[PRE REVIEW]: CRED: a rapid peak caller for Chem-seq data #1374

whedon · 2019-04-14T13:33:36Z

Submitting author: @jlincbio (Jason Lin)
Repository: https://github.com/jlincbio/cred
Version: 0.1
Editor: @lpantano
Reviewers: @darogan

Author instructions

Thanks for submitting your paper to JOSS @jlincbio. Currently, there isn't an JOSS editor assigned to your paper.

@jlincbio if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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The text was updated successfully, but these errors were encountered:

whedon · 2019-04-14T13:33:39Z

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

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

@whedon commands

What happens now?

This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience 😸

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

whedon · 2019-04-14T13:33:40Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-14T13:33:49Z

PDF failed to compile for issue #1374 with the following error:

Can't find any papers to compile :-(

labarba · 2019-04-14T13:40:35Z

👋 @lpantano — It looks like this submission is one you can help us with... I'll assign you as handling editor now, but do let me know if I got this wrong 🤓

labarba · 2019-04-14T13:40:48Z

@whedon assign @lpantano as editor

whedon · 2019-04-14T13:40:51Z

OK, the editor is @lpantano

whedon · 2019-04-15T00:11:39Z

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

whedon · 2019-04-15T00:11:55Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-15T00:12:19Z

PDF failed to compile for issue #1374 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Jason Lin, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:57:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:17:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:109:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:109:in block in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:106:in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

whedon · 2019-04-15T00:18:16Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-15T00:18:46Z

PDF failed to compile for issue #1374 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Jason Lin, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:57:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:17:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:109:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:109:in block in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:106:in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

whedon · 2019-04-15T00:21:22Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-15T00:21:55Z

PDF failed to compile for issue #1374 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Jason Lin, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:57:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:17:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:109:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:109:in block in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:106:in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

whedon · 2019-04-15T00:24:39Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-15T00:25:29Z

👉 Check article proof 📄 👈

whedon · 2019-04-15T03:09:00Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-15T03:10:06Z

👉 Check article proof 📄 👈

jlincbio · 2019-04-15T03:10:41Z

Thanks for picking up the review. I noticed that whedon was unable to generate a PDF, so looked around and fixed some things in the paper. Hopefully this wouldn't affect the review process.

jlincbio · 2019-04-15T05:18:05Z

@labarba @lpantano this is my first time submitting to JOSS (and TBH first time submitting a software paper), so I'm actually not sure on what sort of criteria a suitable reviewer should meet. With that said, looking at the previous JOSS referee list and perhaps one of the following may work?

MDebasish
darogan
arvestad
janpb
standage
jdeligt

I just filtered the list for the following criteria:

Having C/C++ and Perl as the preferred languages
Current research area involves some aspect of biology
No active reviews at the moment

lpantano · 2019-04-16T22:55:26Z

Hi @jlincbio ,

I will take this tool through the process. I just came back from vacations, so give me a couple of days to organize myself.

Cheers

jlincbio · 2019-04-18T23:06:09Z

Thanks for agreeing to handle this submission, @lpantano - it is my first software submission, so I am a bit over-anxious about the whole experience. I made a list of possible referees in an earlier post, but they were not tagged with mentions. If there is anything you need from me please do not hesitate to let me know.

jlincbio · 2019-05-01T16:05:33Z

@lpantano - sorry I don't mean to rush you at all with this, but I am going to be out of the office for a few days next week. Is there anything I should do before that?

lpantano · 2019-05-01T16:47:39Z

Hi @jlincbio

I am still trying to find a reviewer, I hope I can get somebody this week. I think you are all set, it is my fault.

Thanks!

lpantano · 2019-05-01T17:58:31Z

@whedon add @darogan as reviewer

whedon · 2019-05-01T17:58:35Z

OK, @darogan is now a reviewer

lpantano · 2019-05-01T17:58:53Z

@whedon check references

whedon · 2019-05-01T17:58:55Z

Attempting to check references...

whedon · 2019-05-01T17:59:24Z


OK DOIs

- 10.1186/gb-2008-9-9-r137 is OK
- 10.1371/journal.pone.0065598 is OK
- 10.1371/journal.pone.0165581 is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.1137/1.9781611970586 is OK

MISSING DOIs

- https://doi.org/10.2307/2346797 may be missing for title: Algorithm AS 63: The Incomplete Beta Integral

INVALID DOIs

- None

lpantano · 2019-05-01T17:59:37Z

@whedon start review

whedon · 2019-05-01T17:59:41Z

OK, I've started the review over in #1423. Feel free to close this issue now!

whedon added the pre-review label Apr 14, 2019

whedon added C Makefile Perl labels Apr 14, 2019

whedon assigned lpantano Apr 14, 2019

whedon unassigned lpantano May 1, 2019

whedon assigned lpantano May 1, 2019

lpantano closed this as completed May 1, 2019

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[PRE REVIEW]: CRED: a rapid peak caller for Chem-seq data #1374

[PRE REVIEW]: CRED: a rapid peak caller for Chem-seq data #1374

whedon commented Apr 14, 2019 •

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[PRE REVIEW]: CRED: a rapid peak caller for Chem-seq data #1374

[PRE REVIEW]: CRED: a rapid peak caller for Chem-seq data #1374

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