Commit 6e782aeb authored by Maxime Manno's avatar Maxime Manno 🍜
Browse files

Add trimporechop component

parent f01a98e3
......@@ -15,6 +15,7 @@
# along with this program. If not, see <>.
import logging
import os
from ng6.ng6workflow import NG6Workflow
from ng6.utils import Utils
......@@ -29,10 +30,10 @@ class OntQualityCheck (NG6Workflow):
def define_parameters(self, function="process"):
logging.getLogger("jflow").debug("Begin OntQualityCheck.define_parameters! ont_qc")
self.add_parameter("compression", "How should the data be compressed once archived", choices= [ "none", "gz", "bz2"], default = "gz")
#self.add_parameter("nb_threads", "Number of threads to use for fastqc. Each thread will be allocated 250MB of memory.", default=6)
#self.add_parameter("nanoplot_color", "Color of nanoplot")
self.add_parameter("nb_threads", "Number of threads to use for porechop.", default=4)
self.add_parameter("fileformat", "The file format for porechop", choices= [ "fastq", "fasta"], default = "fastq")
self.add_input_file( "summary_file", "Input summary basecalling file", default=None)
self.add_parameter("barcoded", "", choices= [ "yes", "no"], default = "no")
self.add_parameter("barcoded", "Barcoded run or not", choices= [ "yes", "no"], default = "no")
def process(self):
logging.getLogger("jflow").debug("Begin OntQualityCheck.process! test ont_qc")
......@@ -50,4 +51,5 @@ class OntQualityCheck (NG6Workflow):
addrawfiles = self.add_component("AddRawFiles", [self.runobj, self.get_all_reads(), self.compression])
#nanoplot = self.add_component("Nanoplot", [,self.get_all_reads(), self.nb_threads, True, "png", self.nanoplot_color,"nanoplot.tar.gz"])
ontstat = self.add_component("Run_stats", [self.summary_file, self.barcoded])
trim_porechop = self.add_component("Trim_porechop", [self.get_all_reads(), self.nb_threads, self.fileformat , "discard_middle"])
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