Commit 9ea0a4bc authored by Adam Caprez's avatar Adam Caprez
Browse files

Add staging of gem read distribution file

parent be0b317a
...@@ -52,7 +52,8 @@ file_extensions = { ...@@ -52,7 +52,8 @@ file_extensions = {
"yaml": ["yaml"], "yaml": ["yaml"],
"result": ["bed", "narrowPeak", "broadPeak", "tagAlign", "bam"], "result": ["bed", "narrowPeak", "broadPeak", "tagAlign", "bam"],
"txt": ["txt"], "txt": ["txt"],
"chrom_sizes": ["sizes"] "chrom_sizes": ["sizes"],
"read_dist" : ["txt"]
} }
# list of resources that can be specified per job (step) in # list of resources that can be specified per job (step) in
......
...@@ -10,7 +10,9 @@ peak_call: ...@@ -10,7 +10,9 @@ peak_call:
type: file type: file
- prefix: - prefix:
type: string type: string
additional_inputs: null additional_inputs:
- read.dist:
type: file
outputs: outputs:
- results_sorted.narrowPeak: - results_sorted.narrowPeak:
type: file type: file
......
...@@ -8,7 +8,9 @@ gem_callpeak: ...@@ -8,7 +8,9 @@ gem_callpeak:
type: file type: file
- prefix: - prefix:
type: argument type: argument
additional_inputs: null additional_inputs:
- read_dist:
type: file
outputs: outputs:
- bed: - bed:
type: file type: file
......
...@@ -44,7 +44,9 @@ class PeakCallGenerator(ModuleGenerator): ...@@ -44,7 +44,9 @@ class PeakCallGenerator(ModuleGenerator):
"control.bed": file_pair[1]["file_name"], "control.bed": file_pair[1]["file_name"],
"prefix": prefix "prefix": prefix
} }
additional_inputs = {} additional_inputs = {
"read.dist" : self.module.workflow_jobs['gem_callpeak'].raw_files.keys()[0]
}
sample_data = [file_pair[0]["sample"], file_pair[1]["sample"]] sample_data = [file_pair[0]["sample"], file_pair[1]["sample"]]
experiment_ids = file_pair[0]["experiment_ids"] experiment_ids = file_pair[0]["experiment_ids"]
control_ids = file_pair[1]["control_ids"] control_ids = file_pair[1]["control_ids"]
......
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