Extra : inside quotes of salmon_version in cmd_info.json file for salmon v1.5.2

[allyhawkins]

Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?
Alevin-fry

Describe the bug
A clear and concise description of what the bug is.
The new updates to the cmd_info.json file result in an extra : at the end of "salmon_version:" inside the quotes. This results in the json file being read in with the header of that entry being salmon_version: when it should be salmon_version.

Note that this was found when running salmon alevin in the --rad or --justAlign mode and we have not tested if this is also the case when running only salmon alevin.

To Reproduce
Steps and data to reproduce the behavior:
We ran alevin-fry v0.4.1 starting with salmon alevin using --rad on single-cell data in the salmon biocontainer and that led to the cmd_info.json file being output with the extra : on salmon_version.

The biocontainer that we used was: quay.io/biocontainers/salmon:1.5.2--h84f40af_0

Specifically, please provide at least the following information:

• Which version of salmon was used?
  1.5.2
• How was salmon installed (compiled, downloaded executable, through bioconda)?
  used the biocontainer
• Which reference (e.g. transcriptome) was used?
  used the splici index following the alevin-fry tutorial
• Which read files were used?
• Which which program options were used?

salmon alevin -l ISR --chromiumV3 --dumpFeatures --rad

Expected behavior
A clear and concise description of what you expected to happen.
We would expect that the extra : would not be included to be consistent with previous versions of salmon.

Screenshots
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Desktop (please complete the following information):

• OS: [e.g. Ubuntu Linux, OSX]
• Version [ If you are on OSX, the output of sw_vers. If you are on linux the output of uname -a and lsb_release -a]

Additional context
Add any other context about the problem here.

[rob-p]

Thanks for the super-detailed report, @allyhawkins. We'll fix this in the next point release.

[rob-p]

Hi @allyhawkins; this is now fixed in 1.6.0. Thanks again for the report!