Commit be7e18f5 authored by mmassaviol's avatar mmassaviol
Browse files

Debug RNAseq

parent 80085219
......@@ -66,7 +66,7 @@
type: radio,
value: "exactTest",
choices: [exactTest: exactTest, glmLRT: glmLRT],
label: "Test type: exactTest: Computes p-values for differential abundance for each gene between two samples, conditioning on the total count for each gene. The counts in each group are assumed to follow a binomial distribution\nglmLRT: Fits a negative binomial generalized log-linear model to the read counts for each gene and conducts genewise statistical tests.",
label: "Test type: exactTest: Computes p-values for differential abundance for each gene between two samples, conditioning on the total count for each gene. The counts in each group are assumed to follow a binomial distribution. glmLRT: Fits a negative binomial generalized log-linear model to the read counts for each gene and conducts genewise statistical tests.",
},
],
},
......
......@@ -23,14 +23,18 @@ SAMPLES = raw_reads['samples']
def reads():
inputs = dict()
if (config["trimming"] == "null"):
return raw_reads
if (config["SeOrPe"] == "SE"):
inputs["read"] = raw_reads['read']
elif (config["SeOrPe"] == "PE"):
inputs["read"] = raw_reads['read']
inputs["read2"] = raw_reads['read2']
elif (config["trimming"] == "trimmomatic"):
if (config["SeOrPe"] == "SE"):
inputs["read"] = rules.trimmomatic_SE.output.read
elif (config["SeOrPe"] == "PE"):
inputs["read"] = rules.trimmomatic_PE.output.readFP
inputs["read2"] = rules.trimmomatic_PE.output.readRP
return inputs
return inputs
def get_groups():
with open(config["group_file"], mode="r") as infile:
......@@ -52,7 +56,13 @@ def fastqc_PE_inputs():
return inputs
def trimmomatic_inputs():
return raw_reads
inputs = dict()
if (config["SeOrPe"] == "SE"):
inputs["read"] = raw_reads['read']
elif (config["SeOrPe"] == "PE"):
inputs["read"] = raw_reads['read']
inputs["read2"] = raw_reads['read2']
return inputs
def kallisto_inputs():
return reads()
......
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