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Snakefile
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Mon, Feb 24, 13:40

Snakefile
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import os
from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
HTTP = HTTPRemoteProvider()
SAMPLES = ['DATASET_NAME']
for smp in SAMPLES:
print("Sample " + smp + " will be processed")
rule final:
input:
# directory('/tmp/MOUSE_GRCm38.p6'),
expand('/output/{sample}_R1_fastqc.html', sample=SAMPLES),
expand('/output/{sample}_R2_fastqc.html', sample=SAMPLES),
expand('/output/{sample}_trimmed_R1.fastq', sample=SAMPLES),
expand('/output/{sample}_trimmed_R2.fastq', sample=SAMPLES),
expand('/output/{sample}_trimmed_R1_fastqc.html', sample=SAMPLES),
expand('/output/{sample}_trimmed_R2_fastqc.html', sample=SAMPLES),
expand('/output/{sample}_trimmed.fastq', sample=SAMPLES),
rule get_genome:
input:
HTTP.remote("cloud.s3it.uzh.ch:8080/v1/AUTH_576f87a2a18948bdb2da11fdcad29ae2/RNA-genome/GENOME.zip", keep_local=True)
output:
directory('/tmp/MOUSE_GRCm38.p6')
priority:1
run:
outputName = os.path.join('/tmp',os.path.basename(input[0]))
shell("mv {input} {outputName} && unzip {outputName} -d /tmp && rm {outputName}")
rule perform_qc:
input:
R1='/input/{sample}_R1.fastq',
R2='/input/{sample}_R2.fastq',
params:
out_dir = '/output/'
output:
'/output/{sample}_R1_fastqc.html',
'/output/{sample}_R1_fastqc.zip',
'/output/{sample}_R2_fastqc.html',
'/output/{sample}_R2_fastqc.zip',
shell:
r'''
fastqc -o {params.out_dir} -f fastq {input.R1} {input.R2}
'''
rule trimmometic_run:
input:
R1_read='/input/{sample}_R1.fastq',
R2_read='/input/{sample}_R1.fastq',
output:
R1_trimmed='/output/{sample}_trimmed_R1.fastq',
R2_trimmed='/output/{sample}_trimmed_R2.fastq',
R1_unpaired='/output/{sample}_trimmed_upaired_R1.fastq',
R2_unpaired='/output/{sample}_trimmed_upaired_R2.fastq',
message: """---TRIMMOMATIC---"""
shell:
r'''
java -jar /usr/share/java/trimmomatic-0.35.jar PE -phred33 {input.R1_read} {input.R2_read} {output.R1_trimmed} {output.R1_unpaired} {output.R2_trimmed} {output.R2_unpaired} LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30
'''
rule perform_qc_trimmed:
input:
R1_trimmed_qc='/output/{sample}_trimmed_R1.fastq',
R2_trimmed_qc='/output/{sample}_trimmed_R2.fastq',
params:
out_dir = '/output/'
output:
'/output/{sample}_trimmed_R1_fastqc.html',
'/output/{sample}_trimmed_R1_fastqc.zip',
'/output/{sample}_trimmed_R2_fastqc.html',
'/output/{sample}_trimmed_R2_fastqc.zip',
message: """---QC trimmed Data---"""
shell:
r'''
fastqc -outdir {params.out_dir} -f fastq {input.R1_trimmed_qc} {input.R2_trimmed_qc}
'''
rule merge_trimmed_R1_and_R2:
input:
R1_trimmed_qc='/output/{sample}_trimmed_R1.fastq',
R2_trimmed_qc='/output/{sample}_trimmed_R2.fastq',
output:
merged='/output/{sample}_trimmed.fastq',
message: """---Merge trimmed R1 and R2---"""
shell:
r'''
cat {input.R1_trimmed_qc} {input.R2_trimmed_qc} > {output.merged}
'''

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