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atacseq_analysis
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BICF
Astrocyte
atacseq_analysis
Commits
fa52a716
There was a problem fetching the pipeline stages.
Commit
fa52a716
authored
6 years ago
by
Venkat Malladi
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Fix util tests.
parent
0e4adc7a
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Pipeline
#2248
failed with stages
in 9 seconds
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1
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1 changed file
workflow/tests/test_utils.py
+4
-4
4 additions, 4 deletions
workflow/tests/test_utils.py
with
4 additions
and
4 deletions
workflow/tests/test_utils.py
+
4
−
4
View file @
fa52a716
...
...
@@ -17,7 +17,7 @@ def steps():
def
steps_1
(
steps
):
design_file
=
"
test_data/design_ENCSR265ZXX_SE.txt
"
step
=
[
"
grep
A549
%s
"
%
(
design_file
)]
"
grep
ENCLB170KFO
%s
"
%
(
design_file
)]
return
step
...
...
@@ -31,7 +31,7 @@ def steps_2(steps_1):
@pytest.mark.unit
def
test_run_one_step
(
steps_1
,
capsys
):
check_output
=
'
ENCLB1
44FDT
\t
ENCSR2
38SGC
\t
limb
\t
H3K4me1
\t
None
\t
1
\t
ENCLB304SBJ
\t
ENCFF
833BLU
.fastq.gz
'
.
encode
(
'
UTF-8
'
)
check_output
=
'
ENCLB1
70KFO
\t
ENCSR2
65ZXX
\t
A549
\t
None
\t
100nm
\t
Dex
\t
1
\t
ENCFF
115PAE
.fastq.gz
'
.
encode
(
'
UTF-8
'
)
out
,
err
=
utils
.
run_pipe
(
steps_1
)
output
,
errors
=
capsys
.
readouterr
()
assert
"
first step shlex to stdout
"
in
output
...
...
@@ -40,7 +40,7 @@ def test_run_one_step(steps_1, capsys):
@pytest.mark.unit
def
test_run_two_step
(
steps_2
,
capsys
):
check_output
=
'
ENCFF
833BLU.fastq.gz
\n
ENCFF646LXU
.fastq.gz
'
.
encode
(
'
UTF-8
'
)
check_output
=
'
ENCFF
115PAE
.fastq.gz
'
.
encode
(
'
UTF-8
'
)
out
,
err
=
utils
.
run_pipe
(
steps_2
)
output
,
errors
=
capsys
.
readouterr
()
assert
"
intermediate step 2 shlex to stdout
"
in
output
...
...
@@ -49,7 +49,7 @@ def test_run_two_step(steps_2, capsys):
@pytest.mark.unit
def
test_run_last_step_file
(
steps_2
,
capsys
,
tmpdir
):
check_output
=
'
ENCFF
833BLU.fastq.gz
\n
ENCFF646LXU
.fastq.gz
'
check_output
=
'
ENCFF
115PAE
.fastq.gz
'
tmp_outfile
=
tmpdir
.
join
(
'
output.txt
'
)
out
,
err
=
utils
.
run_pipe
(
steps_2
,
tmp_outfile
.
strpath
)
output
,
errors
=
capsys
.
readouterr
()
...
...
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