Commit 965a37cf authored by aknecht2's avatar aknecht2
Browse files

Updated all idr stuff to conform to new standard.

parent 37b424ba
......@@ -114,6 +114,5 @@ class IdrGenerator(ModuleGenerator):
"sorted_sample_1.bed": result_pair[0].full_name,
"sorted_sample_2.bed": result_pair[1].full_name
}
additional_inputs = {}
results = self.create_results(run, result)
return markers, inputs, additional_inputs, self.get_outputs(results)
return markers, inputs, self.get_outputs(results)
idr:
- idr:
inputs:
- sorted_sample_1.bed:
type: file
- sorted_sample_2.bed:
type: file
additional_inputs: null
sorted_sample_1.bed:
param_name: sample_1
sorted_sample_2.bed:
param_name: sample_2
outputs:
- idr.bed:
type: file
idr.bed:
param_name: idr_bed
- sort_awk_sort_peaks:
inputs:
- idr.bed:
type: file
additional_inputs: null
idr.bed:
param_name: peak_results
outputs:
- sorted_idr.bed:
type: file
final_result: true
sorted_idr.bed:
param_name: sorted_peaks
idr:
inputs:
- name: sample_1
sample_1:
type: file
file_type: bed
- name: sample_2
sample_2:
type: file
file_type: bed
additional_inputs: null
outputs:
- name: idr_bed
idr_bed:
type: file
file_type: bed
command: idr
arguments:
- "--samples":
type: list
type: file_list
changeable: false
required: true
has_value: true
default:
- $inputs.0
- $inputs.1
- $sample_1
- $sample_2
- "--rank":
type: numeric
changeable: true
......@@ -39,7 +37,7 @@ idr:
changeable: false
required: true
has_value: true
default: $outputs.0
default: $idr_bed
walltime: 600
memory: 8000
cores: 1
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment