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fastqc.smk
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fastqc.smk
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"""Get fastqc reports"""
#Which rules will be run on the host computer and not sent to nodes
localrules:
multiqc_fastqc_reads,
multiqc_fastqc_barcodes
rule fastqc_barcodes:
"""Create fastqc report"""
input:
get_R1_files,
output:
html='{results_dir}/logs/fastqc/{sample}_R1_fastqc.html',
zip='{results_dir}/logs/fastqc/{sample}_R1_fastqc.zip'
params: '--extract'
wrapper:
'0.27.1/bio/fastqc'
rule fastqc_reads:
"""Create fastqc report"""
input:
get_R2_files,
output:
html='{results_dir}/logs/fastqc/{sample}_R2_fastqc.html',
zip='{results_dir}/logs/fastqc/{sample}_R2_fastqc.zip'
params: '--extract'
wrapper:
'0.27.1/bio/fastqc'
rule multiqc_fastqc_barcodes:
input:
expand('{results_dir}/logs/fastqc/{sample}_R1_fastqc.html', sample=samples.index, results_dir=results_dir)
output:
html='{results_dir}/reports/fastqc_barcodes.html'
params: '-m fastqc --ignore *_R2*'
wrapper:
'0.27.1/bio/multiqc'
rule multiqc_fastqc_reads:
input:
expand('{results_dir}/logs/fastqc/{sample}_R2_fastqc.html', sample=samples.index, results_dir=results_dir)
output:
html='{results_dir}/reports/fastqc_reads.html'
params: '-m fastqc --ignore *_R1*'
wrapper:
'0.27.1/bio/multiqc'