Commit cfe987de authored by Gerald Salin's avatar Gerald Salin

correct bug adding self.runobj to fastqilluminafilter component

parent 62e909d6
......@@ -266,9 +266,11 @@ class Utils(object):
"""
read_1_list = []
read_2_list = []
logging.getLogger("Utils").debug("split_pair. Entering")
if is_casava:
logging.getLogger("Utils").debug("split_pair. is_casava")
for file in file_list:
logging.getLogger("Utils").debug("split_pair. file = " + file)
basename_without_ext = os.path.basename(file).split(".")[0]
file_name_fields = basename_without_ext.split(Utils.CASAVA_FILENAME_SEPARATOR)
read_tag = file_name_fields[Utils.CASAVA_FILENAME['read']-1]
......@@ -278,8 +280,11 @@ class Utils(object):
read_2_list.append(file)
else:
sorted_list = sorted( file_list )
logging.getLogger("Utils").debug("split_pair. file_list = " + ", ".join(file_list))
logging.getLogger("Utils").debug("split_pair. sorted_list = " + ", ".join(sorted_list))
for i in range(0,len(sorted_list),2):
logging.getLogger("Utils").debug("split_pair. sorted_list[i] = " + sorted_list[i])
logging.getLogger("Utils").debug("split_pair. sorted_list[i+1] = " + sorted_list[i+1])
read_1_list.append(sorted_list[i])
read_2_list.append(sorted_list[i+1])
......
......@@ -16,6 +16,8 @@
#
import re, os
import logging
from subprocess import Popen, PIPE
from ng6.analysis import Analysis
......@@ -99,6 +101,8 @@ class FastqIlluminaFilter (Analysis):
def process(self):
# If the file is not zip
if not self.fastq_files[0].endswith(".gz"):
logging.getLogger("FastqIlluminaFilter").debug("process self.fastq_files = " + ",".join(self.fastq_files))
logging.getLogger("FastqIlluminaFilter").debug("process self.fastq_files_filtered = " + ",".join(self.fastq_files_filtered))
self.add_shell_execution(self.get_exec_path("fastq_illumina_filter") + " --keep " + self.keep_option + " -v -o $1 $3 > $2",
cmd_format='{EXE} {OUT} {IN}', map=True,
inputs = self.fastq_files, outputs = [self.fastq_files_filtered, self.stdout])
......
......@@ -92,7 +92,7 @@ class PhiXCheck (CasavaNG6Workflow):
addrawfiles = self.add_component("AddRawFiles", [self.runobj, phiX_R1+phiX_R2, self.compression])
# fastq illumina filter
fastqilluminafilter_phiX = self.add_component("FastqIlluminaFilter", [phiX_R1+phiX_R2, "pass_illumina_filters", None], component_prefix="phiX")
fastqilluminafilter_phiX = self.add_component("FastqIlluminaFilter", [self.runobj,phiX_R1+phiX_R2, "pass_illumina_filters", None], component_prefix="phiX")
# list filtered files
if self.is_paired_end() :
# split read 1 and read 2 from filtered files list
......
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