def __init__(self): opts = (_mapseq_lims_opt, ( "-f", "--fasta_path", "Path to a directory containing a fasta file for each chromosome", { 'default': None } ), ("--mincov", "Minimum coverage to call the SNP.", { 'default': 5 }), ( "--minsnp", "Minimum percentage of reads per allele to call the SNP.", { 'default': 40 } ), ("-b", "--make_bigwigs", "Create genome-wide coverage, heterozygosity and quality bigwigs.", { 'action': "store_true" })) usage = "[-m mapseq_minilims] [--mincov --minsnp]" desc = """Compares sequencing data to a reference assembly to detect SNPs.""" Workflow.__init__(self, module="snp", opts=opts, usage=usage, desc=desc)
def __init__(self): opts = ( _mapseq_lims_opt, ("-p", "--pileup_level", "Target features, inside of quotes, separated by commas. E.g. 'genes,exons,transcripts'.", { 'default': "genes,exons,transcripts" }), ("-j", "--junctions", "Whether or not to search for splice junctions using soapsplice.", { 'action': "store_true", 'default': False }), ("--stranded", "To indicate that the protocol was strand-specific.", { 'action': "store_true", 'default': False }), ) usage = "[-m mapseq_minilims] [-p -j --stranded]" desc = """A High-throughput RNA-seq analysis workflow. It returns text files containing read counts for exons, genes and transcripts for each given BAM file, and the result of a DESeq run (differential expression analysis) for every pair of groups. """ Workflow.__init__(self, module="rnaseq", opts=opts, usage=usage, desc=desc)
def __init__(self): opts = (_mapseq_lims_opt, ) usage = "[-m mapseq_minilims]" desc = """A High-throughput ChIP-seq peak analysis workflow.""" Workflow.__init__(self, module="chipseq", opts=opts, usage=usage, desc=desc)
def __init__(self): opts = (("--noqc", "Skip fastqc step", {'action': "store_true"}), ) usage = "[--noqc]" desc = "A High-throughput sequencing data mapping workflow." Workflow.__init__(self, module="mapseq", opts=opts, usage=usage, desc=desc)
def __init__(self): opts = (_mapseq_lims_opt, ) usage = "[-m mapseq_minilims]" desc = """A High-throughput DNAseI-seq analysis workflow.""" Workflow.__init__(self, module="dnaseseq", name="dnaseseq", opts=opts, usage=usage, desc=desc)
def __init__(self): opts = (_mapseq_lims_opt, ) usage = "[-m mapseq_minilims]" desc = """A High-throughput microbiome analysis workflow. Will return counts per level for the selected microbiome database.""" Workflow.__init__(self, module="microbiome", name="microbiome", opts=opts, usage=usage, desc=desc)
def __init__(self): opts = (_mapseq_lims_opt, ("-f", "--fasta_path", "Path to a directory containing a fasta file for each chromosome", {'default':None}), ("--mincov", "Minimum coverage to call the SNP.", {'default':5}), ("--minsnp", "Minimum percentage of reads per allele to call the SNP.", {'default':40}), ("-b","--make_bigwigs", "Create genome-wide coverage, heterozygosity and quality bigwigs.", {'action':"store_true"})) usage = "[-m mapseq_minilims] [--mincov --minsnp]" desc = """Compares sequencing data to a reference assembly to detect SNPs.""" Workflow.__init__(self,module="snp",opts=opts,usage=usage,desc=desc)
def __init__(self): opts = (_mapseq_lims_opt, ("-p", "--pileup_level", "Target features, inside of quotes, separated by commas. E.g. 'genes,exons,transcripts'.", {'default':"genes,exons,transcripts"}), ("-j", "--junctions", "Whether or not to search for splice junctions using soapsplice.", {'action':"store_true", 'default':False}), ("--stranded", "To indicate that the protocol was strand-specific.", {'action':"store_true", 'default':False}), ) usage = "[-m mapseq_minilims] [-p -j --stranded]" desc = """A High-throughput RNA-seq analysis workflow. It returns text files containing read counts for exons, genes and transcripts for each given BAM file, and the result of a DESeq run (differential expression analysis) for every pair of groups. """ Workflow.__init__(self,module="rnaseq",opts=opts,usage=usage,desc=desc)
def __init__(self): opts = (_mapseq_lims_opt,) usage = "[-m mapseq_minilims]" desc = """A High-throughput ChIP-seq peak analysis workflow.""" Workflow.__init__(self,module="chipseq",opts=opts,usage=usage,desc=desc)
def __init__(self): opts = (("--noqc","Skip fastqc step",{'action':"store_true"}), ("--local_align","Perform local alignment",{'action':"store_true"}),) usage = "[--noqc] [--local_align]" desc = "A High-throughput sequencing data mapping workflow." Workflow.__init__(self,module="mapseq",opts=opts,usage=usage,desc=desc)
def __init__(self): opts = (_mapseq_lims_opt,) usage = "[-m mapseq_minilims]" desc = """A High-throughput DNAseI-seq analysis workflow.""" Workflow.__init__(self,module="dnaseseq",name="dnaseseq",opts=opts,usage=usage,desc=desc)
def __init__(self): opts = (_mapseq_lims_opt,) usage = "[-m mapseq_minilims]" desc = """A High-throughput microbiome analysis workflow. Will return counts per level for the selected microbiome database.""" Workflow.__init__(self,module="microbiome",name="microbiome",opts=opts,usage=usage,desc=desc)
def __init__(self): desc = "Demultiplexing routine for 4C-seq data." Workflow.__init__(self,module="demultiplex",name="demultiplexing",desc=desc)
def __init__(self): desc = "Demultiplexing routine for 4C-seq data." Workflow.__init__(self, module="demultiplex", name="demultiplexing", desc=desc)