Commit 0f77e19b authored by Claire Kuchly's avatar Claire Kuchly
Browse files

modif the new parameter properties - component flash

parent f4b910e7
......@@ -107,7 +107,7 @@ class IlluminaDiversityQC (NG6Workflow):
contamination_search = self.add_component("ContaminationSearch", [filtered_read1_files+filtered_read2_files, self.args["databank"], reads_prefixes], parent = fastqilluminafilter)
# merge overlapping pair
join_pairs = self.add_component("Flash", [filtered_read1_files, filtered_read2_files, self.args["mismatch_ratio"], self.args["min_overlap"], self.args["max_overlap"], self.args["avg_reads_length"], self.args["avg_fragment_length"]], parent=fastqilluminafilter)
join_pairs = self.add_component("Flash", [filtered_read1_files, filtered_read2_files, self.args["mismatch_ratio"], self.args["min_overlap"], self.args["max_overlap"]], parent=fastqilluminafilter)
if self.args["assignation_databank"] is not None :
# subset assignation
......
......@@ -61,7 +61,6 @@ files_read.read_2.flag = R2
files_read.read_2.help = Which read2 files should be used (if single end, leave empty)
files_read.read_2.type = localfile
compression.name = compression
compression.flag = --compression
compression.help = How should data be compressed once archived (none|gz|bz2)
......@@ -82,7 +81,6 @@ databank.type = localfile
assignation_databank.name = assignation databank
assignation_databank.flag = --assignation-databank
assignation_databank.help = Blast databank to classify a subset of sequences
assignation_databank.type = localfile
keep_reads.name = keep_reads
keep_reads.flag = --keep
......@@ -111,4 +109,4 @@ max_overlap.name = Maximum overlap
max_overlap.flag = --max-overlap
max_overlap.help = Maximum overlap length expected in approximately 90 percent of read pairs.
max_overlap.type = int
max_overlap.default = 55
\ No newline at end of file
max_overlap.default = 55
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