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Snakefile
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Snakefile
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# noinspection PyUnresolvedReferences
rule rule_run_fastp:
input:
fq1 = config['args']['fastq1']
params:
fq2 = config['args']['fastq2'],
paired = config['params']['paired'],
output1_file = config['outputs']['fastp']['fqp1'],
output2_file = config['outputs']['fastp']['fqp2'],
log_file = config['logs']['fastp'],
mex_path = config['params']['mex_path']
threads: config['args']['processes']
output:
config['outputs']['fastp']['fqp1']
conda: config['envs']['preprocessing']
script: config['scripts']['fastp']
# noinspection PyUnresolvedReferences
rule rule_run_fastqc:
input:
fq1 = config['outputs']['fastp']['fqp1']
params:
fq2 = config['outputs']['fastp']['fqp2'],
paired = config['params']['paired'],
output_dir = config['outputs']['fastqc'],
log_file = config['logs']['fastqc'],
mex_path = config['params']['mex_path']
threads: config['args']['processes']
output:
config['targets']['fastqc']
conda: config['envs']['preprocessing']
script: config['scripts']['fastqc']
# noinspection PyUnresolvedReferences
rule rule_run_ngs_te_mapper2:
input:
fq1 = config['outputs']['fastp']['fqp1'],
genome = config['args']['genome'],
te_fasta = config['args']['te'],
params:
fq2 = config['outputs']['fastp']['fqp2'],
paired = config['params']['paired'],
tool_config = config['params']['tools_config'],
output_dir = config['outputs']['ngs_te_mapper2'],
log_file = config['logs']['ngs_te_mapper2'],
mex_path = config['params']['mex_path'],
annotation = config['args']['ngs_te_mapper2']['annotation'],
window = config['args']['ngs_te_mapper2']['window'],
min_mapq = config['args']['ngs_te_mapper2']['min_mapq'],
min_af = config['args']['ngs_te_mapper2']['min_af'],
tsd_max = config['args']['ngs_te_mapper2']['tsd_max'],
gap_max = config['args']['ngs_te_mapper2']['gap_max'],
keep_files = config['args']['ngs_te_mapper2']['keep_files'],
threads: config['args']['processes']
output:
config['targets']['ngs_te_mapper2'][0],
config['targets']['ngs_te_mapper2'][1]
conda: config['envs']['ngs_te_mapper2']
script: config['scripts']['ngs_te_mapper2']
# noinspection PyUnresolvedReferences
rule rule_run_vep:
input:
ngs_te_mapper2_vcfs = config['targets']['ngs_te_mapper2'],
params:
log_file = config['logs']['vep'],
mex_path = config['params']['mex_path'],
assembly = config['args']['vep']['assembly'],
cache_dir = config['params']['vep_cache_dir']
threads: config['args']['processes']
output:
config['targets']['vep'][0], config['targets']['vep'][1],
conda: config['envs']['vep']
script: config['scripts']['vep']