Commit 831a5b33 authored by aknecht2's avatar aknecht2
Browse files

Fixed workflow_module to work with single path modules. Added new testing...

Fixed workflow_module to work with single path modules.  Added new testing config files for paired_end reads.
parent 5fa61338
notify:
pegasus_home: "/usr/share/pegasus/"
email: "avi@kurtknecht.com"
profile:
pegasus:
style: "glite"
condor:
grid_resource: "pbs"
universe: "vanilla"
env:
PATH: "/work/walia/common/pymodules/anaconda/bin"
PYTHONPATH: "/work/walia/common/pymodules/anaconda/lib/python2.7/site-packages/"
bwa_sai_to_sam:
arguments: null
walltime: 2000
memory: 2000
bwa_align_single:
arguments:
"-q": 5
"-l": 32
"-k": 2
"-t": 1
walltime: 2000
memory: 2000
bwa_align_paired:
arguments:
"-t": 1
walltime: 2000
memory: 2000
bowtie2_align_single:
arguments: null
walltime: 2000
memory: 2000
bowtie2_align_paired:
arguments: null
walltime: 2000
memory: 2000
samtools_sam_to_bam:
arguments: null
walltime: 2000
memory: 2000
bedtools_bam_to_bed:
arguments: null
walltime: 2000
memory: 2000
macs2_callpeak:
arguments: null
walltime: 2000
memory: 8000
picard_mark_duplicates:
arguments: null
walltime: 2000
memory: 2000
picard_sort_sam:
arguments: null
walltime: 2000
memory: 2000
r_spp_nodups:
arguments: null
walltime: 2000
memory: 2000
samtools_remove_duplicates:
arguments: null
walltime: 2000
memory: 2000
samtools_filter_bam:
arguments: null
walltime: 2000
memory: 2000
runs:
- experiment: "ENCSR922MYB"
align: bwa
peak: spp
- experiment: "ENCSR992MYB"
align: bowtie2
peak: spp
genomes:
bwa:
hg19: "/path/to/genome/base"
mm9: "/path/to/genome/base"
bowtie2:
hg19: "/path/to/genome/base"
mm9: "/path/to/genome/base"
......@@ -33,8 +33,10 @@ class WorkflowModule(object):
self.workflow = {}
self.workflow_jobs = workflow_jobs
self._load_markers(self.data[self.name])
# Deep copy self.order, want to maintain it
self._add_workflow_keys(self.workflow, list(self.order))
if self.markers:
self._add_workflow_keys(self.workflow)
else:
self.workflow = []
self._load_jobs(self.data[self.name], add_markers = dict(self.markers))
except SystemExit as se:
pass
......@@ -51,13 +53,12 @@ class WorkflowModule(object):
return data
return
def _add_workflow_keys(self, workflow, order, index = 0):
marker_key = order[index]
def _add_workflow_keys(self, workflow, index = 0):
marker_key = self.order[index]
for marker in self.markers[marker_key]:
if index < len(order) - 1:
if index < len(self.order) - 1:
workflow[marker] = {}
new_index = index + 1
self._add_workflow_keys(workflow[marker], order, new_index)
self._add_workflow_keys(workflow[marker], int(index + 1))
else:
workflow[marker] = []
return
......
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