Commit a7934074 authored by Penom Nom's avatar Penom Nom
Browse files

fastqc for pacbio_qc wf. default fastqc for all casava wf

parent dc70596f
......@@ -458,6 +458,11 @@ class CasavaNG6Workflow(NG6Workflow):
raise NotImplementedError
def illumina_process(self):
fastqilluminafilter = None
filtered_read1_files = []
filtered_read2_files = []
saved_files = []
if self.is_casava :
if len(self.undetermined_reads1) > 0 :
if self.casava['mismatch_index'] :
......@@ -492,9 +497,6 @@ class CasavaNG6Workflow(NG6Workflow):
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])
# 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)
contam = []
try :
......@@ -507,7 +509,15 @@ class CasavaNG6Workflow(NG6Workflow):
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)
return fastqilluminafilter, filtered_read1_files, filtered_read2_files, saved_files
else :
return None, self.get_all_reads("read1"), self.get_all_reads("read2"), self.get_all_reads()
\ No newline at end of file
fastqilluminafilter = None
filtered_read1_files = self.get_all_reads("read1")
filtered_read2_files = self.get_all_reads("read2")
saved_files = self.get_all_reads()
# 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
\ No newline at end of file
......@@ -37,8 +37,8 @@ class FastQC (Analysis):
@param archive_name : name for the output archive
"""
self.add_input_file_list( "input_files", "Fastq files paths", default=input_files, required=True, file_format = 'fastq')
self.add_parameter("is_casava", "True gathers all different files of one read of one sample (only with name on CASAVA 1.8+ format)", default=is_casava)
self.add_parameter("no_group", "True disables grouping of bases for reads >50bp", default=no_group)
self.add_parameter("is_casava", "True gathers all different files of one read of one sample (only with name on CASAVA 1.8+ format)", default=is_casava, type ='bool')
self.add_parameter("no_group", "True disables grouping of bases for reads >50bp", default=no_group, type='bool')
self.add_parameter("archive_name", "Archive name", default=archive_name)
items = self.input_files
......
......@@ -33,5 +33,6 @@ class PacBioQualityCheck (NG6Workflow):
def process(self):
add_pacbio_raw_file = self.add_component("AddPacBioRawFiles", [self.runobj, self.get_all_reads()])
h5tofastq = self.add_component("H5toFastq", [self.get_all_reads()])
fastqc = self.add_component("FastQC", [h5tofastq.output_fastqs, False, False, "fastqc.tar.gz"], parent = h5tofastq)
\ No newline at end of file
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