[PRE REVIEW]: CRBHits: Conditional Reciprocal Best Hits in R

whedon commented 4 years ago

Submitting author: @kullrich (Kristian Ullrich) Repository: https://gitlab.gwdg.de/mpievolbio-it/joss_crbhits Version: v0.0.1 Editor: Pending Reviewer: Pending Managing EiC: Daniel S. Katz

:warning: JOSS reduced service mode :warning:

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whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

whedon commented 4 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.01 s (156.0 files/s, 20207.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             13              0            120
Markdown                         1             25              0            101
-------------------------------------------------------------------------------
SUM:                             2             38              0            221
-------------------------------------------------------------------------------

Statistical information for the repository '2257' was gathered on 2020/05/26.
No commited files with the specified extensions were found.

whedon commented 4 years ago

Failed to discover a valid open source license.

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

whedon commented 4 years ago

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.21105/joss.00142 may be missing for title: shmlast: an improved implementation of conditional reciprocal best hits with LAST and Python
- https://doi.org/10.1101/gr.113985.110 may be missing for title: Adaptive seeds tame genomic sequence comparison
- https://doi.org/10.1186/s13059-015-0721-2 may be missing for title: OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
- https://doi.org/10.1093/protein/12.2.85 may be missing for title: Twilight zone of protein sequence alignments
- https://doi.org/10.1007/978-3-540-35306-5_10 may be missing for title: SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis
- https://doi.org/10.1016/s1672-0229(10)60008-3 may be missing for title: KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies
- https://doi.org/10.1093/oxfordjournals.molbev.a026236 may be missing for title: Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
- https://doi.org/10.1093/nar/gkr853 may be missing for title: PomBase: a comprehensive online resource for fission yeast

INVALID DOIs

- None

danielskatz commented 4 years ago

👋 @kullrich - this repository seems to include your paper but not the software. JOSS submissions are normally a software repository that also includes a paper. Additionally, the software needs to be a public version control system, and from the paper, it appears that your software is in https://mpievolbio-it.pages.gwdg.de/ which may not be public?

Finally, and as a minor point, you should add DOIs to the papers in your references for the papers that have DOIs. The reference check above provides some suggestions, but it is not always completely accurate.

kullrich commented 4 years ago

The software repo is here:

https://gitlab.gwdg.de/mpievolbio-it/crbhits https://gitlab.gwdg.de/mpievolbio-it/crbhits

I now included the paper.md, paper.bib and figure1.png at the root and added them to .Rbuildignore

Should I do a new submission or can the repo source be changed?

Best regards

Kristian Ullrich

Kristian Ullrich, Ph.D. Scientific IT group Department of Evolutionary Genetics Max Planck Institute for Evolutionary Biology August Thienemann Str. 2 24306 Plön Germany +49 4522 763 313 ullrich@evolbio.mpg.de

-- CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited.

On 26. May 2020, at 17:02, Daniel S. Katz notifications@github.com wrote:

👋 @kullrich https://github.com/kullrich - this repository seems to include your paper but not the software. JOSS submissions are normally a software repository that also includes a paper. Additionally, the software needs to be a public version control system, and from the paper, it appears that your software is in https://mpievolbio-it.pages.gwdg.de/ https://mpievolbio-it.pages.gwdg.de/ which may not be public?

Finally, and as a minor point, you should add DOIs to the papers in your references for the papers that have DOIs. The reference check above provides some suggestions, but it is not always completely accurate.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2257#issuecomment-634081689, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5ZWI3YLJ3ZT2LZME7JQLDRTPKYXANCNFSM4NKMJALQ.

danielskatz commented 4 years ago

If you don't mind making a new submission, it might be slightly easier. I will mark this one as withdrawn

danielskatz commented 4 years ago

@whedon withdraw

whedon commented 4 years ago

Paper withdrawn.

kullrich commented 4 years ago

OK, thanks

Kristian Ullrich, Ph.D. Scientific IT group Department of Evolutionary Genetics Max Planck Institute for Evolutionary Biology August Thienemann Str. 2 24306 Plön Germany +49 4522 763 313 ullrich@evolbio.mpg.de

-- CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited.

On 26. May 2020, at 17:30, Kristian Ullrich ullrich@evolbio.mpg.de wrote:

The software repo is here:

https://gitlab.gwdg.de/mpievolbio-it/crbhits https://gitlab.gwdg.de/mpievolbio-it/crbhits

I now included the paper.md, paper.bib and figure1.png at the root and added them to .Rbuildignore

Should I do a new submission or can the repo source be changed?

Best regards

Kristian Ullrich

Kristian Ullrich, Ph.D. Scientific IT group Department of Evolutionary Genetics Max Planck Institute for Evolutionary Biology August Thienemann Str. 2 24306 Plön Germany +49 4522 763 313 ullrich@evolbio.mpg.de mailto:ullrich@evolbio.mpg.de

-- CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited.

On 26. May 2020, at 17:02, Daniel S. Katz <notifications@github.com mailto:notifications@github.com> wrote:

👋 @kullrich https://github.com/kullrich - this repository seems to include your paper but not the software. JOSS submissions are normally a software repository that also includes a paper. Additionally, the software needs to be a public version control system, and from the paper, it appears that your software is in https://mpievolbio-it.pages.gwdg.de/ https://mpievolbio-it.pages.gwdg.de/ which may not be public?

Finally, and as a minor point, you should add DOIs to the papers in your references for the papers that have DOIs. The reference check above provides some suggestions, but it is not always completely accurate.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2257#issuecomment-634081689, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5ZWI3YLJ3ZT2LZME7JQLDRTPKYXANCNFSM4NKMJALQ.

kullrich commented 4 years ago

Paper was re-submitted but until now the @whedon seems not to have reported any feedback. Might there be an issue because the same title was used for the new submission?

danielskatz commented 4 years ago

I see it in the queue, but the next step is manual, and I haven't gotten to it yet. Last time you were just fortunate that I was working on this at about the same time as you submitted, so you got a very fast manual (not automated) response.

kullrich commented 4 years ago

OK, I understand.

Thank you for the quick response and the nice help about this first issue.

Best regards

Kristian

Kristian Ullrich, Ph.D. Scientific IT group Department of Evolutionary Genetics Max Planck Institute for Evolutionary Biology August Thienemann Str. 2 24306 Plön Germany +49 4522 763 313 ullrich@evolbio.mpg.de

-- CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited.

On 26. May 2020, at 19:12, Daniel S. Katz notifications@github.com wrote:

I see it in the queue, but the next step is manual, and I haven't gotten to it yet. Last time you were just fortunate that I was working on this at about the same time as you submitted, so you got a very fast manual (not automated) response.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2257#issuecomment-634157458, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5ZWI5MSK4W4LYPA4UHE6TRTP2AFANCNFSM4NKMJALQ.

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