def main():
#setup argparser to display help if no arguments
class MyParser(argparse.ArgumentParser):
def error(self, message):
self.print_help()
sys.stderr.write('\nerror: %s\n' % message)
sys.exit(1)
docker_config_path = os.path.abspath(
os.path.dirname(__file__) + '/' + 'core/docker_config.json')
parser = MyParser(
description=f"StaPH-B ToolKit Programs v{autoupdate.version}",
usage=
"staphb-tk [optional arguments] <application> [application arguments]",
add_help=True)
subparsers = parser.add_subparsers(title='custom toolkit applications',
metavar='',
dest="subparser_name",
parser_class=MyParser)
parser.add_argument(
"--docker_config",
"-c",
default=docker_config_path,
metavar="<path>",
help=
"Configuration file for container images and tags; if none provided, default container versions will be used."
)
parser.add_argument(
"--get_docker_config",
default=False,
action="store_true",
help="Get the default docker container configureation file.")
parser.add_argument(
"--list",
"-l",
default=False,
action="store_true",
help="List all of the software available in the toolkit.")
parser.add_argument("--update",
default=False,
action="store_true",
help="Check for and install a ToolKit update.")
parser.add_argument(
"--auto_update",
default=False,
action="store_true",
help="Toggle automatic ToolKit updates. Default is off.")
###custom apps
## Mash Species
parser_mash_species = subparsers.add_parser(
'mash_species',
help=
'MASH_species uses a pre-sketched RefSeq database to identify the isolate species from paired-end read data.',
usage="sb_mash_species <input> [options]")
parser_mash_species.add_argument(
"input",
type=str,
nargs='?',
help="path to dir containing paire-end read files")
parser_mash_species.add_argument("-o",
metavar='path',
default="",
type=str,
help="Path for output directory",
required=False)
#parser for applications
#-----------------------------------------
parser_abricate = subparsers.add_parser('abricate', add_help=False)
parser_augur = subparsers.add_parser('augur', add_help=False)
parser_bbtools = subparsers.add_parser('bbtools', add_help=False)
parser_bwa = subparsers.add_parser('bwa', add_help=False)
parser_canuracon = subparsers.add_parser('canu-racon', add_help=False)
parser_centroid = subparsers.add_parser('centroid', add_help=False)
parser_cfsansnp = subparsers.add_parser('cfsan-snp', add_help=False)
parser_circlator = subparsers.add_parser('circlator', add_help=False)
parser_clustalo = subparsers.add_parser('clustalo', add_help=False)
parser_emmtypingtool = subparsers.add_parser('emm-typing-tool',
add_help=False)
parser_fastani = subparsers.add_parser('fastani', add_help=False)
parser_fastqc = subparsers.add_parser('fastqc', add_help=False)
parser_fasttree = subparsers.add_parser('fasttree', add_help=False)
parser_filtong = subparsers.add_parser('filtlong', add_help=False)
parser_flye = subparsers.add_parser('flye', add_help=False)
parser_iqtree = subparsers.add_parser('iqtree', add_help=False)
parser_ivar = subparsers.add_parser('ivar', add_help=False)
parser_ivar_SC2 = subparsers.add_parser('ivar-SC2', add_help=False)
parser_kma = subparsers.add_parser('kma', add_help=False)
parser_kraken = subparsers.add_parser('kraken', add_help=False)
parser_krakenbuild = subparsers.add_parser('kraken-build', add_help=False)
parser_kraken2 = subparsers.add_parser('kraken2', add_help=False)
parser_kraken2build = subparsers.add_parser('kraken2-build',
add_help=False)
parser_ksnp3 = subparsers.add_parser('ksnp3', add_help=False)
parser_legsta = subparsers.add_parser('legsta', add_help=False)
parser_lyveset = subparsers.add_parser('lyveset', add_help=False)
parser_mafft = subparsers.add_parser('mafft', add_help=False)
parser_mash = subparsers.add_parser('mash', add_help=False)
parser_mashtree = subparsers.add_parser('mashtree', add_help=False)
parser_medaka = subparsers.add_parser('medaka', add_help=False)
parser_minimap2 = subparsers.add_parser('minimap2', add_help=False)
parser_mlst = subparsers.add_parser('mlst', add_help=False)
parser_mugsy = subparsers.add_parser('mugsy', add_help=False)
parser_multiqc = subparsers.add_parser('multiqc', add_help=False)
parser_nanoplot = subparsers.add_parser('nanoplot', add_help=False)
parser_ncbiamrfinder_plus = subparsers.add_parser('ncbi-amrfinder-plus',
add_help=False)
parser_orthofinder = subparsers.add_parser('orthofinder', add_help=False)
parser_pangolin = subparsers.add_parser('pangolin', add_help=False)
parser_pilon = subparsers.add_parser('pilon', add_help=False)
parser_plasmidseeker = subparsers.add_parser('plasmidseeker',
add_help=False)
parser_prokka = subparsers.add_parser('prokka', add_help=False)
parser_quast = subparsers.add_parser('quast', add_help=False)
parser_rasusa = subparsers.add_parser('rasusa', add_help=False)
parser_raxml = subparsers.add_parser('raxml', add_help=False)
parser_roary = subparsers.add_parser('roary', add_help=False)
parser_salmid = subparsers.add_parser('salmid', add_help=False)
parser_samtools = subparsers.add_parser('samtools', add_help=False)
parser_seqsero = subparsers.add_parser('seqsero', add_help=False)
parser_seqsero2 = subparsers.add_parser('seqsero2', add_help=False)
parser_seqyclean = subparsers.add_parser('seqyclean', add_help=False)
parser_seroba = subparsers.add_parser('seroba', add_help=False)
parser_serotypefinder = subparsers.add_parser('serotypefinder',
add_help=False)
parser_shovill = subparsers.add_parser('shovill', add_help=False)
parser_sistr = subparsers.add_parser('sistr', add_help=False)
parser_skesa = subparsers.add_parser('skesa', add_help=False)
parser_snippy = subparsers.add_parser('snippy', add_help=False)
parser_snpdists = subparsers.add_parser('snp-dists', add_help=False)
parser_snpsites = subparsers.add_parser('snp-sites', add_help=False)
parser_spades = subparsers.add_parser('spades', add_help=False)
parser_sratoolkit = subparsers.add_parser('sra-toolkit', add_help=False)
parser_staramr = subparsers.add_parser('staramr', add_help=False)
parser_tiptoft = subparsers.add_parser('tiptoft', add_help=False)
parser_trimmomatic = subparsers.add_parser('trimmomatic', add_help=False)
parser_unicycler = subparsers.add_parser('unicycler', add_help=False)
parser_wtdbg2 = subparsers.add_parser('wtdbg2', add_help=False)
#-----------------------------------------
def print_prog_list():
print("Available programs:")
header = ["Command", "Description", "-------", "-----------"]
print(f"{header[0]:<25}{header[1]:^10}")
print(f"{header[2]:<25}{header[3]:^10}")
for key in progs:
print(f"{key:<25}{progs[key]:^10}")
return
#handle the arguments and perform automatic path replacement
parser_args = parser.parse_known_args()
program = parser_args[0].subparser_name
args = parser_args[1]
#check for updates
if parser_args[0].update:
autoupdate.check_for_updates()
sys.exit(0)
if parser_args[0].auto_update:
#get current status
update_status = autoupdate.check_update_status()
if update_status:
autoupdate.toggle_updater(False)
else:
autoupdate.toggle_updater(True)
if autoupdate.check_update_status():
autoupdate.check_for_updates()
#give user docker config if asked
if parser_args[0].get_docker_config:
cwd = os.getcwd()
copy(
docker_config_path,
os.path.join(
os.getcwd(),
date.today().strftime("%y-%m-%d") + "_docker_config.json"))
sys.exit(0)
#display list of programs if needed
if parser_args[0].list:
print_prog_list()
sys.exit(0)
if program == None:
parser.print_help()
sys.exit(1)
#Run autopathing
arg_string, path_map = path_replacer(args, os.getcwd())
# set the configuration file
if parser_args[0].docker_config == "/core/docker_config.json":
# use default
config_file_path = os.path.abspath(
os.path.dirname(
os.path.realpath(__file__))) + parser_args[0].docker_config
else:
config_file_path = os.path.abspath(parser_args[0].docker_config)
with open(config_file_path, 'r') as config_file:
config = json.load(config_file)
#Custom program specific execution code
#-----------------------------------------
if program == 'mash_species':
#get output dir if supplied, if not set it to cwd
output_dir = None
if not parser_args[0].o:
output_dir = os.getcwd()
else:
try:
output_dir = os.path.abspath(parser_args[0].o)
except (AttributeError, TypeError):
print("Please enter a valid output path.")
sys.exit(1)
#get input path, if not supplied print help
try:
path = os.path.abspath(parser_args[0].input)
except (AttributeError, TypeError) as e:
parser_mash_species.print_help()
print("Please enter a valid input path.")
sys.exit(1)
#create and run the mash species object
mash_species_obj = MashSpecies(path=path, output_dir=output_dir)
mash_species_obj.run()
#Program specific execution code
#-----------------------------------------
if program == 'ivar-SC2':
if not re.search('[a-zA-Z]', arg_string):
arg_string = " "
command = "ivar " + arg_string
program_configuration = config["parameters"]["ivar-SC2"]
if program == 'ivar':
if not re.search('[a-zA-Z]', arg_string):
arg_string = " "
command = "ivar " + arg_string
program_configuration = config["parameters"]["ivar"]
if program == 'wtdbg2':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "wtdbg2 " + arg_string
program_configuration = config["parameters"]["wtdbg2"]
if program == 'trimmomatic':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "trimmomatic " + arg_string
program_configuration = config["parameters"]["trimmomatic"]
if program == 'tiptoft':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "tiptoft " + arg_string
program_configuration = config["parameters"]["tiptoft"]
if program == 'staramr':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "staramr " + arg_string
program_configuration = config["parameters"]["staramr"]
if program == 'sra-toolkit':
if not re.search('[a-zA-Z]', arg_string):
print(
"SRA toolkit tool must be specified, e.g. staphb-tk sra-toolkit fasterq-dump, staphb-tk sra-toolkit sra-pileup, etc. \n\nMore info on SRA Toolkit usage at: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc."
)
sys.exit()
command = " " + arg_string
program_configuration = config["parameters"]["sra-toolkit"]
if program == 'snp-dists':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "snp-dists " + arg_string
program_configuration = config["parameters"]["snp-dists"]
if program == 'snp-sites':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "snp-sites " + arg_string
program_configuration = config["parameters"]["snp-sites"]
if program == 'snippy':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "snippy " + arg_string
program_configuration = config["parameters"]["snippy"]
if program == 'skesa':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "skesa " + arg_string
program_configuration = config["parameters"]["skesa"]
if program == 'sistr':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "sistr " + arg_string
program_configuration = config["parameters"]["sistr"]
if program == 'seroba':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "seroba " + arg_string
program_configuration = config["parameters"]["seroba"]
if program == 'seqsero2':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "SeqSero2_package.py " + arg_string
program_configuration = config["parameters"]["seqsero2"]
if program == 'salmid':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "SalmID.py " + arg_string
program_configuration = config["parameters"]["salmid"]
if program == 'rasusa':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "rasusa " + arg_string
program_configuration = config["parameters"]["rasusa"]
if program == 'plasmidseeker':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "plasmidseeker.pl " + arg_string
program_configuration = config["parameters"]["plasmidseeker"]
if program == 'pangolin':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "--help"
command = "pangolin " + arg_string
program_configuration = config["parameters"]["pangolin"]
if program == 'pilon':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "--help"
command = "pilon " + arg_string
program_configuration = config["parameters"]["pilon"]
if program == 'orthofinder':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "orthofinder " + arg_string
program_configuration = config["parameters"]["orthofinder"]
if program == 'ncbi-amrfinder-plus':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "--help"
command = "amrfinder " + arg_string
program_configuration = config["parameters"]["ncbi-amrfinder-plus"]
if program == 'nanoplot':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "NanoPlot " + arg_string
program_configuration = config["parameters"]["nanoplot"]
if program == 'multiqc':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "multiqc " + arg_string
program_configuration = config["parameters"]["multiqc"]
if program == 'mugsy':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "mugsy " + arg_string
program_configuration = config["parameters"]["mugsy"]
if program == 'mlst':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "mlst " + arg_string
program_configuration = config["parameters"]["mlst"]
if program == 'medaka':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "medaka " + arg_string
program_configuration = config["parameters"]["medaka"]
if program == 'mashtree':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "mashtree " + arg_string
program_configuration = config["parameters"]["mashtree"]
if program == 'legsta':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "legsta " + arg_string
program_configuration = config["parameters"]["legsta"]
if program == 'ksnp3':
if not re.search('[a-zA-Z]', arg_string):
arg_string = ""
command = "kSNP3 " + arg_string
program_configuration = config["parameters"]["ksnp3"]
if program == 'kraken2-build':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "kraken2-build " + arg_string
program_configuration = config["parameters"]["kraken2"]
if program == 'kraken2':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "kraken2 " + arg_string
program_configuration = config["parameters"]["kraken2"]
if program == 'kraken-build':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "kraken-build " + arg_string
program_configuration = config["parameters"]["kraken"]
if program == 'kraken':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "kraken " + arg_string
program_configuration = config["parameters"]["kraken"]
if program == 'kma':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "kma " + arg_string
program_configuration = config["parameters"]["kma"]
if program == 'flye':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "flye " + arg_string
program_configuration = config["parameters"]["flye"]
if program == 'filtlong':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "filtlong " + arg_string
program_configuration = config["parameters"]["filtlong"]
if program == 'fastqc':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "fastqc " + arg_string
program_configuration = config["parameters"]["fastqc"]
if program == 'fasttree':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "FastTree " + arg_string
program_configuration = config["parameters"]["fasttree"]
if program == 'fastani':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "fastANI " + arg_string
program_configuration = config["parameters"]["fastani"]
if program == 'emm-typing-tool':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "emm_typing.py " + arg_string
program_configuration = config["parameters"]["emm-typing-tool"]
if program == 'circlator':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "circlator " + arg_string
program_configuration = config["parameters"]["circlator"]
if program == 'cfsan-snp':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "cfsan_snp_pipeline " + arg_string
program_configuration = config["parameters"]["cfsan-snp-pipeline"]
if program == 'canu-racon':
if not re.search('[a-zA-Z]', arg_string):
print(
"This is a bundled application that requires a specific commands to be used (i.e. staphb-tk canu-racon canu -h) please see the documentation for Canu, Minimap2 and Racon to use."
)
sys.exit()
command = " " + arg_string
program_configuration = config["parameters"]["canu-racon"]
if program == 'bbtools':
if not re.search('[a-zA-Z]', arg_string):
print(
"BBTools shell script must be specified, e.g. staphb-tk bbtools bbmap.sh, staphb-tk bbtools bbduk.sh, etc. \n\nMore info on BBTools at https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/."
)
sys.exit()
command = " " + arg_string
program_configuration = config["parameters"]["bbtools"]
if program == 'raxml':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "raxmlHPC " + arg_string
program_configuration = config["parameters"]["raxml"]
if program == 'spades':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "spades.py " + arg_string
program_configuration = config["parameters"]["spades"]
if program == 'mash':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "mash " + arg_string
program_configuration = config["parameters"]["mash"]
if program == 'seqyclean':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "seqyclean " + arg_string
program_configuration = config["parameters"]["seqyclean"]
if program == 'shovill':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "shovill " + arg_string
program_configuration = config["parameters"]["shovill"]
if program == 'prokka':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "prokka " + arg_string
program_configuration = config["parameters"]["prokka"]
if program == 'clustalo':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "clustalo " + arg_string
program_configuration = config["parameters"]["clustalo"]
if program == 'abricate':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "abricate " + arg_string
program_configuration = config["parameters"]["abricate"]
if program == 'augur':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "augur " + arg_string
program_configuration = config["parameters"]["augur"]
if program == 'iqtree':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "iqtree " + arg_string
program_configuration = config["parameters"]["iqtree"]
if program == 'lyveset':
if not re.search('[a-zA-Z]', arg_string):
print(
"Lyev-SET perl script must be specified, e.g. staphb-tk lyveset launch_set.pl, staphb-tk lyveset set_manage.pl, staphb-tk lyveset run_assembly_readMeterics.pl. \n\nMore info on Lyve-SET usage at: github.com/lskatz/lyve-SET."
)
sys.exit()
command = "" + arg_string
program_configuration = config["parameters"]["lyveset"]
if program == 'quast':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "quast.py " + arg_string
program_configuration = config["parameters"]["quast"]
if program == 'roary':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "roary " + arg_string
program_configuration = config["parameters"]["roary"]
if program == 'seqsero':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "SeqSero.py " + arg_string
program_configuration = config["parameters"]["seqsero"]
if program == 'samtools':
if not re.search('[a-zA-Z]', arg_string):
arg_string = ""
command = "samtools " + arg_string
program_configuration = config["parameters"]["samtools"]
if program == 'serotypefinder':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "serotypefinder.pl " + arg_string
program_configuration = config["parameters"]["serotypefinder"]
if program == 'bwa':
if not re.search('[a-zA-Z]', arg_string):
arg_string = ""
command = "bwa " + arg_string
program_configuration = config["parameters"]["bwa"]
if program == 'minimap2':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "minimap2 " + arg_string
program_configuration = config["parameters"]["minimap2"]
if program == 'centroid':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "centroid.py " + arg_string
program_configuration = config["parameters"]["centroid"]
if program == 'unicycler':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "unicycler " + arg_string
program_configuration = config["parameters"]["unicycler"]
if program == 'mafft':
if not re.search('[a-zA-Z]', arg_string):
arg_string = "-h"
command = "mafft " + arg_string
program_configuration = config["parameters"]["mafft"]
#Run the program
#-----------------------------------------
program_object = sb_prog.Run(command=command,
path=path_map,
image=program_configuration["image"],
tag=program_configuration["tag"])
program_object.run()
def main():
#get nextflow executable
lib_path = os.path.abspath(os.path.dirname(__file__) + '/' + 'lib')
workflows_path = os.path.abspath(os.path.dirname(__file__) + '/' + 'workflows')
nextflow_path = os.path.join(lib_path,'nextflow')
#setup argparser to display help if no arguments
class MyParser(argparse.ArgumentParser):
def error(self, message):
sys.stderr.write('error: %s\n' % message)
self.print_help()
sys.exit(2)
parser = MyParser(description=f"StaPH-B ToolKit Workflows v{autoupdate.version}",usage=f"staphb-wf [optional arguments] <workflow> [workflow arguments]")
parser.add_argument("--update",default=False,action="store_true",help="Check for and install a ToolKit update.")
parser.add_argument("--auto_update",default=False,action="store_true",help="Toggle automatic ToolKit updates. Default is off.")
subparsers = parser.add_subparsers(title='workflows',metavar='',dest="subparser_name")
#parser for workflows
#tredegar-----------------------------------------
parser_tredegar = subparsers.add_parser('tredegar', help='Quality control of WGS read data.', add_help=False)
parser_tredegar.add_argument('reads_path', type=str,help="path to the location of the reads in a fastq format",nargs='?', default=False)
parser_tredegar.add_argument('--output','-o',metavar="<output_path>",type=str,help="Path to ouput directory, default \"tredegar_results\".",default="tredegar_results")
parser_tredegar.add_argument('--profile', type=str,choices=["docker","singularity"],help="Nextflow profile. Default will try docker first, then singularity if the docker executable cannot be found.")
parser_tredegar.add_argument('--config','-c', type=str,help="Nextflow custom configuration.")
parser_tredegar.add_argument('--get_config',action="store_true",help="Get a Nextflow configuration template for tredegar.")
parser_tredegar.add_argument('--resume', default="", action="store_const",const="-resume",help="resume a previous run")
#monroe-----------------------------------------
parser_monroe = subparsers.add_parser('monroe', help='Consensus assembly for SARS-CoV-2 from ARTIC + Illumina protocols.', add_help=False)
monroe_subparsers = parser_monroe.add_subparsers(title='monroe_commands',metavar='',dest='monroe_command')
parser_monroe.add_argument('--get_config',type=str,choices=["pe_assembly", "se_assembly", "clearlabs_assembly", "ont_assembly", "cluster_analysis"],help="Get a Nextflow configuration template for the chosen workflow.")
##monroe_pe_assembly----------------------------
subparser_monroe_pe_assembly = monroe_subparsers.add_parser('pe_assembly',help='Assembly SARS-CoV-2 genomes from paired-end read data generated from ARTIC amplicons', add_help=False)
subparser_monroe_pe_assembly.add_argument('reads_path', type=str,help="path to the location of the reads in a fastq format")
subparser_monroe_pe_assembly.add_argument('--primers', type=str, choices=["V1","V2","V3"], help="indicate which ARTIC primers were used (V1, V2, or V3)")
subparser_monroe_pe_assembly.add_argument('--profile', type=str,choices=["docker", "singularity"],help="Nextflow profile. Default will try docker first, then singularity if the docker executable cannot be found.")
subparser_monroe_pe_assembly.add_argument('--output','-o',metavar="<output_path>",type=str,help="Path to ouput directory, default \"monroe_results\".",default="monroe_results")
subparser_monroe_pe_assembly.add_argument('--resume', default="", action="store_const",const="-resume",help="resume a previous run")
subparser_monroe_pe_assembly.add_argument('--config','-c', type=str,help="Nextflow custom configuration.")
##monroe_se_assembly----------------------------
subparser_monroe_se_assembly = monroe_subparsers.add_parser('se_assembly',help='Assembly SARS-CoV-2 genomes from single-end read data generated from ARTIC amplicons', add_help=False)
subparser_monroe_se_assembly.add_argument('reads_path', type=str,help="path to the location of the single-end reads in a fastq format")
subparser_monroe_se_assembly.add_argument('--primers', type=str, choices=["V1","V2","V3"], help="indicate which ARTIC primers were used (V1, V2, or V3)")
subparser_monroe_se_assembly.add_argument('--profile', type=str,choices=["docker", "singularity"],help="Nextflow profile. Default will try docker first, then singularity if the docker executable cannot be found.")
subparser_monroe_se_assembly.add_argument('--output','-o',metavar="<output_path>",type=str,help="Path to ouput directory, default \"monroe_results\".",default="monroe_results")
subparser_monroe_se_assembly.add_argument('--resume', default="", action="store_const",const="-resume",help="resume a previous run")
subparser_monroe_se_assembly.add_argument('--config','-c', type=str,help="Nextflow custom configuration.")
##monroe_clearlabs_assembly----------------------------
subparser_monroe_clearlabs_assembly = monroe_subparsers.add_parser('clearlabs_assembly',help='Assembly SARS-CoV-2 genomes from Clear Labs ont read data', add_help=False)
subparser_monroe_clearlabs_assembly.add_argument('reads_path', type=str,help="path to the location of the clearlabs reads in a fastq format")
subparser_monroe_clearlabs_assembly.add_argument('--profile', type=str,choices=["docker", "singularity"],help="Nextflow profile. Default will try docker first, then singularity if the docker executable cannot be found.")
subparser_monroe_clearlabs_assembly.add_argument('--output','-o',metavar="<output_path>",type=str,help="Path to ouput directory, default \"monroe_results\".",default="monroe_results")
subparser_monroe_clearlabs_assembly.add_argument('--resume', default="", action="store_const",const="-resume",help="resume a previous run")
subparser_monroe_clearlabs_assembly.add_argument('--config','-c', type=str,help="Nextflow custom configuration.")
##monroe_ont_assembly----------------------------
##medaka nanopolish
subparser_monroe_ont_assembly = monroe_subparsers.add_parser('ont_assembly',help='Assembly SARS-CoV-2 genomes from ONT read data generated from ARTIC amplicons', add_help=False)
subparser_monroe_ont_assembly.add_argument('--fast5_path', type=str,help="path to the location of the reads in a fast5 format")
subparser_monroe_ont_assembly.add_argument('--fastq_path', type=str,help="path to the location of the reads in a fastq format")
subparser_monroe_ont_assembly.add_argument('--demultiplexed', default="false",action="store_const",const="true",help="flag if fastq files have already been demultiplexed")
subparser_monroe_ont_assembly.add_argument('--medaka_model',default="r941_min_high_g360",help="medaka model to use for polishing, default: r941_min_fast_g303")
subparser_monroe_ont_assembly.add_argument('--run_prefix', type=str,help="desired run prefix. Default \"artic_ncov19\"",default="artic_ncov19")
subparser_monroe_ont_assembly.add_argument('--primers', type=str,choices=["V1", "V2", "V3"], help="indicate which ARTIC primers were used (V1, V2, or V3), default V3",default="V3")
subparser_monroe_ont_assembly.add_argument('--config','-c', type=str,help="Nextflow custom configuration.")
subparser_monroe_ont_assembly.add_argument('--output','-o',metavar="<output_path>",type=str,help="Path to ouput directory, default \"monroe_results\".",default="monroe_results")
subparser_monroe_ont_assembly.add_argument('--resume', default="", action="store_const",const="-resume",help="resume a previous run")
subparser_monroe_ont_assembly.add_argument('--profile', type=str,choices=["docker","singularity"],help="Nextflow profile. Default will try docker first, then singularity if the docker executable cannot be found.")
##monroe_cluster_analysis-----------------------
subparser_monroe_cluster_analysis = monroe_subparsers.add_parser('cluster_analysis',help='Perform multiple sequence alinmment of SC2 assemblies to generate a SNP-distance matrix & ML phylogenetic tree', add_help=False)
subparser_monroe_cluster_analysis.add_argument('assemblies_path', type=str,help="path to the location of the SC2 assemblies in a fasta format",nargs='?', default=False)
subparser_monroe_cluster_analysis.add_argument('--output','-o',metavar="<output_path>",type=str,help="Path to ouput directory, default \"monroe_results\".",default="monroe_results")
subparser_monroe_cluster_analysis.add_argument('--rtemplate','-rt', type=str, help="path to report rmarkdown", default=os.path.join(workflows_path,"monroe/report/report.Rmd"))
subparser_monroe_cluster_analysis.add_argument('--profile', type=str,choices=["docker","singularity"],help="Nextflow profile. Default will try docker first, then singularity if the docker executable cannot be found.")
subparser_monroe_cluster_analysis.add_argument('--resume', default="", action="store_const",const="-resume",help="resume a previous run")
subparser_monroe_cluster_analysis.add_argument('--config','-c', type=str,help="Nextflow custom configuration.")
subparser_monroe_cluster_analysis.add_argument('--get_rtemplate',action="store_true",help="Get a Rmd configuration template for report building.")
#foushee-----------------------------------------
parser_foushee = subparsers.add_parser('foushee', help='Reference-free SNP calling for Streptococcus pyogenes isolates.', add_help=False)
parser_foushee.add_argument('reads_path', type=str,help="path to the directory of raw reads in the fastq format",nargs='?', default=False)
parser_foushee.add_argument('--output','-o',metavar="<output_path>",type=str,help="Path to ouput directory, default \"tredegar_results\".",default="foushee_results")
parser_foushee.add_argument('--rtemplate','-rt', type=str, help="path to report rmarkdown", default=os.path.join(workflows_path,"foushee/report/report.Rmd"))
parser_foushee.add_argument('--profile', type=str,choices=["docker","singularity"],help="Nextflow profile. Default will try docker first, then singularity if the docker executable cannot be found.")
parser_foushee.add_argument('--config','-c', type=str,help="Nextflow custom configuration.")
parser_foushee.add_argument('--get_config',action="store_true",help="Get a Nextflow configuration template for foushee.")
parser_foushee.add_argument('--resume', default="", action="store_const",const="-resume",help="resume a previous run")
#dryad-----------------------------------------
parser_dryad = subparsers.add_parser('dryad', help='A comprehensive tree building program.', add_help=False)
subparser_dryad = parser_dryad.add_subparsers(title='dryad apps',metavar='',dest='dryad_app')
subparser_dryad_main = subparser_dryad.add_parser('main',help="dryad workflow")
subparser_dryad_main.add_argument('reads_path', type=str,help="path to the directory of raw reads in the fastq format",nargs='?', default=False)
subparser_dryad_main.add_argument('--output','-o',metavar="<output_path>",type=str,help="path to ouput directory, default \"dryad_results\"",default="dryad_results")
subparser_dryad_main.add_argument('--core-genome','-cg',default=False, action="store_true", help="construct a core-genome tree")
subparser_dryad_main.add_argument('--snp','-s',default=False, action="store_true", help="construct a SNP tree, requires a reference sequence in fasta format (-r)")
subparser_dryad_main.add_argument('-r',metavar='<path>', type=str,help="reference sequence for SNP pipeline")
subparser_dryad_main.add_argument('-ar',default=False, action="store_true", help="detect AR mechanisms")
subparser_dryad_main.add_argument('--profile', type=str,choices=["docker", "singularity"],help="specify nextflow profile, dryad will try to use docker first, then singularity")
subparser_dryad_main.add_argument('--config','-c', type=str,help="Nextflow custom configuration")
subparser_dryad_main.add_argument('--get_config',action="store_true",help="get a Nextflow configuration template for dryad")
subparser_dryad_main.add_argument('--resume', default="", action="store_const",const="-resume",help="resume a previous run")
subparser_dryad_main.add_argument('--report',action="store_true",help="generte a pdf report")
subparser_dryad_report = subparser_dryad.add_parser('rebuild_report',help='rebuild a previously generated PDF report')
subparser_dryad_report.add_argument('rmd',type=str,help="path to Rmarkdown file (.Rmd)",nargs='?', default=False)
subparser_dryad_report.add_argument('snp_matrix',type=str,help="path to snp matrix",nargs='?', default=False)
subparser_dryad_report.add_argument('cg_tree',type=str,help="path to core genome tree",nargs='?', default=False)
subparser_dryad_report.add_argument('--output','-o',metavar="<output_path>",type=str,help="path to ouput directory, default \"./\"",default="./")
subparser_dryad_report.add_argument('--ar',type=str,help="path to ar TSV file")
subparser_dryad_report.add_argument('--profile', type=str,choices=["docker", "singularity"],help="specify nextflow profile, dryad_report will try to use docker first, then singularity")
subparser_dryad_report.add_argument('--get_config',action="store_true",help="get a Nextflow configuration template for dryad")
subparser_dryad_report.add_argument('--config','-c', type=str,help="Nextflow custom configuration")
#hickory-----------------------------------------
parser_hickory = subparsers.add_parser('hickory', help='Determining an ideal reference genome.', add_help=False)
parser_hickory.add_argument('reads_path', type=str,help="path to the location of the reads in a fastq format",nargs='?', default=False)
parser_hickory.add_argument('--output','-o',metavar="<output_path>",type=str,help="Path to ouput directory, default \"hickory_results\".",default="hickory_results")
parser_hickory.add_argument('--profile', type=str,choices=["docker","singularity"],help="Nextflow profile. Default will try docker first, then singularity if the docker executable cannot be found.")
parser_hickory.add_argument('--config','-c', type=str,help="Nextflow custom configuration.")
parser_hickory.add_argument('--get_config',action="store_true",help="Get a Nextflow configuration template for hickory.")
parser_hickory.add_argument('--resume', default="", action="store_const",const="-resume",help="resume a previous run")
#cutshaw-----------------------------------------
parser_cutshaw = subparsers.add_parser('cutshaw', help='WGS competency assessment and instrument validation.', add_help=False)
parser_cutshaw.add_argument('reads_path', type=str,help="path to the location of the reads in a fastq format",nargs='?', default=False)
parser_cutshaw.add_argument('--isolate_key', type=str,help="path to the location of the isolation key file",nargs='?', default=False)
parser_cutshaw.add_argument('--report_title', type=str,help="title of the cutshaw report (e.g. name of instrument or scientist being assessed); must enclose in quotes",default="Unnamed Assessment")
parser_cutshaw.add_argument('--output','-o',metavar="<output_path>",type=str,help="Path to ouput directory, default \"cutshaw_results\".",default="cutshaw_results")
parser_cutshaw.add_argument('--profile', type=str,choices=["docker","singularity"],help="Nextflow profile. Default will try docker first, then singularity if the docker executable cannot be found.")
parser_cutshaw.add_argument('--config','-c', type=str,help="Nextflow custom configuration.")
parser_cutshaw.add_argument('--get_config',action="store_true",help="Get a Nextflow configuration template for cutshaw.")
parser_cutshaw.add_argument('--resume', default="", action="store_const",const="-resume",help="resume a previous run")
#cecret-----------------------------------------
parser_cecret = subparsers.add_parser('cecret', help='Consensus fasta creation of amplicon-based SARS-CoV-2 Illumina sequencing.', add_help=False)
parser_cecret.add_argument('reads_path', type=str,help="path to the location of reads in a fastq format",nargs='?', default=False)
parser_cecret.add_argument('--reads_type',type=str,choices=["paired","single"],help="Specify either \"paired\"-end or \"single\"-end reads, default \"paired\".",default="paired")
parser_cecret.add_argument('--annotation',action="store_true",help="Annotate fastas instead of creating fastas.")
parser_cecret.add_argument('--output','-o',metavar="<output_path>",type=str,help="Path to ouput directory, default \"cecret\".",default="cecret")
parser_cecret.add_argument('--profile',type=str,choices=["docker","singularity"],help="Nextflow profile. Default will try docker first, then singularity if the docker executable cannot be found.")
parser_cecret.add_argument('--config','-c',type=str,help="Nextflow custom configuration.")
parser_cecret.add_argument('--get_config',action="store_true",help="Get a Nextflow configuration template for cecret.")
parser_cecret.add_argument('--resume', default="", action="store_const",const="-resume",help="resume a previous run")
#----------------------------------------------
args = parser.parse_args()
#check if we are using docker or singularity
if which('docker'):
profile = '-profile docker'
elif which('singularity'):
profile = '-profile singularity'
else:
profile = ''
#check for updates
if args.update:
autoupdate.check_for_updates()
if args.auto_update:
#get current status
update_status = autoupdate.check_update_status()
if update_status:
autoupdate.toggle_updater(False)
else:
autoupdate.toggle_updater(True)
if autoupdate.check_update_status():
autoupdate.check_for_updates()
if args.subparser_name == None:
parser.print_help()
sys.exit(1)
program = args.subparser_name
#current time for log files
exec_time = datetime.now().strftime("%y_%m_%d_%H_%M_%S_")
#################################
#Program specific execution code#
#################################
#tredegar--------------------------------
if program == 'tredegar':
#tredegar path
tredegar_path = os.path.join(workflows_path,"tredegar/")
#give config to user if requested
if args.get_config:
config_path = os.path.join(tredegar_path,"configs/tredegar_config_template.config")
dest_path = os.path.join(os.getcwd(),date.today().strftime("%y-%m-%d")+"_tredegar.config")
copyfile(config_path,dest_path)
sys.exit()
#check for reads_path
if not args.reads_path:
parser_tredegar.print_help()
print("Please specify a path to a directory containing the raw reads.")
sys.exit(1)
#check for config or profile
config = ""
if args.config:
config = "-C " + os.path.abspath(args.config)
profile = ""
elif args.profile:
profile = f"-profile {args.profile}"
elif not profile:
print('Singularity or Docker is not installed or not in found in PATH.')
sys.exit(1)
#set work dir into local logs dir if profile not aws
work = ""
if profile and not args.config:
work = f"-w {args.output}/logs/work"
#build command
command = nextflow_path
command = command + f" {config} run {tredegar_path}/tredegar.nf {profile} {args.resume} --reads {args.reads_path} --outdir {args.output} -with-trace {args.output}/logs/{exec_time}Tredegar_trace.txt -with-report {args.output}/logs/{exec_time}Tredegar_execution_report.html {work}"
print(command)
#run command using nextflow in a subprocess
print("Starting the Tredegar pipeline:")
child = pexpect.spawn(command)
child.interact()
#monroe----------------------------------
if program == 'monroe':
#monroe path
monroe_path = os.path.join(workflows_path,"monroe/")
#give config to user if requested
if args.get_config == "pe_assembly":
config_path = os.path.join(monroe_path,"configs/pe_user_config.config")
dest_path = os.path.join(os.getcwd(),date.today().strftime("%y-%m-%d")+"_pe_assembly.config")
copyfile(config_path,dest_path)
sys.exit()
elif args.get_config == "se_assembly":
config_path = os.path.join(monroe_path,"configs/se_user_config.config")
dest_path = os.path.join(os.getcwd(),date.today().strftime("%y-%m-%d")+"_se_assembly.config")
copyfile(config_path,dest_path)
sys.exit()
elif args.get_config == "clearlabs_assembly":
config_path = os.path.join(monroe_path,"configs/clearlabs_user_config.config")
dest_path = os.path.join(os.getcwd(),date.today().strftime("%y-%m-%d")+"_clearlabs_assembly.config")
copyfile(config_path,dest_path)
sys.exit()
elif args.get_config == "ont_assembly":
config_path = os.path.join(monroe_path,"configs/ont_user_config.config")
dest_path = os.path.join(os.getcwd(),date.today().strftime("%y-%m-%d")+"_ont_assembly.config")
copyfile(config_path,dest_path)
sys.exit()
elif args.get_config == "cluster_analysis":
config_path = os.path.join(monroe_path,"configs/cluster_user_config.config")
dest_path = os.path.join(os.getcwd(),date.today().strftime("%y-%m-%d")+"_cluster_analysis.config")
copyfile(config_path,dest_path)
sys.exit()
if args.monroe_command == None:
parser_monroe.print_help()
sys.exit(1)
#check for config or profile
config = ""
if args.config:
config = "-C " + os.path.abspath(args.config)
profile = ""
elif args.profile:
profile = f"-profile {args.profile}"
elif not profile:
print('Singularity or Docker is not installed or not in found in PATH.')
sys.exit(1)
#set work dir into local logs dir if profile not aws
work = ""
if profile and not args.config:
work = f"-w {args.output}/logs/work"
if args.monroe_command == 'pe_assembly':
#check for either standard ARTIC primer version, or a custom config
if not args.config and not args.primers:
raise Exception(f"argument --primers: no primer set selected, choose from ('V1', 'V2', 'V3') or use a custom configuration.")
if not args.config:
primer_set = f"/configs/artic_{args.primers}_nCoV-2019.bed"
profile = profile + f" --primerSet {primer_set}"
#build command
command = nextflow_path + f" {config} run {monroe_path}/monroe_pe_assembly.nf {profile} {args.resume} --pipe pe --reads {args.reads_path} --outdir {args.output} -with-trace {args.output}/logs/{exec_time}Monroe_trace.txt -with-report {args.output}/logs/{exec_time}Monroe_execution_report.html {work}"
#run command using nextflow in a subprocess
print("Starting the Monroe paired-end assembly:")
child = pexpect.spawn(command)
child.interact()
if args.monroe_command == 'se_assembly':
#check for either standard ARTIC primer version, or a custom config
if not args.config and not args.primers:
raise Exception(f"argument --primers: no primer set selected, choose from ('V1', 'V2', 'V3') or use a custom configuration.")
if not args.config:
primer_set = f"/configs/artic_{args.primers}_nCoV-2019.bed"
profile = profile + f" --primerSet {primer_set}"
#build command
command = nextflow_path + f" {config} run {monroe_path}/monroe_se_assembly.nf {profile} {args.resume} --pipe pe --reads {args.reads_path} --outdir {args.output} -with-trace {args.output}/logs/{exec_time}Monroe_trace.txt -with-report {args.output}/logs/{exec_time}Monroe_execution_report.html {work}"
#run command using nextflow in a subprocess
print("Starting the Monroe single-end assembly:")
child = pexpect.spawn(command)
child.interact()
if args.monroe_command == 'clearlabs_assembly':
#build command
command = nextflow_path + f" {config} run {monroe_path}/monroe_clearlabs_assembly.nf {profile} {args.resume} --pipe clearlabs --reads {args.reads_path} --outdir {args.output} -with-trace {args.output}/logs/{exec_time}Monroe_trace.txt -with-report {args.output}/logs/{exec_time}Monroe_execution_report.html {work}"
#run command using nextflow in a subprocess
print("Starting the Monroe Clear Labs assembly:")
child = pexpect.spawn(command)
child.interact()
if args.monroe_command == 'cluster_analysis':
#give report template to user if requested
if args.get_rtemplate:
rtemplate_path = os.path.join(monroe_path,"report/report.Rmd")
dest_path = os.path.join(os.getcwd(),date.today().strftime("%y-%m-%d")+"_cluster_analysis_report.Rmd")
copyfile(rtemplate_path,dest_path)
sys.exit()
#check for assemblies path
if not args.assemblies_path:
subparser_monroe_cluster_analysis.print_help()
print("Please specify a path to a directory containing the raw reads.")
sys.exit(1)
#build command
command = nextflow_path + f" {config} run {monroe_path}/monroe_cluster_analysis.nf {profile} {args.resume} --pipe cluster --assemblies {args.assemblies_path} --report {args.rtemplate} --outdir {args.output} -with-trace {args.output}/logs/{exec_time}Monroe_trace.txt -with-report {args.output}/logs/{exec_time}Monroe_execution_report.html {work}"
#run command using nextflow in a subprocess
print("Starting the Monroe cluster analysis:")
child = pexpect.spawn(command)
child.interact()
if args.monroe_command == 'ont_assembly':
#build command
if args.fast5_path:
read_paths = f"--fast5_dir {args.fast5_path}"
elif args.fastq_path:
read_paths = f"--fastq_dir {args.fastq_path}"
else:
subparser_monroe_ont_assembly.print_help()
print("Please provide path to fast5 files to perform basecalling or fastq files, note: basecalling requires GPU")
sys.exit(1)
command = nextflow_path + f" {config} run {monroe_path}/monroe_ont_assembly.nf {profile} {args.resume} {read_paths} --pipe ont --primers {args.primers} --outdir {args.output} --run_prefix {args.run_prefix} --medaka_model {args.medaka_model} --demultiplexed {args.demultiplexed} -with-trace {args.output}/logs/{exec_time}Monroe_trace.txt -with-report {args.output}/logs/{exec_time}Monroe_execution_report.html {work}"
#run command using nextflow in a subprocess
print("Starting the Monroe ONT assembly:")
child = pexpect.spawn(command)
child.interact()
#foushee---------------------------------
if program == 'foushee':
#tredegar path
foushee_path = os.path.join(workflows_path,"foushee/")
#give config to user if requested
if args.get_config:
config_path = os.path.join(foushee_path,"configs/foushee_config_template.config")
dest_path = os.path.join(os.getcwd(),date.today().strftime("%y-%m-%d")+"_foushee.config")
copyfile(config_path,dest_path)
sys.exit()
#check for reads_path
if not args.reads_path:
parser_foushee.print_help()
print("Please specify a path to a directory containing the raw reads.")
sys.exit(1)
#check for config or profile
config = ""
if args.config:
config = "-C " + os.path.abspath(args.config)
profile = ""
elif args.profile:
profile = f"-profile {args.profile}"
elif not profile:
print('Singularity or Docker is not installed or not in found in PATH.')
sys.exit(1)
#set work dir into local logs dir if profile not aws
work = ""
if profile and not args.config:
work = f"-w {args.output}/logs/work"
#build command
command = nextflow_path
command = command + f" {config} run {foushee_path}/foushee.nf {profile} {args.resume} --reads {args.reads_path} --report {args.rtemplate} --outdir {args.output} -with-trace {args.output}/logs/{exec_time}Foushee_trace.txt -with-report {args.output}/logs/{exec_time}Foushee_execution_report.html {work}"
print(command)
#run command using nextflow in a subprocess
print("Starting the Foushee pipeline:")
child = pexpect.spawn(command)
child.interact()
#dryad-----------------------------------
if program == 'dryad':
#dryad path
dryad_path = os.path.join(workflows_path,"dryad/")
if args.dryad_app == None:
parser_dryad.print_help()
sys.exit(1)
#give config to user if requested
if args.get_config:
config_path = os.path.join(dryad_path,"configs/dryad_config_template.config")
dest_path = os.path.join(os.getcwd(),date.today().strftime("%y-%m-%d")+"_dryad.config")
copyfile(config_path,dest_path)
sys.exit()
#rebuild report subroutine
if args.dryad_app == "rebuild_report":
#check for rmd path
if not args.rmd or not args.snp_matrix or not args.cg_tree:
subparser_dryad_report.print_help()
sys.exit(1)
#check for config or profile
config = ""
if args.config:
config = "-C " + os.path.abspath(args.config)
profile = ""
elif args.profile:
if which(args.profile):
profile = '-profile ' + args.profile
else:
print(f"{args.profile} is not installed or found in PATH.")
elif not profile:
print('Singularity or Docker is not installed or not found in PATH.')
sys.exit(1)
#set work dir into local logs dir if profile not aws
work = ""
output_path = os.path.join(os.getcwd(),'rebuild_results')
output_work = os.path.join(output_path,'report_work')
if profile and not args.config:
work = f"-w {output_work}"
rmd = os.path.abspath(args.rmd)
logo_path = os.path.join(dryad_path, 'assets/dryad_logo_250.png')
snp_mat = "--snp_matrix " + os.path.abspath(args.snp_matrix)
cg_tree = "--cg_tree " + os.path.abspath(args.cg_tree)
if args.ar:
ar_tsv = "--ar_tsv " + os.path.abspath(args.ar)
else:
ar_tsv = ""
#build command
command = nextflow_path
command = command + f" {config} run {dryad_path}/rebuild_report.nf {profile} --logo {logo_path} --outdir {output_path} --rmd {rmd} {snp_mat} {cg_tree} {ar_tsv} -with-trace {args.output}/logs/{exec_time}dryad_trace.txt -with-report {args.output}/logs/{exec_time}dryad_execution_report.html {work}"
#run command using nextflow in a subprocess
print("Rebuilding Dryad Report:")
child = pexpect.spawn(command)
child.interact()
#dryad main application
if args.dryad_app == "main":
#check for reads_path
if not args.reads_path:
subparser_dryad_main.print_help()
print("Please specify a path to a directory containing the raw reads.")
sys.exit(1)
#check for reference sequence
if args.snp and args.r == None:
subparser_dryad_main.print_help()
print("Please specify a reference sequence for the SNP pipeline.")
sys.exit(1)
#check for config or profile
config = ""
if args.config:
config = "-C " + os.path.abspath(args.config)
profile = ""
elif args.profile:
if which(args.profile):
profile = '-profile ' + args.profile
else:
print(f"{args.profile} is not installed or found in PATH.")
elif not profile:
print('Singularity or Docker is not installed or not found in PATH.')
sys.exit(1)
#set work dir into local logs dir if profile not aws
work = ""
if profile and not args.config:
work = f"-w {args.output}/logs/work"
#build nextflow command
logo_path = os.path.join(dryad_path,"assets/dryad_logo_250.png")
selections = ""
if args.ar:
selections += " --ar"
if args.core_genome:
selections += " --cg"
if args.snp:
selections += f" --snp --snp_reference {args.r}"
if args.report and args.snp and args.core_genome:
report_template_path = os.path.join(dryad_path,"report/report.Rmd")
selections += f" --report {report_template_path} --logo {logo_path}"
#path for multiqc config
mqc_config_path = f"--multiqc_config " + os.path.join(dryad_path,"configs/multiqc_config.yaml")
mqc_logo_path = f"--multiqc_logo " + logo_path
#add other arguments
other_args = f"--outdir {args.output}"
#build command
command = nextflow_path
command = command + f" {config} run {dryad_path}/dryad.nf {profile} {args.resume} --reads {args.reads_path} {selections} {other_args} {mqc_config_path} {mqc_logo_path} -with-trace {args.output}/logs/{exec_time}dryad_trace.txt -with-report {args.output}/logs/{exec_time}dryad_execution_report.html {work}"
#run command using nextflow in a subprocess
print("Starting the Dryad pipeline:")
child = pexpect.spawn(command)
child.interact()
#hickory--------------------------------
if program == 'hickory':
#Hickory path
hickory_path = os.path.join(workflows_path,"hickory/")
#give config to user if requested
if args.get_config:
config_path = os.path.join(hickory_path,"configs/hickory_config_template.config")
dest_path = os.path.join(os.getcwd(),date.today().strftime("%y-%m-%d")+"_hickory.config")
copyfile(config_path,dest_path)
sys.exit()
#check for reads_path
if not args.reads_path:
parser_hickory.print_help()
print("Please specify a path to a directory containing the raw reads.")
sys.exit(1)
#check for config or profile
config = ""
if args.config:
config = "-C " + os.path.abspath(args.config)
profile = ""
elif args.profile:
profile = f"-profile {args.profile}"
elif not profile:
print('Singularity or Docker is not installed or not in found in PATH.')
sys.exit(1)
#set work dir into local logs dir if profile not aws
work = ""
if profile and not args.config:
work = f"-w {args.output}/logs/work"
#build command
command = nextflow_path
command = command + f" {config} run {hickory_path}/hickory.nf {profile} {args.resume} --reads {args.reads_path} --outdir {args.output} -with-trace {args.output}/logs/{exec_time}hickory_trace.txt -with-report {args.output}/logs/{exec_time}hickory_execution_report.html {work}"
print(command)
#run command using nextflow in a subprocess
print("Starting the Hickory pipeline:")
child = pexpect.spawn(command)
child.interact()
#cutshaw--------------------------------
if program == 'cutshaw':
#cutshaw path
cutshaw_path = os.path.join(workflows_path,"cutshaw/")
#give config to user if requested
if args.get_config:
config_path = os.path.join(cutshaw_path,"configs/cutshaw_config_template.config")
dest_path = os.path.join(os.getcwd(),date.today().strftime("%y-%m-%d")+"_cutshaw.config")
copyfile(config_path,dest_path)
sys.exit()
#check for reads_path
if not args.reads_path:
parser_cutshaw.print_help()
print("Please specify a path to a directory containing the raw reads.")
sys.exit(1)
#check for config or profile
config = ""
if args.config:
config = "-C " + os.path.abspath(args.config)
profile = ""
elif args.profile:
profile = f"-profile {args.profile}"
elif not profile:
print('Singularity or Docker is not installed or not in found in PATH.')
sys.exit(1)
#set work dir into local logs dir if profile not aws
work = ""
if profile and not args.config:
work = f"-w {args.output}/logs/work"
#build command
command = nextflow_path
print(args.report_title)
command = command + f" {config} run {cutshaw_path}/cutshaw.nf {profile} {args.resume} --reads {args.reads_path} --pt_genomes {cutshaw_path}/pt_genomes/* --isolate_key {args.isolate_key} --title \"{args.report_title}\" --outdir {args.output} -with-trace {args.output}/logs/{exec_time}Cutshaw_trace.txt -with-report {args.output}/logs/{exec_time}Cutshaw_execution_report.html {work}"
print(command)
#run command using nextflow in a subprocess
print("Starting the Cutshaw pipeline:")
child = pexpect.spawn(command)
child.interact()
#cecret--------------------------------
if program == 'cecret':
#cecret path
cecret_path = os.path.join(workflows_path,"cecret/")
#give config to user if requested
if args.get_config:
config_path = os.path.join(cecret_path,"configs/cecret_config_template.config")
dest_path = os.path.join(os.getcwd(),date.today().strftime("%y-%m-%d")+"_cecret.config")
copyfile(config_path,dest_path)
sys.exit()
#check for reads_path
if not args.reads_path:
parser_cecret.print_help()
print("Please specify a path to a directory containing paired end raw reads.")
print("Note: Can specify an empty directory if single reads parameter is set.")
sys.exit()
#check for config or profile
config = ""
if args.config:
config = "-C " + os.path.abspath(args.config)
profile = ""
elif args.profile:
profile = f"-profile {args.profile}"
elif not profile:
print('Singularity or Docker is not installed or not in found in PATH.')
sys.exit(1)
reads_type = ""
if args.reads_type == "paired":
reads_type = "--reads"
elif args.reads_type == "single":
reads_type = "--single_reads"
elif not args.reads_type:
print("Type of reads not specified for some reason")
sys.exit(1)
if args.annotation:
flow = 'cecret_annotation.nf'
reads_type = '--fastas'
else:
flow = 'cecret.nf'
#set work dir into local logs dir if profile not aws
work = ""
if profile and not args.config:
work = f"-w {args.output}/logs/work"
#build command
command = nextflow_path
command = command + f" {config} run {cecret_path}/{flow} {profile} {args.resume} {reads_type} {args.reads_path} --outdir {args.output} -with-trace {args.output}/logs/{exec_time}cecret_trace.txt -with-report {args.output}/logs/{exec_time}cecret_execution_report.html {work}"
print(command)
#run command using nextflow in a subprocess
print("Starting the cecret workflow:")
child = pexpect.spawn(command)
child.interact()