Open editorialbot opened 1 week ago
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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
β
OK DOIs
- 10.1101/2023.04.29.23289314 is OK
- 10.1038/nbt.3820 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1093/bioinformatics/btx192 is OK
- 10.5281/zenodo.10463781 is OK
- 10.1093/gigascience/giab008 is OK
- 10.1101/gr.107524.110 is OK
- 10.1038/nbt.3820 is OK
- 10.1093/bioinformatics/btw354 is OK
- 10.1038/s41587-020-0439-x is OK
- 10.1093/bioinformatics/btq033 is OK
- 10.5281/zenodo.13147688 is OK
- 10.5281/zenodo.13601364 is OK
π‘ SKIP DOIs
- No DOI given, and none found for title: The nf-core framework for community-curated bioinf...
- No DOI given, and none found for title: CreateSequenceDictionary (Picard)
- No DOI given, and none found for title: Picard toolkit
- No DOI given, and none found for title: CollectHsMetrics (Picard)
- No DOI given, and none found for title: CollectMultipleMetrics (Picard)
- No DOI given, and none found for title: HTS format specifications
- No DOI given, and none found for title: Babraham Bioinformatics - FastQC A Quality Control...
- No DOI given, and none found for title: Twist Methylome
- No DOI given, and none found for title: Twist Methylome
- No DOI given, and none found for title: target-methylseq-qc website
β MISSING DOIs
- None
β INVALID DOIs
- None
Software report:
github.com/AlDanial/cloc v 1.90 T=0.05 s (1532.4 files/s, 244651.6 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
CSS 5 39 20 2238
JavaScript 11 235 226 2112
SVG 3 3 3 2081
HTML 4 53 10 1537
YAML 27 74 30 905
JSON 7 2 0 635
XML 2 0 0 518
Markdown 9 295 0 494
Groovy 4 76 103 354
TeX 1 31 0 339
Python 2 61 90 183
CSV 3 0 0 10
TOML 1 1 2 7
Bourne Shell 1 0 0 5
-------------------------------------------------------------------------------
SUM: 80 870 484 11418
-------------------------------------------------------------------------------
Commit count by author:
111 Abhinav Sharma
1 Patricia
1 t4ly4
Paper file info:
π Wordcount for paper.md
is 1753
β
The paper includes a Statement of need
section
License info:
β
License found: MIT License
(Valid open source OSI approved license)
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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β οΈ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.
CC @agudeloromero @t4ly4
@abhi18av Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:
.bib
file, and call @editorialbot check references
here to check them again. @editorialbot invite @csoneson as editor
Invitation to edit this submission sent!
In principle I'm happy to edit this, but would like to first wait for the author's responses to @Kevin-Mattheus-Moerman's queries above.
@abhi18av Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:
Dear @Kevin-Mattheus-Moerman and @csoneson , thank you for your time to evaluate this manuscript!
I have addressed the comments inline.
- β Please study the above reference check βοΈ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your
.bib
file, and call@editorialbot check references
here to check them again.
Sure, I have updated the DOI for a few more citations, however as some entries don't have an associated publication (such as picard
) or there's no consensus on how to cite (such as HTS specification
https://github.com/samtools/hts-specs/issues/179 ), I have simply used the @online
bib resource annotation for those.
If there's a better way or a JOSS convention to address this, please let us know and we will be happy to accommodate.
- β I may have missed it, but can you confirm this project features (automated) testing? If so it may be good to link to this in the README.
Ah yes, there are a bunch of Github actions in the repo which are triggered upon relevant events.
In addition, I have added an explanation in the REAMDE for the bundled test dataset which we provide to users for quick testing https://github.com/wal-yan/target-methylseq-qc?tab=readme-ov-file#testing .
- β Could you help me understand the above code report, and potentially add to it in terms of nextflow contributions? What aspects of the report would you say is your core achievement/new contribution? In addition, can you help estimate the lines of code number for the nextflow work? We ask this as some tools exist e.g. to automatically generate JavaScript GUI related code for instance. So any help to judge the "weight/size" of this submission would be appreciated.
In terms of the cloc
report from https://github.com/openjournals/joss-reviews/issues/7238#issuecomment-2352844762, I must say that numbers hide the overall big picture, but thank you for raising this.
The principle changes regarding the implementation logic are of course in the Nextflow/Groovy layer, however as Nextflow is just the DSL for the orchestration of tasks, we have worked on other layers/languages as well.
The samplesheet check (written in Python) is specific to this pipeline and checks for the overall validity of the samplesheet as a pre-flight
check, in addition to the test samplesheet files in CSV format (assets/test_samplesheet_bed_filter.csv
and assets/test_samplesheet_picard_profiler.csv
.
Furthermore, once the analysis is done, the generated results are merged and pushed to MultiQC
which relies on a customized YAML file (assets/multiqc_config.yml
) in order to present the principal summary report.
Finally in terms of the UI for Nextflow Schema renderers, the JSON format has been customized to reflect the principal parameters of the pipeline corresponding to different modes.
I must also highlight that the creation of test_*
profiles is done in *`conf/config** scripts which are also
Groovy/Nextflowscripts but __do not__ get picked up by
cloc` as any language in the overall counts.
Therefore, kindly take this into consideration π
@editorialbot check references
@editorialbot generate pdf
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
β
OK DOIs
- 10.1101/2023.04.29.23289314 is OK
- 10.1038/nbt.3820 is OK
- 10.1038/s41587-020-0439-x is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1093/bioinformatics/btx192 is OK
- 10.5281/zenodo.10463781 is OK
- 10.1093/gigascience/giab008 is OK
- 10.1101/gr.107524.110 is OK
- 10.1038/nbt.3820 is OK
- 10.1093/bioinformatics/btw354 is OK
- 10.1038/s41587-020-0439-x is OK
- 10.1093/bioinformatics/btq033 is OK
- 10.5281/zenodo.8251379 is OK
- 10.5281/zenodo.13597863 is OK
π‘ SKIP DOIs
- No DOI given, and none found for title: CreateSequenceDictionary (Picard)
- No DOI given, and none found for title: Picard toolkit
- No DOI given, and none found for title: CollectHsMetrics (Picard)
- No DOI given, and none found for title: CollectMultipleMetrics (Picard)
- No DOI given, and none found for title: HTS format specifications
- No DOI given, and none found for title: Babraham Bioinformatics - FastQC A Quality Control...
- No DOI given, and none found for title: Twist Methylome
- No DOI given, and none found for title: Twist Methylome
- No DOI given, and none found for title: target-methylseq-qc website
β MISSING DOIs
- None
β INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Five most similar historical JOSS papers:
Acanthophis: a comprehensive plant hologenomics pipeline
Submitting author: @kdm9
Handling editor: @marcosvital (Active)
Reviewers: @bricoletc, @gbouras13, @abhishektiwari
Similarity score: 0.7247
MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis
Submitting author: @ParkvilleData
Handling editor: @jmschrei (Active)
Reviewers: @Ebedthan, @rjorton
Similarity score: 0.7067
nf-gwas-pipeline: A Nextflow Genome-Wide Association Study Pipeline
Submitting author: @ZeyuanSong
Handling editor: @lpantano (Active)
Reviewers: @preetida, @rspirgel
Similarity score: 0.6974
CheckQC: Quick quality control of Illumina sequencing runs
Submitting author: @johandahlberg
Handling editor: @pjotrp (Retired)
Reviewers: @brainstorm
Similarity score: 0.6879
RNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and ease
Submitting author: @serine
Handling editor: @pjotrp (Retired)
Reviewers: @andrewyatz
Similarity score: 0.6763
β οΈ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.
@editorialbot query scope
Submission flagged for editorial review.
@abhi18av thanks for providing those additional details. I have just flagged this submission for a scope review by our editorial board. This is because I need some help to determine if this work is in scope, and if the pipeline/workflow you present meets our substantial scholarly effort criterion.
The scope review should take about 2 weeks to complete.
Submitting author: !--author-handle-->@abhi18av<!--end-author-handle-- (Abhinav Sharma) Repository: https://github.com/wal-yan/target-methylseq-qc Branch with paper.md (empty if default branch): master Version: v2.0.0 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman
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