Commit b8a18706 authored by Penom Nom's avatar Penom Nom
Browse files

Fix bug in filtered file list R1 and filtered file list R2 order.

parent bacfcb46
......@@ -106,12 +106,15 @@ class Casava18 (NG6Workflow):
# fastq illumina filter
group_prefix = Utils.get_group_basenames(self.read1_files+self.read2_files, "read")
fastqilluminafilter = self.add_component("FastqIlluminaFilter", [self.read1_files+self.read2_files, self.args["keep_reads"], group_prefix, self.runobj.name+"_fastqilluminafilter.tar.gz"])
# concatenate fastq
concatenatefastq = self.add_component("ConcatenateFilesGroups", [self.read1_files+self.read2_files, group_prefix.keys()])
# Split read 1 and read 2 from filtered files list
# split read 1 and read 2 from filtered files list
[filtered_read1_files, filtered_read2_files] = Utils.split_pair(fastqilluminafilter.fastq_files_filtered, True)
filtered_read1_files.sort()
filtered_read1_files.sort()
group_prefix = Utils.get_group_basenames(filtered_read1_files+filtered_read2_files, "read")
# concatenate fastq
concatenatefastq = self.add_component("ConcatenateFilesGroups", [filtered_read1_files+filtered_read2_files, group_prefix.keys()])
# archive the files
addrawfiles = self.add_component("AddRawFiles", [self.runobj, concatenatefastq.concat_files, self.args["compression"]])
......
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