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)