Commit ee8a85a3 authored by aknecht2's avatar aknecht2
Browse files

Added job yaml file. Updated workflow_job parsing to handle rawfolder argument.

parent c17b5649
music_punctate:
inputs:
- name: prefix
type: string
- name: control.bed
type: file
file_type: bed
- name: signal.bed
type: file
file_type: bed
additional_inputs:
- name: mapp_inputs
type: list
file_type: bin
outputs:
- name: scale_129.bed
type: file
file_type: bed
- name: scale_194.bed
type: file
file_type: bed
- name: scale_291.bed
type: file
file_type: bed
- name: scale_437.bed
type: file
file_type: bed
- name: scale_656.bed
type: file
file_type: bed
- name: scale_985.bed
type: file
file_type: bed
- name: scale_1477.bed
type: file
file_type: bed
- name: scale_2216.bed
type: file
file_type: bed
command: run_music.py
arguments:
- "--prefix":
type: string
changeable: false
required: true
has_value: true
default: "$inputs.0"
- "--peak_type":
type: string
changeable: false
required: true
has_value: true
default: "punctate"
- "--controls":
type: file
changeable: false
required: true
has_value: true
default: "$inputs.1"
- "--signals":
type: file
changeable: false
required: true
has_value: true
default: "$inputs.2"
- "--mapp":
type: rawfolder
changeable: true
required: true
has_value: true
- "--lmapp":
type: numeric
changeable: true
required: true
has_value: true
default: 50
walltime: 240
memory: 16000
cores: 1
nodes: 1
......@@ -294,9 +294,19 @@ class WorkflowJob(object):
valid_arg, msg = self._is_valid_arg(arg_name, arg_info)
if valid_arg:
# If the argument is a rawfile, add it to the raw_file list for use in the DAX
# This is for files that are on disk and need to be staged
if arg_info["type"] == "rawfile":
arg_value = self._get_arg_value(arg_name, arg_info)
self.raw_files[os.path.basename(arg_value)] = {"path": arg_value}
# Sometimes we have a folder full of files we need to include,
# in this case, use the rawfolder argument to stage all files
# within the folder.
elif arg_info["type"] == "rawfolder":
arg_value = self._get_arg_value(arg_name, arg_info)
for root, dirs, files in os.walk(arg_value):
for f in files:
self.raw_files[f] = {"path": "%s/%s" % (arg_value, f)}
break
else:
self.errors.append(msg)
if self.params.get("arguments") is not None:
......
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