def requires(self):
if self.pre_process_reads == "yes" and self.read_library_type == "pe":
return [
bbduk(sampleName=i) for i in [
line.strip() for line in open((
os.path.join(os.getcwd(), "config", "pe_samples.lst")))
]
]
if self.pre_process_reads == "yes" and self.read_library_type == "se":
return [
bbduk(sampleName=i) for i in [
line.strip() for line in open((
os.path.join(os.getcwd(), "config", "se_samples.lst")))
]
]
if self.pre_process_reads == "no" and self.read_library_type == "pe":
return [
reformat(sampleName=i) for i in [
line.strip() for line in open((
os.path.join(os.getcwd(), "config", "pe_samples.lst")))
]
]
if self.pre_process_reads == "no" and self.read_library_type == "se":
return [
reformat(sampleName=i) for i in [
line.strip() for line in open((
os.path.join(os.getcwd(), "config", "se_samples.lst")))
]
]
def requires(self): if self.seq_platforms == "pe" and self.pre_process_reads=="yes": return [cleanFastq(seq_platforms="pe",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]] if self.seq_platforms == "pe" and self.pre_process_reads=="no": return [reformat(seq_platforms="pe",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]] # Paired-end with Mate-pair if self.seq_platforms == "pe-mp" and self.pre_process_reads =="yes": return [ [cleanFastq(seq_platforms="pe",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]], [cleanFastq(seq_platforms="mp",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")))]] ] if self.seq_platforms == "pe-mp" and self.pre_process_reads =="no": return [ [reformat(seq_platforms="pe",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]], [reformat(seq_platforms="mp",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")))]] ]
def requires(self):
if self.seq_platform == "pacbio" and self.pre_process_reads == "yes":
return [
filtlong(seq_platforms="pac", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "pac_samples.lst")))
]
]
if self.seq_platform == "pacbio" and self.pre_process_reads == "no":
return [
reformat(seq_platforms="pac", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "pac_samples.lst")))
]
]
if self.seq_platform == "nanopore" and self.pre_process_reads == "yes":
return [
filtlong(seq_platforms="ont", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "ont_samples.lst")))
]
]
if self.seq_platform == "nanopore" and self.pre_process_reads == "no":
return [
reformat(seq_platforms="ont", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "ont_samples.lst")))
]
]
def requires(self): if (self.pre_process_reads == "yes"): return [bbduk(sampleName=self.sampleName), makeTx2Gene()] if (self.pre_process_reads == "no"): return [reformat(sampleName=self.sampleName), makeTx2Gene()]
def requires(self):
if (self.pre_process_reads == "yes"):
return [
bbduk(sampleName=self.sampleName,
read_library_type=self.read_library_type),
makeTx2Gene(annotation_file_type=self.annotation_file_type)
]
if (self.pre_process_reads == "no"):
return [
reformat(sampleName=self.sampleName,
read_library_type=self.read_library_type),
makeTx2Gene(annotation_file_type=self.annotation_file_type)
]
def requires(self):
if self.pre_process_reads == "yes":
return [
cleanFastq(seq_platforms="pe", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "pe_samples.lst")))
]
]
if self.pre_process_reads == "no":
return [
reformat(seq_platforms="pe", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "pe_samples.lst")))
]
]
def requires(self):
if self.seq_platforms == "pe" and self.pre_process_reads == "yes":
return [
[
cleanFastq(seq_platforms="pe", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "pe_samples.lst")))
]
],
[
kmergenie_formater_cleanFastq(
os.path.join(os.getcwd(), "sample_list",
"pe_samples.lst"))
],
]
if self.seq_platforms == "pe" and self.pre_process_reads == "no":
return [
[
reformat(seq_platforms="pe", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "pe_samples.lst")))
]
],
[
kmergenie_formater_reformat(
os.path.join(os.getcwd(), "sample_list",
"pe_samples.lst"))
],
]
if self.seq_platforms == "pe-mp" and self.pre_process_reads == "yes":
return [[
cleanFastq(seq_platforms="pe", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "pe_samples.lst")))
]
],
[
kmergenie_formater_cleanFastq(
os.path.join(os.getcwd(), "sample_list",
"pe_samples.lst"))
],
[
cleanFastq(seq_platforms="mp", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "mp_samples.lst")))
]
]]
if self.seq_platforms == "pe-mp" and self.pre_process_reads == "no":
return [[
reformat(seq_platforms="pe", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "pe_samples.lst")))
]
],
[
kmergenie_formater_reformat(
os.path.join(os.getcwd(), "sample_list",
"pe_samples.lst"))
],
[
reformat(seq_platforms="mp", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "mp_samples.lst")))
]
]]
if self.seq_platforms == "pe-pac" and self.pre_process_reads == "yes":
return [
[
cleanFastq(
seq_platforms="pe", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "pe_samples.lst")))
]
],
[
kmergenie_formater_cleanFastq(
os.path.join(os.getcwd(), "sample_list",
"pe_samples.lst"))
],
[
filtlong(seq_platforms="pac", sampleName=i) for i in [
line.strip()
for line in open((os.path.join(
os.getcwd(), "sample_list", "pac_samples.lst")))
]
]
]
if self.seq_platforms == "pe-pac" and self.pre_process_reads == "no":
return [
[
reformat(
seq_platforms="pe", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "pe_samples.lst")))
]
],
[
kmergenie_formater_reformat(
os.path.join(os.getcwd(), "sample_list",
"pe_samples.lst"))
],
[
reformat(seq_platforms="pac", sampleName=i) for i in [
line.strip()
for line in open((os.path.join(
os.getcwd(), "sample_list", "pac_samples.lst")))
]
]
]
if self.seq_platforms == "pe-ont" and self.pre_process_reads == "yes":
return [
[
cleanFastq(
seq_platforms="pe", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "pe_samples.lst")))
]
],
[
kmergenie_formater_cleanFastq(
os.path.join(os.getcwd(), "sample_list",
"pe_samples.lst"))
],
[
filtlong(platform="pac", sampleName=i) for i in [
line.strip()
for line in open((os.path.join(
os.getcwd(), "sample_list", "ont_samples.lst")))
]
]
]
if self.seq_platforms == "pe-ont" and self.pre_process_reads == "no":
return [
[
reformat(
seq_platforms="pe", sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "pe_samples.lst")))
]
],
[
kmergenie_formater_reformat(
os.path.join(os.getcwd(), "sample_list",
"pe_samples.lst"))
],
[
reformat(seq_platforms="ont", sampleName=i) for i in [
line.strip()
for line in open((os.path.join(
os.getcwd(), "sample_list", "ont_samples.lst")))
]
]
]
def requires(self):
if self.read_library_type == "pe-lr" and self.pre_process_reads=="yes":
return [
[bbduk(read_library_type="pe", sampleName=i)
for i in [line.strip()
for line in
open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]],
[minia_pe_bbduk(os.path.join(os.getcwd(), "sample_list", "pe_samples.lst"))],
[bbduk(read_library_type="lr",sampleName=i)
for i in [line.strip()
for line in
open((os.path.join(os.getcwd(), "sample_list", "lr_samples.lst")))]]
]
if self.read_library_type == "pe-lr" and self.pre_process_reads=="no":
return [
[reformat(read_library_type="pe", sampleName=i)
for i in [line.strip()
for line in
open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]],
[minia_pe_reformat(os.path.join(os.getcwd(), "sample_list", "pe_samples.lst"))],
[reformat(read_library_type="lr",sampleName=i)
for i in [line.strip()
for line in
open((os.path.join(os.getcwd(), "sample_list", "lr_samples.lst")))]]
]
if self.read_library_type == "pe-mp-lr" and self.pre_process_reads=="yes":
return [
[bbduk(read_library_type="pe", sampleName=i)
for i in [line.strip()
for line in
open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]],
[bbduk(read_library_type="mp", sampleName=i)
for i in [line.strip()
for line in
open((os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")))]],
[minia_pe_mp_bbduk((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")),
(os.path.join(os.getcwd(), "sample_list", "mp_samples.lst"))
)],
[bbduk(read_library_type="lr",sampleName=i)
for i in [line.strip()
for line in
open((os.path.join(os.getcwd(), "sample_list", "lr_samples.lst")))]]
]
if self.read_library_type == "pe-mp-lr" and self.pre_process_reads=="no":
return [
[reformat(read_library_type="pe", sampleName=i)
for i in [line.strip()
for line in
open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]],
[reformat(read_library_type="mp", sampleName=i)
for i in [line.strip()
for line in
open((os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")))]],
[minia_pe_mp_reformat((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")),
(os.path.join(os.getcwd(), "sample_list", "mp_samples.lst"))
)],
[bbduk(read_library_type="lr",sampleName=i)
for i in [line.strip()
for line in
open((os.path.join(os.getcwd(), "sample_list", "lr_samples.lst")))]]
]
