Commit af90f42f authored by Jerome Mariette's avatar Jerome Mariette
Browse files

integration of Dynamic components into ng6

parent 18f27f0c
......@@ -44,7 +44,7 @@ class R454QualityCheck (NG6Workflow):
[mids_config_file, midscheme] = self.runobj.export_mids_to_newbler_cfg_file(self.args["demux_error"])
# extract sff per mids
sfffile = self.add_component("SFFfile", [self.args["data_file"], run_name, midscheme, mids_config_file])
sff_to_process = glob.glob(os.path.join(sfffile.output_directory, "*.sff"))
sff_to_process = sfffile.splited_sffs
# extract the files to process
sff_extract = self.add_component("SFFextract", [sff_to_process], parent=sfffile)
fastq_to_process = sff_extract.fastq_files
......@@ -19,7 +19,7 @@ import os
from subprocess import Popen, PIPE
from jflow.component import Component
from jflow.iotypes import OutputFile, InputFile, Formats
from jflow.iotypes import OutputFile, InputFile, OutputFileEndsWith, Formats
from ng6.analysis import Analysis
from weaver.function import ShellFunction
......@@ -28,15 +28,13 @@ from weaver.abstraction import Map
class SFFfile (Analysis):
def __init__(self):
Analysis.__init__(self, is_dynamic=True)
def define_parameters(self, sff_file, files_prefix, midscheme, mids_config_file):
self.sff_file = InputFile(sff_file, Formats.SFF)
self.files_prefix = os.path.join(self.output_directory, files_prefix)
self.midscheme = midscheme
self.mids_config_file = mids_config_file
basename = os.path.splitext(os.path.basename(sff_file))[0]
self.splited_sffs = OutputFileEndsWith(self.output_directory, ".sff", Formats.SFF)
self.stdout = OutputFile(os.path.join(self.output_directory, basename+".stdout"))
def define_analysis(self):
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