(inactive) SEQprocess

[hgwoo]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/SYSMED/SEQprocess

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[bioc-issue-bot]

Hi @hgwoo

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: SEQprocess
Type: Package
Title: R-based pipelines for NGS data processing
Version: 0.99.0
Date: 2018-1-3
Author: Hyun Goo Woo
Maintainer: Hyun Goo Woo  <HyunGooWoo@gmail.com>
Description: R-based pipelines for NGS data processing
License: GPL2
biocViews: Alignment, Annotation, Preprocessing, QualityControl, GenomeAssembly
RoxygenNote: 6.0.1
Suggests: knitr, markdown, BiocStyle
Depends: R (>= 3.3.2)
Encoding: UTF-8

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[mtmorgan]

Your package does not have a vignette with evaluated code chunks, and does not (re) use standard and well-established Bioconductor representations for NGS analysis (e.g., GenomicRanges, SummarizedExperiment, rtracklayer::import()). Use of these data structures enables interoperability between packages and facilitates robust software developement. With a vignette or use of Bioconductor objects, your package is not appropriate for Bioconductor.

If you revise your package around these concerns, and follow the Bioconductor guidelines in the new submission form, then please post a comment including @mtmorgan and indicating that your package ready for reconsideration.

[hgwoo]

@bioc-issue-bot #669

[mtmorgan]

Is your package now ready for moderation and review?

[hgwoo]

Hi @mtmorgan ,

SEQprocess provides pipelines that perform quality control, sequence alignment, variant calling, and annotation of sequence variations. Processing of NGS data are carried out by multiple methods according to the data types to be analyzed. These multiple processes can be run sequentially as a single and customized pipeline. (using fastQC, tophat2, bwa, cufflinks, gatk, picard, annovar.....)

I would like to submit the SEQprocess package to bioconductor, please let me know what you need to modify or add. Thank you!

[mtmorgan]

My original comment was here https://github.com/Bioconductor/Contributions/issues/634#issuecomment-362240916

Looking again, I do not think your package fits well with Bioconductor -- it relies heavily on external tools that our build system will not have available. The vignette cannot be evaluated and the software tested in an automated way. Bioconductor users expect to work with well-defined objects and perform in-memory, interactive computation whereas your package provides a way of orchestrating a work flow of third-party tools. I am going to decline this package for these reasons.