Commit 954d4052 authored by WJH58's avatar WJH58
Browse files

bowtie2 version changed

parent 60251e93
channels:
- bioconda
dependencies:
- bowtie2=2.4.2
- bowtie2=2.3.2
......@@ -118,6 +118,19 @@ rule trimmomatic:
SLIDINGWINDOW:4:15 \
MINLEN:40 &>{log}
"""
rule trimmed_fastqc:
input:
forward_reads = WORKING_DIR + "trimmed/{samples}_forward.fastq.gz",
reverse_reads = WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz"
output:
RESULT_DIR + "fastqc/{samples}_{R}_trimmed_fastqc.html"
params:
RESULT_DIR + "fastqc/"
conda:
"envs/fastqc.yaml"
shell:
"fastqc --outdir={params} {input.forward_reads} {input.reverse_reads} &>{log}"
rule fastqc:
input:
......
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