Commit e2995d71 authored by Maxime Manno's avatar Maxime Manno 🍜 Committed by Maxime Manno
Browse files

test

parents 1527e5e2 5159767a
......@@ -176,6 +176,10 @@ class FastQC (Analysis):
for metric in metrics :
self._add_result_element("metrics", "metric", metric, metric)
# Finaly create and add the archive to the analysis
print(results_files)
print("archive_name " , self.archive_name)
self.archive_name = self.archive_name.replace("/","-")
print("archive_name " , self.archive_name)
self._create_and_archive(results_files, self.archive_name)
def get_version(self):
......
......@@ -40,7 +40,7 @@ class FastqIlluminaFilter (Analysis):
def define_analysis(self):
self.name = "IlluminaFilter"
self.description = "Filters FASTQ file generated by CASAVA 1.8"
self.description = "Filters FASTQ file generated by CASAVA 2.20"
self.software = "fastq_illumina_filter"
self.options = "--keep " + self.keep_option + " -v"
......
......@@ -101,8 +101,8 @@ class GeneDiversity (NG6Workflow):
def define_parameters(self, function="process"):
self.add_multiple_parameter_list("merge", "The list of samples to merge")
self.add_parameter("name", "Merge group name", required=True, add_to="merge")
self.add_parameter_list("sample_name", "The name of the sample", required=True, add_to="merge")
self.add_parameter("name", "Merge group name", required=False, add_to="merge")
self.add_parameter_list("sample_name", "The name of the sample", required=False, add_to="merge")
self.add_input_file("database", "The reference set contains protein representative sequences of the gene target" +
"and should be compiled to have a good coverage of diversity of the gene family", required=True, group="Gene section")
......@@ -149,7 +149,7 @@ class GeneDiversity (NG6Workflow):
trim_R2 = self.add_component("Trimmer", [self.get_all_reads('read2'), 1, self.trim_read_2], component_prefix="R2")
# Make some statistics on raw file
fastqc = self.add_component("FastQC", [trim_R1.output_files + trim_R2.output_files, False, True])
#fastqc = self.add_component("FastQC", [trim_R1.output_files + trim_R2.output_files, False, True])
# Merge overlapping pair
join_pairs = self.add_component("Flash", [trim_R1.output_files, trim_R2.output_files, self.mismatch_ratio, self.min_overlap, self.max_overlap])
......
......@@ -61,5 +61,5 @@ class UsearchDereplication (Component):
self.add_output_file_list("stderr", "stderr", pattern='{basename_woext}.stderr', items=self.input_fasta)
def process(self):
dereplicate = ShellFunction( self.get_exec_path("usearch") + " -derep_" + self.method + " $1 -output $2 " + self.options + " 2> $3", cmd_format='{EXE} {IN} {OUT}' )
dereplicate = ShellFunction( self.get_exec_path("usearch") + " -derep_" + self.method + " $1 -fastaout $2 " + self.options + " 2> $3", cmd_format='{EXE} {IN} {OUT}' )
dereplicate = MultiMap(dereplicate, inputs=self.input_fasta, outputs=[self.output_files, self.stderr])
\ No newline at end of file
......@@ -28,7 +28,7 @@ class OntQualityCheck (NG6Workflow):
def define_parameters(self, function="process"):
logging.getLogger("jflow").debug("Begin OntQualityCheck.define_parameters! ont_qc")
self.add_parameter("compression", "How should the data be compressed once archived", choices= [ "none", "gz", "bz2"], default = "none")
self.add_parameter("compression", "How should the data be compressed once archived", choices= [ "none", "gz", "bz2"], default = "gz")
#self.add_parameter("nb_threads", "Number of threads to use for fastqc. Each thread will be allocated 250MB of memory.", default=6)
#self.add_parameter("nanoplot_color", "Color of nanoplot")
self.add_input_file( "summary_file", "Input summary basecalling file", default=None)
......@@ -48,6 +48,6 @@ class OntQualityCheck (NG6Workflow):
self.compression = "gz"
addrawfiles = self.add_component("AddRawFiles", [self.runobj, self.get_all_reads(), self.compression])
#nanoplot = self.add_component("Nanoplot", [sample.name,self.get_all_reads(), self.nb_threads, True, "png", self.nanoplot_color,"nanoplot.tar.gz"])
nanoplot = self.add_component("Nanoplot", [sample.name,self.get_all_reads(), self.nb_threads, True, "png", self.nanoplot_color,"nanoplot.tar.gz"])
ontstat = self.add_component("Run_stats", [self.summary_file, self.barcoded])
This diff is collapsed.
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment