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