Commit 2474ad4c authored by Penom Nom's avatar Penom Nom
Browse files

No commit message

No commit message
parent 6961cbd6
#
# Copyright (C) 2012 INRA
# Copyright (C) 2015 INRA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
......@@ -32,13 +32,12 @@ from ng6.run import Run
from ng6.sample import Sample
from ng6.utils import Utils
from workflows.types import date, adminlogin, casavadir, existingproject, samplemetadata
class BasicNG6Workflow (Workflow):
def __init__(self, args={}, id=None, function= "process"):
Workflow.__init__(self, args, id, function)
self.add_parameter("admin_login", "Who is the project administrator", required = True, type = adminlogin, display_name="Admin login")
self.add_parameter("admin_login", "Who is the project administrator", required = True, type = 'ng6userlogin', display_name="Admin login")
def add_component(self, component_name, args=[], kwargs={}, component_prefix="default", parent=None, addto="run"):
# first build and check if this component is OK
......@@ -130,10 +129,10 @@ class NG6Workflow (BasicNG6Workflow):
self.reads2_indexes = []
def _add_run_parameters(self):
self.add_parameter("project_name", "The project name the run belongs to", required = True, type = existingproject, group="Run information")
self.add_parameter("project_name", "The project name the run belongs to", required = True, type = 'existingproject', group="Run information")
self.add_parameter("run_name", "Give a name to your run", flag = "--name", required = True, display_name="Name", group="Run information")
self.add_parameter("run_description", "Give a description to your run", flag = "--description", required = True, display_name="Description", group="Run information")
self.add_parameter("run_date", "When were the data produced", flag = "--date", required = True, type = date, display_name="Date", group="Run information")
self.add_parameter("run_date", "When were the data produced", flag = "--date", required = True, type = 'date', display_name="Date", group="Run information")
self.add_parameter("data_nature", "Are Sequences cDNA, genomique, RNA, ...", required = True, display_name="Data nature", group="Run information")
self.add_parameter("sequencer", "Which sequencer produced the data", required = True, display_name="Sequencer", group="Run information")
self.add_parameter("species", "Which species has been sequenced", required = True, display_name="Species", group="Run information")
......@@ -147,7 +146,7 @@ class NG6Workflow (BasicNG6Workflow):
self.add_parameter("type", "Read orientation and type", choices = Sample.AVAILABLE_TYPES, default='se', add_to = "input_sample")
self.add_parameter("insert_size", "Insert size for paired end reads", type = int, add_to = "input_sample")
self.add_parameter("species", "Species related to this sample", add_to = "input_sample")
self.add_parameter_list("metadata", "Add metadata to the sample", type=samplemetadata ,add_to = "input_sample")
self.add_parameter_list("metadata", "Add metadata to the sample", type='samplemetadata' ,add_to = "input_sample")
self.add_input_file_list("read1", "Read 1 data file path", required = True, add_to = "input_sample")
self.add_input_file_list("read2", "Read 2 data file path", add_to = "input_sample")
......
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