Snakemake workflow as a module to test reproducibility

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smk-wk-as-module
smk-wk-as-module
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Toy Snakemake workflow to be deployed as a module to test reproducibility

Code Snippets

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wrapper:
    "v1.1.0/bio/cutadapt/pe"
SnakeMake From line 34 of workflow/Snakefile 
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shell:
    "vsearch --fastx_uniques {input} --fastaout {output} --fasta_width 0 --threads {threads}"
SnakeMake VSEARCH From line 44 of workflow/Snakefile 
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shell:
    "wc -l {input} > {output}"
SnakeMake From line 52 of workflow/Snakefile 
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__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell


n = len(snakemake.input)
assert n == 2, "Input must contain 2 (paired-end) elements."

extra = snakemake.params.get("extra", "")
adapters = snakemake.params.get("adapters", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)

assert (
    extra != "" or adapters != ""
), "No options provided to cutadapt. Please use 'params: adapters=' or 'params: extra='."

shell(
    "cutadapt"
    " {adapters}"
    " {extra}"
    " -o {snakemake.output.fastq1}"
    " -p {snakemake.output.fastq2}"
    " -j {snakemake.threads}"
    " {snakemake.input}"
    " > {snakemake.output.qc} {log}"
)
Python Snakemake Cutadapt From line 3 of pe/wrapper.py
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/cpauvert/smk-wk-as-module
Name: smk-wk-as-module
Version: 1
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Copyright: Public Domain
License: None
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