def run_HybridSPAdes(self, ctx, params):
    '\n        Run HybridSPAdes on paired end libraries with PacBio CLR and Oxford Nanopore reads\n        :param params: instance of type "HybridSPAdesParams" (------To run\n           HybridSPAdes 3.13.0 you need at least one library of the following\n           types:------ 1) Illumina paired-end/high-quality\n           mate-pairs/unpaired reads 2) IonTorrent paired-end/high-quality\n           mate-pairs/unpaired reads 3) PacBio CCS reads Version 3.13.0 of\n           SPAdes supports paired-end reads, mate-pairs and unpaired reads.\n           SPAdes can take as input several paired-end and mate-pair\n           libraries simultaneously. workspace_name - the name of the\n           workspace from which to take input and store output.\n           output_contigset_name - the name of the output contigset\n           read_libraries - a list of Illumina or IonTorrent\n           paired-end/high-quality mate-pairs/unpaired reads\n           long_reads_libraries - a list of PacBio, Oxford Nanopore Sanger\n           reads and/or additional contigs dna_source - the source of the DNA\n           used for sequencing \'single_cell\': DNA amplified from a single\n           cell via MDA anything else: Standard DNA sample from multiple\n           cells. Default value is None. pipeline_options - a list of string\n           specifying how the SPAdes pipeline should be run kmer_sizes -\n           (optional) K-mer sizes, Default values: 21, 33, 55, 77, 99, 127\n           (all values must be odd, less than 128 and listed in ascending\n           order) In the absence of these values, K values are automatically\n           selected. min_contig_length - integer to filter out contigs with\n           length < min_contig_length from the HybridSPAdes output. Default\n           value is 0 implying no filter. @optional dna_source @optional\n           pipeline_options @optional kmer_sizes @optional min_contig_length)\n           -> structure: parameter "workspace_name" of String, parameter\n           "output_contigset_name" of String, parameter "reads_libraries" of\n           list of type "ReadsParams" (parameter groups--define attributes\n           for specifying inputs with YAML data set file (advanced) The\n           following attributes are available: - orientation ("fr", "rf",\n           "ff") - type ("paired-end", "mate-pairs", "hq-mate-pairs",\n           "single", "pacbio", "nanopore", "sanger", "trusted-contigs",\n           "untrusted-contigs") - interlaced reads (comma-separated list of\n           files with interlaced reads) - left reads (comma-separated list of\n           files with left reads) - right reads (comma-separated list of\n           files with right reads) - single reads (comma-separated list of\n           files with single reads or unpaired reads from paired library) -\n           merged reads (comma-separated list of files with merged reads)) ->\n           structure: parameter "lib_ref" of type "obj_ref" (An X/Y/Z style\n           KBase object reference), parameter "orientation" of String,\n           parameter "lib_type" of String, parameter "long_reads_libraries"\n           of list of type "LongReadsParams" -> structure: parameter\n           "long_reads_ref" of type "obj_ref" (An X/Y/Z style KBase object\n           reference), parameter "long_reads_type" of String, parameter\n           "dna_source" of String, parameter "pipeline_options" of list of\n           String, parameter "kmer_sizes" of list of Long, parameter\n           "min_contig_length" of Long, parameter "create_report" of type\n           "bool" (A boolean. 0 = false, anything else = true.)\n        :returns: instance of type "SPAdesOutput" (Output parameters for\n           SPAdes run. report_name - the name of the KBaseReport.Report\n           workspace object. report_ref - the workspace reference of the\n           report.) -> structure: parameter "report_name" of String,\n           parameter "report_ref" of String\n        '
    self.log('Running run_HybridSPAdes with params:\n{}'.format(json.dumps(params, indent=1)))
    spades_assembler = SPAdesAssembler(self.cfg, ctx.provenance())
    output = spades_assembler.run_hybrid_spades(params)
    if (not isinstance(output, dict)):
        raise ValueError(('Method run_HybridSPAdes return value ' + 'output is not type dict as required.'))
    return [output]
Run HybridSPAdes on paired end libraries with PacBio CLR and Oxford Nanopore reads
:param params: instance of type "HybridSPAdesParams" (------To run
   HybridSPAdes 3.13.0 you need at least one library of the following
   types:------ 1) Illumina paired-end/high-quality
   mate-pairs/unpaired reads 2) IonTorrent paired-end/high-quality
   mate-pairs/unpaired reads 3) PacBio CCS reads Version 3.13.0 of
   SPAdes supports paired-end reads, mate-pairs and unpaired reads.
   SPAdes can take as input several paired-end and mate-pair
   libraries simultaneously. workspace_name - the name of the
   workspace from which to take input and store output.
   output_contigset_name - the name of the output contigset
   read_libraries - a list of Illumina or IonTorrent
   paired-end/high-quality mate-pairs/unpaired reads
   long_reads_libraries - a list of PacBio, Oxford Nanopore Sanger
   reads and/or additional contigs dna_source - the source of the DNA
   used for sequencing 'single_cell': DNA amplified from a single
   cell via MDA anything else: Standard DNA sample from multiple
   cells. Default value is None. pipeline_options - a list of string
   specifying how the SPAdes pipeline should be run kmer_sizes -
   (optional) K-mer sizes, Default values: 21, 33, 55, 77, 99, 127
   (all values must be odd, less than 128 and listed in ascending
   order) In the absence of these values, K values are automatically
   selected. min_contig_length - integer to filter out contigs with
   length < min_contig_length from the HybridSPAdes output. Default
   value is 0 implying no filter. @optional dna_source @optional
   pipeline_options @optional kmer_sizes @optional min_contig_length)
   -> structure: parameter "workspace_name" of String, parameter
   "output_contigset_name" of String, parameter "reads_libraries" of
   list of type "ReadsParams" (parameter groups--define attributes
   for specifying inputs with YAML data set file (advanced) The
   following attributes are available: - orientation ("fr", "rf",
   "ff") - type ("paired-end", "mate-pairs", "hq-mate-pairs",
   "single", "pacbio", "nanopore", "sanger", "trusted-contigs",
   "untrusted-contigs") - interlaced reads (comma-separated list of
   files with interlaced reads) - left reads (comma-separated list of
   files with left reads) - right reads (comma-separated list of
   files with right reads) - single reads (comma-separated list of
   files with single reads or unpaired reads from paired library) -
   merged reads (comma-separated list of files with merged reads)) ->
   structure: parameter "lib_ref" of type "obj_ref" (An X/Y/Z style
   KBase object reference), parameter "orientation" of String,
   parameter "lib_type" of String, parameter "long_reads_libraries"
   of list of type "LongReadsParams" -> structure: parameter
   "long_reads_ref" of type "obj_ref" (An X/Y/Z style KBase object
   reference), parameter "long_reads_type" of String, parameter
   "dna_source" of String, parameter "pipeline_options" of list of
   String, parameter "kmer_sizes" of list of Long, parameter
   "min_contig_length" of Long, parameter "create_report" of type
   "bool" (A boolean. 0 = false, anything else = true.)
:returns: instance of type "SPAdesOutput" (Output parameters for
   SPAdes run. report_name - the name of the KBaseReport.Report
   workspace object. report_ref - the workspace reference of the
   report.) -> structure: parameter "report_name" of String,
   parameter "report_ref" of String
def run_HybridSPAdes(self, ctx, params):
    '\n        Run HybridSPAdes on paired end libraries with PacBio CLR and Oxford Nanopore reads\n        :param params: instance of type "HybridSPAdesParams" (------To run\n           HybridSPAdes 3.13.0 you need at least one library of the following\n           types:------ 1) Illumina paired-end/high-quality\n           mate-pairs/unpaired reads 2) IonTorrent paired-end/high-quality\n           mate-pairs/unpaired reads 3) PacBio CCS reads Version 3.13.0 of\n           SPAdes supports paired-end reads, mate-pairs and unpaired reads.\n           SPAdes can take as input several paired-end and mate-pair\n           libraries simultaneously. workspace_name - the name of the\n           workspace from which to take input and store output.\n           output_contigset_name - the name of the output contigset\n           read_libraries - a list of Illumina or IonTorrent\n           paired-end/high-quality mate-pairs/unpaired reads\n           long_reads_libraries - a list of PacBio, Oxford Nanopore Sanger\n           reads and/or additional contigs dna_source - the source of the DNA\n           used for sequencing \'single_cell\': DNA amplified from a single\n           cell via MDA anything else: Standard DNA sample from multiple\n           cells. Default value is None. pipeline_options - a list of string\n           specifying how the SPAdes pipeline should be run kmer_sizes -\n           (optional) K-mer sizes, Default values: 21, 33, 55, 77, 99, 127\n           (all values must be odd, less than 128 and listed in ascending\n           order) In the absence of these values, K values are automatically\n           selected. min_contig_length - integer to filter out contigs with\n           length < min_contig_length from the HybridSPAdes output. Default\n           value is 0 implying no filter. @optional dna_source @optional\n           pipeline_options @optional kmer_sizes @optional min_contig_length)\n           -> structure: parameter "workspace_name" of String, parameter\n           "output_contigset_name" of String, parameter "reads_libraries" of\n           list of type "ReadsParams" (parameter groups--define attributes\n           for specifying inputs with YAML data set file (advanced) The\n           following attributes are available: - orientation ("fr", "rf",\n           "ff") - type ("paired-end", "mate-pairs", "hq-mate-pairs",\n           "single", "pacbio", "nanopore", "sanger", "trusted-contigs",\n           "untrusted-contigs") - interlaced reads (comma-separated list of\n           files with interlaced reads) - left reads (comma-separated list of\n           files with left reads) - right reads (comma-separated list of\n           files with right reads) - single reads (comma-separated list of\n           files with single reads or unpaired reads from paired library) -\n           merged reads (comma-separated list of files with merged reads)) ->\n           structure: parameter "lib_ref" of type "obj_ref" (An X/Y/Z style\n           KBase object reference), parameter "orientation" of String,\n           parameter "lib_type" of String, parameter "long_reads_libraries"\n           of list of type "LongReadsParams" -> structure: parameter\n           "long_reads_ref" of type "obj_ref" (An X/Y/Z style KBase object\n           reference), parameter "long_reads_type" of String, parameter\n           "dna_source" of String, parameter "pipeline_options" of list of\n           String, parameter "kmer_sizes" of list of Long, parameter\n           "min_contig_length" of Long, parameter "create_report" of type\n           "bool" (A boolean. 0 = false, anything else = true.)\n        :returns: instance of type "SPAdesOutput" (Output parameters for\n           SPAdes run. report_name - the name of the KBaseReport.Report\n           workspace object. report_ref - the workspace reference of the\n           report.) -> structure: parameter "report_name" of String,\n           parameter "report_ref" of String\n        '
    self.log('Running run_HybridSPAdes with params:\n{}'.format(json.dumps(params, indent=1)))
    spades_assembler = SPAdesAssembler(self.cfg, ctx.provenance())
    output = spades_assembler.run_hybrid_spades(params)
    if (not isinstance(output, dict)):
        raise ValueError(('Method run_HybridSPAdes return value ' + 'output is not type dict as required.'))
    return [output]