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Holland Computing Center
chipathlon
Commits
4a164e8b
Commit
4a164e8b
authored
9 years ago
by
aknecht2
Browse files
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Added bedtools bamtobed.
parent
277de0d8
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Changes
3
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3 changed files
chipathlon/jobs/modules/peak_call.yaml
+4
-4
4 additions, 4 deletions
chipathlon/jobs/modules/peak_call.yaml
chipathlon/jobs/modules/remove_duplicates.yaml
+8
-0
8 additions, 0 deletions
chipathlon/jobs/modules/remove_duplicates.yaml
chipathlon/workflow.py
+3
-3
3 additions, 3 deletions
chipathlon/workflow.py
with
15 additions
and
7 deletions
chipathlon/jobs/modules/peak_call.yaml
+
4
−
4
View file @
4a164e8b
...
...
@@ -2,9 +2,9 @@ peak_call:
-
spp[tool]
:
-
r_spp_nodups
:
inputs
:
-
exp.b
am
:
-
exp.b
ed
:
type
:
file
-
control.b
am
:
-
control.b
ed
:
type
:
file
additional_inputs
:
null
outputs
:
...
...
@@ -25,9 +25,9 @@ peak_call:
-
macs2[tool]
:
-
macs2_callpeak
:
inputs
:
-
exp.b
am
:
-
exp.b
ed
:
type
:
file
-
control.b
am
:
-
control.b
ed
:
type
:
file
-
prefix
:
type
:
argument
...
...
This diff is collapsed.
Click to expand it.
chipathlon/jobs/modules/remove_duplicates.yaml
+
8
−
0
View file @
4a164e8b
...
...
@@ -25,3 +25,11 @@ remove_duplicates:
type
:
file
-
quality.qc
:
type
:
file
-
bedtools_bam_to_bed
:
inputs
:
-
no_dups.bam
:
type
:
file
additional_inputs
:
null
outputs
:
-
no_dups.bed
:
type
:
file
This diff is collapsed.
Click to expand it.
chipathlon/workflow.py
+
3
−
3
View file @
4a164e8b
...
...
@@ -359,8 +359,8 @@ class Workflow(object):
# remove_duplicates returns prefix_no_dups.bam
# REMEMBER: experiment is always first
final_prefix
=
run
[
"
prefix
"
][
0
]
+
"
_
"
+
run
[
"
prefix
"
][
1
]
inputs
[
"
exp.b
am
"
]
=
run
[
"
prefix
"
][
0
]
+
"
_no_dups.b
am
"
inputs
[
"
control.b
am
"
]
=
run
[
"
prefix
"
][
1
]
+
"
_no_dups.b
am
"
inputs
[
"
exp.b
ed
"
]
=
run
[
"
prefix
"
][
0
]
+
"
_no_dups.b
ed
"
inputs
[
"
control.b
ed
"
]
=
run
[
"
prefix
"
][
1
]
+
"
_no_dups.b
ed
"
if
run
[
"
peak
"
]
==
"
spp
"
:
pass
elif
run
[
"
peak
"
]
==
"
macs2
"
:
...
...
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