Commit ee7d99f5 authored by aknecht2's avatar aknecht2
Browse files

Updated peak call yaml and generator to new format.

parent 0ed97a3b
......@@ -79,7 +79,7 @@ class PeakCallGenerator(ModuleGenerator):
inputs = {
"chrom.sizes": run.genome.get_chrom_sizes()["name"],
"control.bed": call_pair[0].full_name,
"exp.bed": call_pair[1].full_name,
"signal.bed": call_pair[1].full_name,
# 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.
......@@ -98,10 +98,10 @@ class PeakCallGenerator(ModuleGenerator):
inputs = {
"chrom.sizes": run.genome.get_chrom_sizes()["name"],
"control.bed": call_pair[0].full_name,
"exp.bed": call_pair[1].full_name,
"signal.bed": call_pair[1].full_name,
"prefix": result.prefix,
"genome_dir": run.genome.assembly,
"read.dist": self.module.workflow_jobs["gem_callpeak"].raw_files.keys()[0],
# "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)
......@@ -116,7 +116,7 @@ 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
}
return (self.get_markers(run), inputs)
......@@ -130,7 +130,7 @@ 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
}
return (self.get_markers(run), inputs)
......
......@@ -160,161 +160,142 @@ peak_call:
- narrow[peak_type]:
- gem_callpeak:
inputs:
- chrom.sizes:
type: file
- exp.bed:
type: file
- control.bed:
type: file
- prefix:
type: string
- genome_dir:
type: string
additional_inputs:
- read.dist:
type: file
- chr_fasta:
type: list
prefix:
param_name: prefix
chrom.sizes:
param_name: chrom.sizes
signal.bed:
param_name: signal.bed
control.bed:
param_name: control.bed
genome_dir:
param_name: genome
chr_fasta:
param_name: chr_fasta
outputs:
- GEM_events.narrowPeak:
type: file
name_template: "$prefix$/$prefix$_GEM_events.narrowPeak"
- GPS_events.narrowPeak:
type: file
name_template: "$prefix$/$prefix$_GPS_events.narrowPeak"
GEM_events.narrowPeak:
param_name: gem_peak_result
name_template: "$prefix$/$prefix$_GEM_events.narrowPeak"
GPS_events.narrowPeak:
param_name: gps_peak_result
name_template: "$prefix$/$prefix$_GPS_events.narrowPeak"
- sort_awk_sort_peaks:
inputs:
- GEM_events.narrowPeak:
type: file
additional_inputs: null
GEM_events.narrowPeak:
param_name: peak_results
outputs:
- results_GEM_sorted.bed:
type: file
final_result: true
results_GEM_sorted.bed:
param_name: sorted_peaks
final_result: true
- sort_awk_sort_peaks:
inputs:
- GPS_events.narrowPeak:
type: file
additional_inputs: null
GPS_events.narrowPeak:
param_name: peak_results
outputs:
- results_GPS_sorted.bed:
type: file
final_result: true
results_GPS_sorted.bed:
param_name: sorted_peaks
final_result: true
- spp[tool]:
- cp:
inputs:
- exp.bed:
type: file
additional_inputs: null
signal.bed:
param_name: input_file
outputs:
- exp.tagAlign:
type: file
signal.tagAlign:
param_name: output_file
- cp:
inputs:
- control.bed:
type: file
additional_inputs: null
control.bed:
param_name: input_file
outputs:
- control.tagAlign:
type: file
control.tagAlign:
param_name: output_file
- narrow[peak_type]:
- spp_nodups_narrow:
inputs:
- exp.tagAlign:
type: file
- control.tagAlign:
type: file
additional_inputs: null
signal.tagAlign:
param_name: signal.tagAlign
control.tagAlign:
param_name: control.tagAlign
outputs:
- results.narrowPeak.gz:
type: file
- results.pdf:
type: file
- results.ccscore:
type: file
results.narrowPeak.gz:
param_name: peak_results
results.pdf:
param_name: plots_df
results.ccscore:
param_name: score
- sort_awk_sort_peaks:
inputs:
- results.narrowPeak.gz:
type: file
additional_inputs: null
results.narrowPeak.gz:
param_name: peak_results
outputs:
- results_sorted.bed:
type: file
final_result: true
results_sorted.bed:
param_name: sorted_peaks
- broad[peak_type]:
- spp_nodups_broad:
inputs:
- exp.tagAlign:
type: file
- control.tagAlign:
type: file
additional_inputs: null
signal.tagAlign:
param_name: signal.tagAlign
control.tagAlign:
param_name: control.tagAlign
outputs:
- results.broadPeak.gz:
type: file
- results.pdf:
type: file
- results.ccscore:
type: file
results.broadPeak.gz:
param_name: peak_results
results.pdf:
param_name: plots_df
results.ccscore:
param_name: score
- sort_awk_sort_peaks:
inputs:
- results.broadPeak.gz:
type: file
additional_inputs: null
results.broadPeak.gz:
param_name: peak_results
outputs:
- results_sorted.bed:
type: file
final_result: true
results_sorted.bed:
param_name: sorted_peaks
- macs2[tool]:
- narrow[peak_type]:
- macs2_narrow:
inputs:
- exp.bed:
type: file
- control.bed:
type: file
- prefix:
type: string
additional_inputs: null
prefix:
param_name: prefix
control.bed:
param_name: control.bed
signal.bed:
param_name: signal.bed
outputs:
- peaks.narrowPeak:
type: file
- peaks.xls:
type: file
- summits.bed:
type: file
peaks.narrowPeak:
param_name: result_peaks
peaks.xls:
param_name: excel_result
summits.bed:
param_name: result_summit
- sort_awk_sort_peaks:
inputs:
- peaks.narrowPeak:
type: file
additional_inputs: null
peaks.narrowPeak:
param_name: result_peaks
outputs:
- results_sorted.bed:
type: file
final_result: true
results_sorted.bed:
param_name: sorted_peaks
- broad[peak_type]:
- macs2_broad:
inputs:
- exp.bed:
type: file
- control.bed:
type: file
- prefix:
type: string
additional_inputs: null
prefix:
param_name: prefix
control.bed:
param_name: control.bed
signal.bed:
param_name: signal.bed
outputs:
- peaks.broadPeak:
type: file
- peaks.xls:
type: file
- summits.bed:
type: file
peaks.broadPeak:
param_name: result_peaks
peaks.xls:
param_name: excel_result
summits.bed:
param_name: result_summit
- sort_awk_sort_peaks:
inputs:
- peaks.broadPeak:
type: file
additional_inputs: null
peaks.broadPeak:
param_name: result_peaks
outputs:
- results_sorted.bed:
type: file
final_result: true
results_sorted.bed:
param_name: sorted_peaks
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