Commit faac4939 authored by aknecht2's avatar aknecht2
Browse files

Fixed lots of minor bugs to make sure the workflow actually generates! Running tests now.

parent d0f38192
......@@ -69,8 +69,8 @@ executables = [
"chip-job-peakranger-format",
"chip-job-sort-peak",
"chip-job-zcat-peak",
"chip-job-zerone-add-cols",
"chip-job-hd-add-cols"
"chip-job-zerone-format",
"chip-job-hd-format"
]
# Java needs to have -Xmx specified...
......
......@@ -161,8 +161,7 @@ class PeakCallGenerator(ModuleGenerator):
"control.bam": call_pair[0].full_name,
"signal.bam": call_pair[1].full_name
}
additional_inputs = {}
return (self.get_markers(run), inputs, additional_inputs)
return (self.get_markers(run), inputs)
def _hiddendomains(self, run, result):
"""
......@@ -178,8 +177,7 @@ class PeakCallGenerator(ModuleGenerator):
"signal.bed": call_pair[1].full_name,
"prefix": result.prefix
}
additional_inputs = {}
return (self.get_markers(run), inputs, additional_inputs)
return (self.get_markers(run), inputs)
def _pepr(self, run, result):
"""
......@@ -195,8 +193,7 @@ class PeakCallGenerator(ModuleGenerator):
"prefix": result.prefix,
"peak_type": run.peak_type
}
additional_inputs = {}
return (self.get_markers(run), inputs, additional_inputs)
return (self.get_markers(run), inputs)
def _make_call_pairs(self, run, result_list):
"""
......
......@@ -337,7 +337,7 @@ peak_call:
chrom.sizes:
param_name: chrom_sizes
prefix:
type: string
param_name: prefix
outputs:
result.bed:
param_name: result_peaks
......@@ -352,10 +352,10 @@ peak_call:
- hiddendomains_format:
inputs:
result.bed:
type: file
param_name: result_peaks
outputs:
results_sorted.bed:
type: file
param_name: full_result
final_result: true
- pepr[tool]:
- pepr_callpeak:
......
......@@ -23,11 +23,11 @@ hiddendomains_callpeak:
file_type: txt
control_bins:
type: file
file_type: bxt
file_type: txt
treatment_bins:
type: file
file_type: txt
command: hiddendomains
command: hiddenDomains
arguments:
- "-B":
type: string
......@@ -53,7 +53,7 @@ hiddendomains_callpeak:
has_value: true
default: "$chrom_sizes"
- "-o":
type: file
type: string
changeable: false
required: true
has_value: true
......
......@@ -3,7 +3,6 @@ hiddendomains_format:
result_peaks:
type: file
file_type: bed
additional_inputs: null
outputs:
full_result:
type: file
......
......@@ -17,7 +17,7 @@ pepr_callpeak:
pepr_params:
type: file
file_type: txt
command: pepr
command: PePr
arguments:
- "-c":
type: list
......@@ -38,7 +38,7 @@ pepr_callpeak:
- $signal.bed
- $signal.bed
- "-n":
type: file
type: string
changeable: true
required: true
has_value: true
......
#!/bin/bash
. /util/opt/lmod/lmod/init/profile
module load hiddendomains/2.3
hiddenDomains "$@"
#!/bin/bash
. /util/opt/lmod/lmod/init/profile
module load pepr/1.1
PePr "$@"
#!/bin/bash
#set -eu -o pipefail
#set -o pipefail
. /util/opt/lmod/lmod/init/profile
module load picard/2.9
# Use Java installed with Anaconda to ensure correct version
java="$ENV_PREFIX/bin/java"
# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java"
if [ ! -z "${JAVA_HOME:=}" ]; then
if [ -e "$JAVA_HOME/bin/java" ]; then
java="$JAVA_HOME/bin/java"
fi
fi
picard "$@"
#!/bin/bash
. /util/opt/lmod/lmod/init/profile
module load zerone/1.0
zerone "$@"
......@@ -242,7 +242,6 @@ class Workflow(object):
# Load each yaml_job as an actual object
for root, dirs, files in os.walk("%s/%s" % (os.path.dirname(os.path.realpath(__file__)), chipathlon.conf.job_params)):
for f in files:
print(f)
yaml_job = chipathlon.workflow_job.WorkflowJob(os.path.join(root, f), self.params.get(f.split(".")[0]), self.debug)
if yaml_job.is_valid():
if yaml_job.command in self.executables:
......
......@@ -566,9 +566,9 @@ class WorkflowJob(object):
# Need to figure out 2 things:
# 1. Should we add the argument name?
# 2. What's the correct value to add?
add_value = self._interpolate_value(inputs, outputs, arg_name, arg_info)
if self.debug:
print "%s: Loading argument: %s, info: %s, value: %s" % (self, arg_name, arg_info, add_value)
print "\t%s: Loading argument: %s, info: %s" % (self, arg_name, arg_info)
add_value = self._interpolate_value(inputs, outputs, arg_name, arg_info)
# Only add arguments that have a value
if add_value is not None:
# Need to add in the arg_name and the arg_value
......
......@@ -22,7 +22,9 @@ setup(
"scripts/chip-job-peakranger-format",
"scripts/chip-job-save-result",
"scripts/chip-job-sort-peak",
"scripts/chip-job-zcat-peak"
"scripts/chip-job-zcat-peak",
"scripts/chip-job-zerone-format",
"scripts/chip-job-hd-format"
],
install_requires=["pymongo","pyyaml"],
zip_safe=False
......
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