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Use fastqc wrapper #80

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Smeds opened this issue Mar 16, 2021 · 1 comment
Open

Use fastqc wrapper #80

Smeds opened this issue Mar 16, 2021 · 1 comment
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enhancement New feature or request good first issue Good for newcomers

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@Smeds
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Smeds commented Mar 16, 2021

Twist_DNA/src/Snakemake/rules/QC/fastqc.smk

Lines 38 to 39 in 8a1d086

shell:
"(fastqc --quiet -t {threads} --outdir {params.outdir} {input}) &> {log}"

Twist_DNA/src/Snakemake/rules/QC/fastqc.smk

Lines 57 to 58 in 8a1d086

shell:
"(fastqc --quiet -t {threads} --outdir {params.outdir} {input}) &> {log}"

Start using wrapper
https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/fastqc.html
@Smeds Smeds added enhancement New feature or request good first issue Good for newcomers labels Mar 16, 2021
@jonca79
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jonca79 commented Mar 16, 2021

Could be problems with the temporary directory and singularity permissions

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@Smeds @jonca79