From ee8a85a3fea6987b26da3c5fa1856e1d15a956bd Mon Sep 17 00:00:00 2001
From: aknecht2 <aknecht2@unl.edu>
Date: Fri, 28 Apr 2017 13:24:04 -0500
Subject: [PATCH] Added job yaml file. Updated workflow_job parsing to handle
rawfolder argument.
---
chipathlon/jobs/params/music_punctate.yaml | 89 ++++++++++++++++++++++
chipathlon/workflow_job.py | 10 +++
2 files changed, 99 insertions(+)
create mode 100644 chipathlon/jobs/params/music_punctate.yaml
diff --git a/chipathlon/jobs/params/music_punctate.yaml b/chipathlon/jobs/params/music_punctate.yaml
new file mode 100644
index 0000000..6b12172
--- /dev/null
+++ b/chipathlon/jobs/params/music_punctate.yaml
@@ -0,0 +1,89 @@
+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
diff --git a/chipathlon/workflow_job.py b/chipathlon/workflow_job.py
index 1bad4b5..36df2d9 100644
--- a/chipathlon/workflow_job.py
+++ b/chipathlon/workflow_job.py
@@ -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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