pcr_product_anl

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pcr_product_anl
pcr_product_anl
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Usage

''' snakemake
--cores 10
--snakefile /TBI/Share/BioPeople/siyoo/Pipelines/customppl_anlbio_motif/workflow/Snakefile
--configfile /TBI/Share/BioPeople/siyoo/Pipelines/customppl_anlbio_motif/config/config.yaml
--

Code Snippets

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shell:
    "flash"
    " -d {params.outdir}"
    " -o {params.prefix}"
    " --compress"
    " --compress-prog=gzip"
    " --suffix=gz"
    " --threads {threads}"
    " {input.fq1}"
    " {input.fq2}"
    " > {params.outdir}/{params.prefix}.mylog"
SnakeMake From line 27 of rules/other.smk 
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shell:
    'python {config[script_home]}/take_product.py'
    ' --primer5 {params.primer5}'
    ' --primer3 {params.primer3}'
    ' --infqgz {input.fqgz}'
    ' --prefix {params.prefix}'
SnakeMake From line 50 of rules/other.smk 
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shell:
    'python {config[script_home]}/take_product.py'
    ' --primer5 {params.primer5}'
    ' --primer3 {params.primer3}'
    ' --infqgz {input.fqgz}'
    ' --prefix {params.prefix}'
SnakeMake From line 68 of rules/other.smk 
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shell:
    'python {config[script_home]}/take_product.py'
    ' --primer5 {params.primer5}'
    ' --primer3 {params.primer3}'
    ' --infqgz {input.fqgz}'
    ' --prefix {params.prefix}'
SnakeMake From line 86 of rules/other.smk 
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shell:
    "cat {input.ext_fna}"
    " {input.nc1_fna}"
    " {input.nc2_fna}"
    " > {output.merge_fna}"
SnakeMake From line 100 of rules/other.smk 
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shell:
    'python {config[script_home]}/count_product.py'
    ' --ifn {input.merge_fna}'
    ' --ofn {output.clone_fna}'
SnakeMake From line 111 of rules/other.smk 
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shell:
    'python {config[script_home]}/lm.py'
    ' --infa {input.fna}'
    ' --prefix {params.prefix}'
    ' --seqtype fna'
SnakeMake From line 126 of rules/other.smk 
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shell:
    "cat {input.ext_faa}"
    " {input.nc1_faa}"
    " {input.nc2_faa}"
    " > {output.merge_faa}"
SnakeMake From line 139 of rules/other.smk 
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shell:
    'python {config[script_home]}/count_product.py'
    ' --ifn {input.merge_faa}'
    ' --ofn {output.clone_faa}'
SnakeMake From line 150 of rules/other.smk 
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shell:
    'python {config[script_home]}/lm.py'
    ' --infa {input.faa}'
    ' --prefix {params.prefix}'
    ' --seqtype faa'
SnakeMake From line 165 of rules/other.smk
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/seung1yoo/pcr_product_anl
Name: pcr_product_anl
Version: 1
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Downloaded: 0
Copyright: Public Domain
License: MIT License
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