Commit d71edb64 authored by Penom Nom's avatar Penom Nom
Browse files

contamination and addraw for all

parent 49b6358c
......@@ -496,25 +496,28 @@ class CasavaNG6Workflow(NG6Workflow):
reads_prefixes = (Utils.get_group_basenames(saved_files, "read")).keys()
concatenatefastq = self.add_component("ConcatenateFilesGroups", [saved_files, reads_prefixes])
saved_files = concatenatefastq.concat_files
addrawfiles = self.add_component("AddRawFiles", [self.runobj, saved_files, self.compression])
contam = []
try :
contam.append(self.get_resource("phix_bwa"))
contam.append(self.get_resource("ecoli_bwa"))
contam.append(self.get_resource("yeast_bwa"))
except : pass
# contamination_search
if contam :
if self.contamination_databank: contam.extend(self.contamination_databank)
contamination_search = self.add_component("ContaminationSearch", [filtered_read1_files+filtered_read2_files, contam, reads_prefixes], parent = fastqilluminafilter)
else :
reads_prefixes = None
fastqilluminafilter = None
filtered_read1_files = self.get_all_reads("read1")
filtered_read2_files = self.get_all_reads("read2")
saved_files = self.get_all_reads()
# add raw
addrawfiles = self.add_component("AddRawFiles", [self.runobj, saved_files, self.compression])
contam = []
try :
contam.append(self.get_resource("phix_bwa"))
contam.append(self.get_resource("ecoli_bwa"))
contam.append(self.get_resource("yeast_bwa"))
except : pass
# contamination_search
if contam :
if self.contamination_databank: contam.extend(self.contamination_databank)
contamination_search = self.add_component("ContaminationSearch", [filtered_read1_files+filtered_read2_files, contam, reads_prefixes], parent = fastqilluminafilter)
# make some statistics on raw file
fastqc = self.add_component("FastQC", [filtered_read1_files+filtered_read2_files, (self.group_prefix is not None), self.no_group, "fastqc.tar.gz"], parent = fastqilluminafilter)
return fastqilluminafilter, filtered_read1_files, filtered_read2_files, saved_files
......
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