Commit 344012ba authored by aknecht2's avatar aknecht2
Browse files

Updated peak call generator, removed additional_inputs.

parent 7f47a480
......@@ -49,11 +49,9 @@ class PeakCallGenerator(ModuleGenerator):
"prefix": result.prefix,
"control.bed": call_pair[0].full_name,
"signal.bed": call_pair[1].full_name
#"mapp_files": self.module.workflow_jobs["music_punctate"].raw_files.keys()
}
additional_inputs = {
"mapp_files": self.module.workflow_jobs["music_punctate"].raw_files.keys()
}
return self.get_markers(run), inputs, additional_inputs
return (self.get_markers(run), inputs)
def _peakranger(self, run, result):
"""
......@@ -65,11 +63,10 @@ class PeakCallGenerator(ModuleGenerator):
call_pair = self.call_pairs[result.full_name]
inputs = {
"control.bed": call_pair[0].full_name,
"exp.bed": call_pair[1].full_name,
"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 _ccat(self, run, result):
"""
......@@ -83,14 +80,12 @@ class PeakCallGenerator(ModuleGenerator):
"chrom.sizes": run.genome.get_chrom_sizes()["name"],
"control.bed": call_pair[0].full_name,
"exp.bed": call_pair[1].full_name,
"conf.txt": self.module.workflow_jobs["ccat_callpeak"].raw_files.keys()[0],
# The prefix mod is because ccat files have double extensions,
# and we can't control the names of the output files directly,
# only with the prefix.
"prefix": result.prefix
}
additional_inputs = {}
return (self.get_markers(run), inputs, additional_inputs)
return (self.get_markers(run), inputs)
def _gem(self, run, result):
"""
......@@ -105,13 +100,11 @@ class PeakCallGenerator(ModuleGenerator):
"control.bed": call_pair[0].full_name,
"exp.bed": call_pair[1].full_name,
"prefix": result.prefix,
"genome_dir": run.genome.assembly
}
additional_inputs = {
"genome_dir": run.genome.assembly,
"read.dist": self.module.workflow_jobs["gem_callpeak"].raw_files.keys()[0],
"chr_fasta": [fasta["name"] for fasta in run.genome.get_chr_fasta_files()]
}
return (self.get_markers(run), inputs, additional_inputs)
return (self.get_markers(run), inputs)
def _spp(self, run, result):
"""
......@@ -125,8 +118,7 @@ class PeakCallGenerator(ModuleGenerator):
"control.bed": call_pair[0].full_name,
"exp.bed": call_pair[1].full_name
}
additional_inputs = {}
return (self.get_markers(run), inputs, additional_inputs)
return (self.get_markers(run), inputs)
def _macs2(self, run, result):
"""
......@@ -141,8 +133,7 @@ class PeakCallGenerator(ModuleGenerator):
"exp.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 _make_call_pairs(self, run, result_list):
"""
......@@ -234,6 +225,6 @@ class PeakCallGenerator(ModuleGenerator):
:type result: :py:class:`~chipathlon.result.Result`
"""
prev_results = self.get_prev_results(run, result)
markers, inputs, additional_inputs = self.generate_calls[run.peak](run, result)
markers, inputs = self.generate_calls[run.peak](run, result)
results = self.create_results(run, result)
return markers, inputs, additional_inputs, self.get_outputs(results)
return markers, inputs, self.get_outputs(results)
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