Commit 8c4ebe50 authored by AntonieV's avatar AntonieV
Browse files

some changes in fastqc and multiqc handling

parent 23b3c017
......@@ -51,27 +51,22 @@ def get_individual_fastq(wildcards):
elif wildcards.read == "2":
return units.loc[ (wildcards.sample, wildcards.unit), "fq2" ]
def get_fastqc_list(wildcards):
return multiqc_input
##### FastQC #####
multiqc_input = []
for (sample, unit) in units.index:
reads = [ "1", "2" ]
if is_single_end(sample, unit):
reads = [ "0" ]
multiqc_input.extend(
expand (
[
"results/qc/fastqc/{sample}.{unit}.{reads}.fq_fastqc.zip",
"results/qc/fastqc/{sample}.{unit}.{reads}.fq.html",
],
sample = sample,
unit = unit,
reads = reads
def get_multiqc_input(wildcards):
multiqc_input = []
for (sample, unit) in units.index:
reads = [ "1", "2" ]
if is_single_end(sample, unit):
reads = [ "0" ]
multiqc_input.extend(
expand (
[
"results/qc/fastqc/{sample}.{unit}.{reads}_fastqc.zip",
"results/qc/fastqc/{sample}.{unit}.{reads}.html"
],
sample = sample,
unit = unit,
reads = reads
)
)
)
return multiqc_input
......@@ -2,8 +2,8 @@ rule fastqc:
input:
get_individual_fastq
output:
html="results/qc/fastqc/{sample}.{unit}.{read}.fq.html",
zip="results/qc/fastqc/{sample}.{unit}.{read}.fq_fastqc.zip"
html="results/qc/fastqc/{sample}.{unit}.{read}.html",
zip="results/qc/fastqc/{sample}.{unit}.{read}_fastqc.zip"
log:
"logs/fastqc/{sample}.{unit}.{read}.log"
wrapper:
......@@ -11,7 +11,7 @@ rule fastqc:
rule multiqc:
input:
get_fastqc_list
get_multiqc_input
output:
"results/qc/multiqc/multiqc.html"
......
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