def prepare(args): # NOTE this needs to match the arguments in parse_args and the targets in payload # commas at the beginning of each option are used when that section has # parameters from other functions. options = { "fastq_opts": { "input": "'{input}'", }, "write_opts": { "output": ", ofile='{output}'", }, "method_name": { "method": "{method}", }, "method_opts": { "min_quality": ", min_quality={min_quality}", }, "discard_opts": { "discard": "{discard}", }, } ngl_options = ngl_prepare_options(args, options) payload_tpl = """\ ngless "0.0" input = fastq({fastq_opts}) preprocess(input) using |read|: read = {method_name}(read{method_opts}) if len(read) < {discard_opts}: discard write(input{write_opts}) """.format(**ngl_options) return ngl_prepare_payload(args, payload_tpl)
def prepare(args): # NOTE this needs to match the arguments in parse_args and the targets in payload # commas at the beginning of each option are used when that section has # parameters from other functions. The keys are iterated in alphabetical order # so only the first needs to have a comma. options = { "sam_opts": { "input": "'{input}'", }, "count_opts": { "features": ", features=['seqname']", "multiple": "multiple={{{multiple}}}", }, "write_opts": { "output": ", ofile='{output}'", }, } ngl_options = ngl_prepare_options(args, options) payload_tpl = """\ ngless "0.0" write(count(samfile({sam_opts}){count_opts}){write_opts})\ """.format(**ngl_options) return ngl_prepare_payload(args, payload_tpl)
def prepare(args): # NOTE this needs to match the arguments in parse_args and the targets in payload # commas at the beginning of each option are used when that section has # parameters from other functions. options = { "input_opts": { "input": "'{input}'", }, "write_opts": { "output": ", ofile='{output}'", }, "action_opts": { "action": "{action}", }, "cond_opts": { "conditions": ngl_as_list("{conditions}", wrap_with="{}"), }, } ngl_options = ngl_prepare_options(args, options) payload_tpl = """\ ngless "0.0" mapped = samfile({input_opts}) selected = select(mapped, {action_opts}={cond_opts}) write(selected{write_opts}) """.format(**ngl_options) return ngl_prepare_payload(args, payload_tpl)
def prepare(args): # NOTE this needs to match the arguments in parse_args and the targets in payload # commas at the beginning of each option are used when that section has # parameters from other functions. options = { "input_opts": { "input": "'{input}'", "input_reverse": "'{input_reverse}'", "input_singles": "singles='{input_singles}'", }, "write_opts": { "output": ", ofile='{output}'", }, "target_name": { "target": "{target}", }, "target_opts": { "reference": ", reference='{reference}'", "fasta": ", fafile='{fasta}'", }, } ngl_options = ngl_prepare_options(args, options) payload_tpl = """\ ngless "0.0" input = {target_name}({input_opts}) mapped = map(input{target_opts}) write(mapped{write_opts}) """.format(**ngl_options) return ngl_prepare_payload(args, payload_tpl)
def prepare(args): # NOTE this needs to match the arguments in parse_args and the targets in payload # commas at the beginning of each option are used when that section has # parameters from other functions. options = { "input_opts": { "input": "'{input}'", }, "write_opts": { "output": ", ofile='{output}'", }, "target_opts": { "max_copies": ", max_copies={max_copies}", }, } ngl_options = ngl_prepare_options(args, options) payload_tpl = """\ ngless "0.0" input = fastq({input_opts}) unique = unique(input{target_opts}) write(unique{write_opts}) """.format(**ngl_options) return ngl_prepare_payload(args, payload_tpl)
def prepare(args): # NOTE this needs to match the arguments in parse_args and the targets in payload # commas at the beginning of each option are used when that section has # parameters from other functions. options = { "input_opts": { "input": "'{input}'", }, "write_opts": { "output": ", ofile='{output}'", }, } ngl_options = ngl_prepare_options(args, options) payload_tpl = """\ ngless "0.0" mapped = samfile({input_opts}) stats = mapstats(mapped) write(stats{write_opts}) """.format(**ngl_options) return ngl_prepare_payload(args, payload_tpl)