flagFile = outputs
                runStageCheck('deriveRepAlleleMatrix', flagFile, input, output, reference, replicon, consensus, repliconStats, merge_prefix)
            stage_count += (len(full_sequence_list)*len(replicons))

# checkpoint_deriveRepAlleleMatrix
            @merge(deriveRepAlleleMatrix, [outTempPrefix+'checkpoint.txt', outSuccessPrefix + "deriveRepAlleleMatrix.checkpoint.Success"])
            def checkpoint_deriveRepAlleleMatrix(inputs,outputs):
                output, flagFile = outputs
                runStageCheck('checkpoint', flagFile, outTempPrefix, 'deriveRepAlleleMatrix')
            stage_count += 1

            def matrixByRep():
                for repliconName in replicons:
                    output  = outTempPrefix + refName + '_' + repliconName[0] + '_alleles.csv'
                    flagFile = outSuccessPrefix + refName + '_' + repliconName[0] + '.collateRepAlleleMatrix.Success'
                    rep_name = refName + '_' + repliconName[0]
                    yield([input==None, [output, flagFile], rep_name])

            @follows(checkpoint_deriveRepAlleleMatrix)
            @files(matrixByRep)
            def collateRepAlleleMatrix(input, outputs, rep_name):
                output, flagFile = outputs
                runStageCheck('collateRepAlleleMatrix', flagFile, outTempPrefix, output, full_sequence_list_string, rep_name)
            stage_count += len(replicons)

        # parse SNP table to create alignment for tree
        @transform(collateRepAlleleMatrix, regex(r"(.*)\/(.+)_alleles.csv"), [outPrefix + r"\2_alleles_var_cons"+str(conservation)+".csv", outSuccessPrefix + r"\2_alleles.parseSNPsNoGBK.Success"])
        def parseSNPsNoGBK(inputs, outputs):
            output, flagFile = outputs
            input,_success = inputs
            runStageCheck('parseSNPsNoGBK', flagFile, input, str(conservation), outPrefix)
        if runType == "phylogeny":
            stage_count += len(replicons)
        else:
            stage_count += len(core_replicons)

        if conservation != 0.95:
            @transform(collateRepAlleleMatrix, regex(r"(.*)\/(.+)_alleles.csv"), [outPrefix + r"\2_alleles_var_cons0.95.csv", outSuccessPrefix + r"\2_alleles.parseSNPsNoGBK_95.Success"])
            def parseSNPsNoGBK_95(inputs, outputs):
                output, flagFile = outputs
                input,_success = inputs
                conservation_temp = 0.95
                runStageCheck('parseSNPsNoGBK', flagFile, input, str(conservation_temp), outPrefix)
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)
            
            # create distance matrices based on pair-wise differences in SNPs
            if DifferenceMatrix:
                @follows(parseSNPsNoGBK_95)
                @transform(parseSNPsNoGBK, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outPrefix + r"\2_SNP_diff.nxs", outSuccessPrefix + r"\2_alleles.getDifferenceMatrix.Success"])        
                def getDifferenceMatrix(inputs, outputs):
                    output, flagFile = outputs
                    input, _success = inputs
                    runStageCheck('getDifferenceMatrix', flagFile, input)
                if runType == "phylogeny":
                    stage_count += len(replicons)
                else:
                    stage_count += len(core_replicons)

        elif DifferenceMatrix:        
            # create distance matrices based on pair-wise differences in SNPs
            @transform(parseSNPsNoGBK, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outPrefix + r"\2_SNP_diff.nxs", outSuccessPrefix + r"\2_alleles.getDifferenceMatrix.Success"])        
            def getDifferenceMatrix(inputs, outputs):
                output, flagFile = outputs
                input, _success = inputs
                runStageCheck('getDifferenceMatrix', flagFile, input)        
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)

        # generate tree
        if conservation != 0.95:
            @follows(parseSNPsNoGBK_95)
            @transform(parseSNPsNoGBK, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outPrefix + r"\2_alleles_var_cons"+str(conservation)+".tree", outSuccessPrefix + r"\2_alleles.makeTree.Success"])
            def makeTree(inputs, outputs):
                output, flagFile = outputs
                input, _success = inputs
                input = input[:-4] + ".mfasta"
                do_tree = False
                (isolate_count, snp_count) = getFastaDetails(input)
                if not force_no_tree:
                    if isolate_count <= 500:
                        do_tree = True
                    elif isolate_count > 500 and force_tree:
                        do_tree = True
                if do_tree:
                    runStageCheck('makeTree', flagFile, input, output)
                else:
                    runStageCheck('makeNoTree', flagFile, input, output)
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)
        else:
            @transform(parseSNPsNoGBK, regex(r"(.*)\/(.+)_alleles_var_cons"+str(conservation)+".csv"), [outPrefix + r"\2_alleles_var_cons"+str(conservation)+".tree", outSuccessPrefix + r"\2_alleles.makeTree.Success"])
            def makeTree(inputs, outputs):
                output, flagFile = outputs
                input, _success = inputs
                input = input[:-4] + ".mfasta"
                do_tree = False
                (isolate_count, snp_count) = getFastaDetails(input)
                if not force_no_tree:
                    if isolate_count <= 500:
                        do_tree = True
                    elif isolate_count > 500 and force_tree:
                        do_tree = True
                if do_tree:
                    runStageCheck('makeTree', flagFile, input, output)
                else:
                    runStageCheck('makeNoTree', flagFile, input, output)
            if runType == "phylogeny":
                stage_count += len(replicons)
            else:
                stage_count += len(core_replicons)

print str(stage_count + 1) + " jobs to be executed in total"
if success_count > 0:
    print str(stage_count+1-success_count) + " jobs left to execute"

# *** Clean up *** 
if outMerge != "":
    if not refGenbank:
        if DifferenceMatrix:
            # delete output directory to finish
            @follows(getDifferenceMatrix, makeTree)
            @files(input==None, outMerge + "finish.deleteDir.Success")
            def deleteDir(input, flagFile):            
                if stage_count > getSuccessCount(outSuccessPrefix):
                    print "\nSome stages have completed without success"
                    print "Pipeline Stopped: check for errors in the log files\n"
                else:
                    make_sequence_list(outMerge, full_sequence_list)
                    make_run_report(outMerge, merge_run, version, run_history, 
                                    pipeline_options.reference, refName, refGenbank, replicons, 
                                    full_sequence_list, readType, runType, core_replicons, 
                                    mapping, bowtie_map_type, replaceReads, minDepth, 
                                    coverFail, depthFail, mappedFail, sdOutgroupMultiplier, 
                                    check_reads_mapped, conservation, modules, bowtie_X_value, 
                                    read_history, sequences)
                    runStageCheck('deleteDir', flagFile, outPrefix)
        else:
            # delete output directory to finish
            @follows(makeTree)
            @files(input==None, outMerge + "finish.deleteDir.Success")
            def deleteDir(input, flagFile):            
                if stage_count > getSuccessCount(outSuccessPrefix):
                    print "\nSome stages have completed without success"
                    print "Pipeline Stopped: check for errors in the log files\n"
                else:
                    make_sequence_list(outMerge, full_sequence_list)
                    make_run_report(outMerge, merge_run, version, run_history, 
                                    pipeline_options.reference, refName, refGenbank, replicons, 
                                    full_sequence_list, readType, runType, core_replicons, 
                                    mapping, bowtie_map_type, replaceReads, minDepth, 
                                    coverFail, depthFail, mappedFail, sdOutgroupMultiplier, 
                                    check_reads_mapped, conservation, modules, bowtie_X_value, 
                                    read_history, sequences)
                    runStageCheck('deleteDir', flagFile, outPrefix)
    else:
        if DifferenceMatrix:
            # delete output directory to finish
            @follows(parseGeneContent, getDifferenceMatrix, makeTree)
            @files(input==None, outMerge + "finish.deleteDir.Success")
            def deleteDir(input, flagFile):
                if stage_count > getSuccessCount(outSuccessPrefix):
                    print "\nSome stages have completed without success"
                    print "Pipeline Stopped: check for errors in the log files\n"
                else:
                    make_sequence_list(outMerge, full_sequence_list)
                    make_run_report(outMerge, merge_run, version, run_history, 
                                    pipeline_options.reference, refName, refGenbank, replicons, 
                                    full_sequence_list, readType, runType, core_replicons, 
                                    mapping, bowtie_map_type, replaceReads, minDepth, 
                                    coverFail, depthFail, mappedFail, sdOutgroupMultiplier, 
                                    check_reads_mapped, conservation, modules, bowtie_X_value, 
                                    read_history, sequences)
                    runStageCheck('deleteDir', flagFile, outPrefix)
        else:
            # delete output directory to finish
            @follows(parseGeneContent, makeTree)
            @files(input==None, outMerge + "finish.deleteDir.Success")
            def deleteDir(input, flagFile):
                if stage_count > getSuccessCount(outSuccessPrefix):
                    print "\nSome stages have completed without success"
                    print "Pipeline Stopped: check for errors in the log files\n"
                else:
                    make_sequence_list(outMerge, full_sequence_list)
                    make_run_report(outMerge, merge_run, version, run_history, 
                                    pipeline_options.reference, refName, refGenbank, replicons, 
                                    full_sequence_list, readType, runType, core_replicons, 
                                    mapping, bowtie_map_type, replaceReads, minDepth, 
                                    coverFail, depthFail, mappedFail, sdOutgroupMultiplier, 
                                    check_reads_mapped, conservation, modules, bowtie_X_value, 
                                    read_history, sequences)
                    runStageCheck('deleteDir', flagFile, outPrefix)    

else:
    if not refGenbank:
        if DifferenceMatrix:
            # delete outTemp directory to finish
            @follows(getDifferenceMatrix, makeTree)
            @files(input==None, outPrefix + "finish.deleteDir.Success")
            def deleteDir(input, flagFile):
                if stage_count > getSuccessCount(outSuccessPrefix):
                    print "\nSome stages have completed without success"
                    print "Pipeline Stopped: check for errors in the log files\n"
                else:
                    make_sequence_list(outPrefix, full_sequence_list)
                    make_run_report(outPrefix, merge_run, version, run_history, 
                                    pipeline_options.reference, refName, refGenbank, replicons, 
                                    full_sequence_list, readType, runType, core_replicons, 
                                    mapping, bowtie_map_type, replaceReads, minDepth, 
                                    coverFail, depthFail, mappedFail, sdOutgroupMultiplier, 
                                    check_reads_mapped, conservation, modules, bowtie_X_value, 
                                    read_history, sequences)
                    runStageCheck('deleteDir', flagFile, outTempPrefix)
        else:
            # delete outTemp directory to finish
            @follows(makeTree)
            @files(input==None, outPrefix + "finish.deleteDir.Success")
            def deleteDir(input, flagFile):
                if stage_count > getSuccessCount(outSuccessPrefix):
                    print "\nSome stages have completed without success"
                    print "Pipeline Stopped: check for errors in the log files\n"
                else:
                    make_sequence_list(outPrefix, full_sequence_list)
                    make_run_report(outPrefix, merge_run, version, run_history, 
                                    pipeline_options.reference, refName, refGenbank, replicons, 
                                    full_sequence_list, readType, runType, core_replicons, 
                                    mapping, bowtie_map_type, replaceReads, minDepth, 
                                    coverFail, depthFail, mappedFail, sdOutgroupMultiplier, 
                                    check_reads_mapped, conservation, modules, bowtie_X_value, 
                                    read_history, sequences)
                    runStageCheck('deleteDir', flagFile, outTempPrefix)
    else:
        if DifferenceMatrix:
            # delete outTemp directory to finish
            @follows(parseGeneContent, getDifferenceMatrix, makeTree)
            @files(input==None, outPrefix + "finish.deleteDir.Success")
            def deleteDir(input, flagFile):
                if stage_count > getSuccessCount(outSuccessPrefix):
                    print "\nSome stages have completed without success"
                    print "Pipeline Stopped: check for errors in the log files\n"
                else:
                    make_sequence_list(outPrefix, full_sequence_list)
                    make_run_report(outPrefix, merge_run, version, run_history, 
                                    pipeline_options.reference, refName, refGenbank, replicons, 
                                    full_sequence_list, readType, runType, core_replicons, 
                                    mapping, bowtie_map_type, replaceReads, minDepth, 
                                    coverFail, depthFail, mappedFail, sdOutgroupMultiplier, 
                                    check_reads_mapped, conservation, modules, bowtie_X_value, 
                                    read_history, sequences)
                    runStageCheck('deleteDir', flagFile, outTempPrefix)
        else:
            # delete outTemp directory to finish
            @follows(parseGeneContent, makeTree)
            @files(input==None, outPrefix + "finish.deleteDir.Success")
            def deleteDir(input, flagFile):
                if stage_count > getSuccessCount(outSuccessPrefix):
                    print "\nSome stages have completed without success"
                    print "Pipeline Stopped: check for errors in the log files\n"
                else:
                    make_sequence_list(outPrefix, full_sequence_list)
                    make_run_report(outPrefix, merge_run, version, run_history, 
                                    pipeline_options.reference, refName, refGenbank, replicons, 
                                    full_sequence_list, readType, runType, core_replicons, 
                                    mapping, bowtie_map_type, replaceReads, minDepth, 
                                    coverFail, depthFail, mappedFail, sdOutgroupMultiplier, 
                                    check_reads_mapped, conservation, modules, bowtie_X_value, 
                                    read_history, sequences)
                    runStageCheck('deleteDir', flagFile, outTempPrefix)

#end of pipeline