[PRE REVIEW]: QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data

[editorialbot]

Submitting author: @ManavalanG (Manavalan Gajapathy)
Repository: https://github.com/uab-cgds-worthey/quac
Branch with paper.md (empty if default branch): joss_manuscript
Version: 1.3
Editor: @lpantano
Reviewers: @brentp, @Redmar-van-den-Berg
Managing EiC: Kevin M. Moerman

Status

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

@ManavalanG if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (815.4 files/s, 74219.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
YAML                            21             71             29           1213
Python                          14            318            306           1183
Markdown                        17            324              0            874
Jinja Template                   1             19              0            591
TeX                              1             24              0            208
Bourne Shell                     1             17             10             39
JSON                             1              0              0             23
INI                              1              5              0             17
TOML                             1              1              0              7
-------------------------------------------------------------------------------
SUM:                            58            779            345           4155
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1877

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/bioinformatics/btw354 is OK
- 10.1038/s41436-020-01084-8 is OK
- 10.1038/s41525-020-00154-9 is OK
- 10.1093/bioinformatics/btv566 is OK
- 10.1093/bioinformatics/btx699 is OK
- 10.1093/gigascience/gix090 is OK
- 10.1093/gigascience/giab008 is OK
- 10.1101/gr.246934.118 is OK
- 10.1186/s13073-020-00761-2 is OK
- 10.12688/f1000research.15931.2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[Kevin-Mattheus-Moerman]

@editorialbot invite @lpantano as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@lpantano I was wondering if this submission is something you could help edit. Note I was close to recommending a scope review here given its relatively small size. If you have any concerns let me know. Thanks!

[lpantano]

Ok, thanks!, let me take a closer look tomorrow.

[lpantano]

@editorialbot assign me as editor

[editorialbot]

Assigned! @lpantano is now the editor

[lpantano]

@editorialbot add @brentp as reviewer

[editorialbot]

@brentp added to the reviewers list!

[lpantano]

Hi @naumenko-sa, would you like to review this tool?

[lpantano]

Hi @Redmar-van-den-Berg, would you be interested on reviewing this tool? This are the guidelines we use: https://joss.readthedocs.io/en/latest/review_criteria.html. Let me know if you are interested. Thanks

[lpantano]

Hi @ManavalanG, still trying to find the second reviewer. Do you have any recommendation?

[Redmar-van-den-Berg]

@lpantano I'll have a look!

[Redmar-van-den-Berg]

I'm trying to follow along with https://quac.readthedocs.io/en/stable/system_testing/, and I've run into 2 issues

1. The pipeline does not create the output and log folders automatically, so the user has to create the folders manually before the pipeline is started
2. There is no automatic way to fetch the required reference files that are described in configs/workflow.yaml

[lpantano]

@Redmar-van-den-Berg , Let me add you as a reviewer and then I can start the process. I will copy this comment in the new issue that it will be the formal process.

[lpantano]

@editorialbot add @Redmar-van-den-Berg as reviewer

[editorialbot]

@Redmar-van-den-Berg added to the reviewers list!

[lpantano]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #5313.