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Harded-coded directory in MultiQC #1

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y1zhou opened this issue Dec 1, 2021 · 0 comments
Open

Harded-coded directory in MultiQC #1

y1zhou opened this issue Dec 1, 2021 · 0 comments
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enhancement New feature or request

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@y1zhou
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y1zhou commented Dec 1, 2021

In rule multiqc:

output:
directory("results/qc/multiqc/multiqc_data"),
"results/qc/multiqc/multiqc_report.html"
priority: 9
conda:
"../envs/qc.yml"
shell:
"""multiqc {input.reports} \
--sample-names {input.sample_names} \
--outdir results/qc/multiqc \
-m fastqc
"""

MultiQC expects a directory path to the --outdir argument, which means output and --outdir are both hard-coded in this implementation. There should be a way to move results/qc/multiqc to params.

@y1zhou y1zhou added the enhancement New feature or request label Dec 1, 2021
@y1zhou y1zhou self-assigned this Dec 1, 2021
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