Commit 72951bad authored by Gerald Salin's avatar Gerald Salin
Browse files

add conf files to tests addrun, add projet and addanalysis

remove BasicAnalyse class from addanalysis workflow, using the
BasicAnalysis Class from components directory instead
parent 0a1e8399
......@@ -81,7 +81,7 @@ class AddAnalysis (BasicNG6Workflow):
if parent.id not in analyses_ids :
display_error_message("The parent analysis associated with id '%s' does not belong to the %s id '%s' " % (parent.id, addto, self.project_id or self.run_id) )
basicanalysis = self.add_component("BasicAnalyse", [files_to_save, self.analysis_name,
basicanalysis = self.add_component("BasicAnalysis", [files_to_save, self.analysis_name,
self.analysis_description, self.analysis_software, self.analysis_software_options,
self.analysis_software_version, self.compression, self.delete,
self.archive_name], addto=addto, parent = parent)
......
#
# Copyright (C) 2012 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
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
--data-file
workflows\illumina_diversity_qc\data\casava_directory_test\Project_Demo_project\Sample_Demo\Demo_AGAGAG_L001_R1_001.fastq.gz
--analysis-name
Add an analysis, storing fastq file
--analysis-description
Juste copy a fastq file
--analysis-software
cp
--analysis-software-options
-f
--analysis-software-version
1.2
#
# Copyright (C) 2012 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
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
from ng6.analysis import Analysis
class BasicAnalyse (Analysis):
def define_parameters(self, files, name, description, software, options, version, compression="none",
delete=False, archive_name=None):
self.add_input_file_list( "files", "The files to be archived.", default=files, required=True )
self.add_parameter( "name", "The analysis name", default=name, required = True )
self.add_parameter( "description", "Analysis description", default=description, required = True )
self.add_parameter( "software", "The analysis software", default=software, required = True )
self.add_parameter( "options", "The analysis software options", default=options, required = True )
self.add_parameter( "version", "The analysis software version", default=version, required = True )
self.add_parameter( "compression", "File compression once archived", default=compression)
self.add_parameter( "delete", "Should the input data be deleted once the process is over", type = bool, default=delete)
self.add_parameter( "archive_name", "Give a name to the final archive", default=archive_name)
self.is_editable = True
def define_analysis(self): pass
def process(self): pass
def get_version(self): return ""
def post_process(self):
self._archive_files(self.files, self.compression, self.archive_name, self.delete)
\ No newline at end of file
#
# Copyright (C) 2012 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
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
--name
Demo project 2
--description
Test adding a project
#
# Copyright (C) 2012 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
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
--project-name
Demo project
--name
Adding a run to a project
--description
Test adding a run to a project
--date
25/08/2018
--data-nature
gDNA
--sequencer
MiSeqX
--species
bug
--type
Lane 1
\ No newline at end of file
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