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.read_library_type == "nano-raw" or self.read_library_type == "pacbio-raw":
return [
filtlong(sampleName=i) for i in [
line.strip() for line in open((os.path.join(
os.getcwd(), "sample_list", "lr_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")))]]
]
#Paired-end with Pacbio
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")))]],
[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")))]],
[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")))]]
]
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")))
]
]
]