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Holland Computing Center
chipathlon
Commits
738e3744
Commit
738e3744
authored
Mar 30, 2016
by
aknecht2
Browse files
Fixed peak calling workflow generation, updated configuration and yaml files.
parent
acdc8601
Changes
6
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Inline
Side-by-side
chipathlon/conf.py
View file @
738e3744
...
...
@@ -21,7 +21,9 @@ file_extensions = {
"bwa_genome"
:
[
"amb"
,
"ann"
,
"bwt"
,
"pac"
,
"sa"
],
"bowtie2_genome"
:
[
"1.bt2"
,
"2.bt2"
,
"3.bt2"
,
"4.bt2"
,
"rev.1.bt2"
,
"rev.2.bt2"
],
"quality"
:
[
"quality"
],
"qc"
:
[
"qc"
]
"qc"
:
[
"qc"
],
"pdf"
:
[
"pdf"
],
"ccscore"
:
[
"ccscore"
]
}
# list of resources that can be specified per job (step) in
...
...
chipathlon/jobs/params/macs2_callpeak.yaml
View file @
738e3744
...
...
@@ -6,6 +6,7 @@ macs2_callpeak:
type
:
file
-
prefix
:
type
:
argument
additional_inputs
:
null
outputs
:
-
bed
:
type
:
file
...
...
chipathlon/jobs/params/r_spp_nodups.yaml
View file @
738e3744
...
...
@@ -4,6 +4,7 @@ r_spp_nodups:
type
:
file
-
bam
:
type
:
file
additional_inputs
:
null
outputs
:
-
bed
:
type
:
file
...
...
@@ -42,17 +43,17 @@ r_spp_nodups:
changeable
:
false
required
:
true
has_value
:
true
default
:
$outputs.
1
default
:
$outputs.
0
-
"
-savp"
:
changeable
:
false
required
:
true
has_value
:
true
default
:
$outputs.
2
default
:
$outputs.
1
-
"
-out"
:
changeable
:
false
required
:
true
has_value
:
true
default
:
$outputs.
3
default
:
$outputs.
2
-
"
-fdr"
:
changeable
:
true
required
:
false
...
...
chipathlon/jobs/params/sort_awk_sort_peaks.yaml
View file @
738e3744
...
...
@@ -2,6 +2,7 @@ sort_awk_sort_peaks:
inputs
:
-
bed
:
type
:
file
additional_inputs
:
null
outputs
:
-
bed
:
type
:
file
...
...
chipathlon/jobs/params/zcat_awk_sort_peaks.yaml
View file @
738e3744
...
...
@@ -2,6 +2,7 @@ zcat_awk_sort_peaks:
inputs
:
-
bed
:
type
:
file
additional_inputs
:
null
outputs
:
-
bed
:
type
:
file
...
...
chipathlon/workflow.py
View file @
738e3744
...
...
@@ -58,6 +58,7 @@ class Workflow(object):
self
.
_add_download
()
self
.
_add_align
()
self
.
_add_remove_duplicates
()
self
.
_add_peak_calling
()
# Create pegasus important stuff
self
.
_create_setup
()
self
.
_add_notify
()
...
...
@@ -334,11 +335,9 @@ class Workflow(object):
# prefix and add in as input_files
# remove_duplicates returns prefix_no_dups.bam
# REMEMBER: experiment is always first
final_prefix
=
""
for
i
,
file_tuple
in
enumerate
(
pair
):
prefix
=
run
[
"prefix"
][
i
]
inputs
[
"exp.bam"
]
=
prefix
+
"_no_dups.bam"
final_prefix
+=
prefix
final_prefix
=
run
[
"prefix"
][
0
]
+
"_"
+
run
[
"prefix"
][
1
]
inputs
[
"exp.bam"
]
=
run
[
"prefix"
][
0
]
+
"_no_dups.bam"
inputs
[
"control.bam"
]
=
run
[
"prefix"
][
1
]
+
"_no_dups.bam"
if
run
[
"peak"
]
==
"spp"
:
pass
elif
run
[
"peak"
]
==
"macs2"
:
...
...
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