Commit cd128f6a authored by aknecht2's avatar aknecht2
Browse files

Fixed peakranger again...?

parent a0085119
......@@ -40,11 +40,11 @@ peakranger_callpeak:
has_value: true
default: "bed"
- "-d":
type: string
type: file
changeable: false
required: true
has_value: true
default: "$prefix"
default: "$signal.bed"
- "-c":
type: file
changeable: false
......@@ -52,11 +52,11 @@ peakranger_callpeak:
has_value: true
default: "$control.bed"
- "-o":
type: file
type: string
changeable: false
required: true
has_value: true
default: "$signal.bed"
default: "$prefix"
- "-p":
type: numeric
changeable: true
......
......@@ -557,7 +557,7 @@ class WorkflowJob(object):
"""
arg_list = []
# Java tools need to have -Xmx specified...
if self.executable in chipathlon.conf.java_tools:
if self.job_data["command"] in chipathlon.conf.java_tools:
arg_list.append("-Xmx%sM" % (self.params.get("memory", self.job_data["memory"])))
# Go through each argument
for arg_dict in self.job_data["arguments"]:
......
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