[JOSS] @mberacochea's feedback for the JOSS submission

[mberacochea]

Hello,

This ticket is to gather my review comments for the JOSS submission (https://github.com/openjournals/joss-reviews/issues/5397).

Functionality

Installation

• [x] #36
  • Added a comment -> https://github.com/jhayer/baargin/issues/36
• [x] #41

Functionality

TODO: I will run the pipeline once the installation instructions have been amended.

Documentation

A statement of need

• [x] #27
  • README greatly improved -> https://github.com/jhayer/baargin/pull/22

    Installation instructions

• [x] #37
  • README greatly improved, with better installation instructions -> https://github.com/jhayer/baargin/pull/22

    Automated tests

• [x] #48

  Community guidelines

• [x] #28
  • Added -> https://github.com/jhayer/baargin/pull/25/files

Software paper

State of field

• [x] #30
  • Added -> https://github.com/jhayer/baargin/commit/dd2e39fac8a4214a12fbe4432ccf4fd1d836e583

    Quality of writing

• [x] Line 61: instead of " The contigs are taxonomically assigned using Kraken2.." -> "Taxonomic assignment of the contigs is performed using Kraken2..."
• [x] Line 67: instead of "A quality check of the assembly is achieved by Quast..." -> "A quality check of the assembly is conducted using Quast...".
• [x] Line 73: "The contigs are then submitted to a plasmid identification with PlasmidFinder" -> "The contigs are subsequently submitted to plasmid identification using PlasmidFinder."
• [x] Line 98: " that belong the expected taxon" -> "that belong to the expected taxon"
• [x] Nextflow is written as "NextFlow" and "Nextflow" throughout the text.

Other comments

Overall the nextflow code is correct and easy to follow. I would recommend to split the pipeline into several sub-workflows, that helps with the readability.

• [x] #31
  • Fixed -> https://github.com/jhayer/baargin/pull/33
• [x] #38
  • Fixed https://github.com/jhayer/baargin/pull/39
• [x] #32
  • Fixed -> https://github.com/jhayer/baargin/pull/33
• [x] #42
  • Fixed -> https://github.com/jhayer/baargin/pull/43
• [x] #45
  • Fixed -> https://github.com/jhayer/baargin/pull/46]

[mberacochea]

OK, my first review is completed now. @jhayer please, if you disagree with any of my comments please let me know :).

[jhayer]

Thank you for your review @mberacochea. We will go through all the comments and fix everything by the end of next week.

[jhayer]

Hi @mberacochea, We now finally went through all your comments and fixed everything. Thank you for your valuable input.

[mberacochea]

Hi @jhayer ... apologies it took me so long to reply. I'm running the test dataset now, I'll post an update as soon as I have the results of that.

[mberacochea]

Well.. I was able to run the test data set. I think this PR can be closed :)