BD rhapsody sequence analysis

[rcannood]

Description

• bd_rhapody_sequence_analysis: BD Rhapsody Sequence Analysis CWL pipeline (PR BD rhapsody sequence analysis #96).

Issue ticket number

Closes #xxxx

Checklist before requesting a review

• I have performed a self-review of my code

• Conforms to the Contributing guidelines

• Proposed changes are described in the CHANGELOG.md

• I have tested my code with viash ns test --parallel -q <name or namespace>

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Documentation
  • Bug fixes

[DriesSchaumont]

I would propose to also create an unpublished component for this, so that it it easier to run and manage the dependencies

[rcannood]

🙅 No thank you! It will never be used as part of a pipeline or a standalone component. The script uses just base tidyverse. And oh, one dynutils statement which probably has an equivalent function in the tidyverse.

[DriesSchaumont]

Ok, but in that case I would add a short README with perhaps the following:

• What the script does
• The dependencies required
• How to run the script

Just in case somebody wants to work on this in the future

[rcannood]

done!

[DriesSchaumont]

Suggested change

	template = (arg.get("info") or {}).get("template")
	template = (arg.get("info", {})).get("template")

[rcannood]

It's a pitfall but this doesn't work! Because info might be null which causes arg.get("info", {}) to return None.

[DriesSchaumont]

Ah, so if I understand correctly you get a TypeError when calling .get("template"). Could you add a small comment

[rcannood]

Added note. Sorry for the delay!

[DriesSchaumont]

Does the cwl pipeline create a log file by itself? Otherwise I would prefer to use check_output and write it ourself from stdout and stderr.

[rcannood]

Do you mean out = subprocess.check_output(cmd_pars).decode("utf-8") and then printing the stdout?

[DriesSchaumont]

Yes, printing it, or writing it to an output file.

[rcannood]

I want to view the output as it comes out of the process ^^

[DriesSchaumont]

Printing it is also fine. But right now, neither one of those is happening (because check_call is used). https://docs.python.org/3/library/subprocess.html#subprocess.check_call

Code needing to capture stdout or stderr should use [run()](https://docs.python.org/3/library/subprocess.html#subprocess.run) instead:

[rcannood]

I don't understand. subprocess.check_call does exactly what I want it to do.

>>> out = subprocess.check_call(["echo", "hi"])
hi

For sure, subprocess.run seems to do exactly the same:

>>> out = subprocess.run(["echo", "hi"], check=True)
hi

I guess I don't understand what the difference between the two variants is and why you'd like me to use subprocess.run over subprocess.check_call.

[DriesSchaumont]

Turns out that the pipeline already returns its own log in the output, so this has become a non-issue 👍

[DriesSchaumont]

Ok, but in that case I would add a short README with perhaps the following:

• What the script does
• The dependencies required
• How to run the script

Just in case somebody wants to work on this in the future

[DriesSchaumont]

Printing it is also fine. But right now, neither one of those is happening (because check_call is used). https://docs.python.org/3/library/subprocess.html#subprocess.check_call

Code needing to capture stdout or stderr should use [run()](https://docs.python.org/3/library/subprocess.html#subprocess.run) instead: