feat: enable output of unmapped reads

[kashyapchhatbar]

Description

Ability to save unmapped reads in fastq or fastq.gz formats using the --outReadsUnmapped Fastx option in STAR

QC

• I confirm that:

For all wrappers added by this PR,

• there is a test case which covers any introduced changes,
• input: and output: file paths in the resulting rule can be changed arbitrarily,
• either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
• rule names in the test case are in snake_case and somehow tell what the rule is about or match the tools purpose or name (e.g., map_reads for a step that maps reads),
• all environment.yaml specifications follow the respective best practices,
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
• all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
• stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
• temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to (see here; this also means that using any Python tempfile default behavior works),
• the meta.yaml contains a link to the documentation of the respective tool or command,
• Snakefiles pass the linting (snakemake --lint),
• Snakefiles are formatted with snakefmt,
• Python wrapper scripts are formatted with black.
• Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays).

[kashyapchhatbar]

Thanks for making it clearer. I had to change the code in the wrapper also, the test is failing. I will check locally and update it.

[kashyapchhatbar]

I have updated the files and all the tests are running and making sense. Hopefully, it is good to merge now.

[kashyapchhatbar]

While it is a nice attempt to convert the unmapped files to a list, it doesn't work out nicely downstream. The test fails because the shell function from snakemake doesn't deal with ints properly.

[kashyapchhatbar]

This will still not work because shell function converts everything to string and that's why you can't do the i+1 thing

[fgvieira]

Seems to be working now! Just reformat it...
Can you just make sure that it is running as it should? Maybe run it locally with -p and check if the gzip/cat commands are all correct.

Great work!

[kashyapchhatbar]

Thanks, I won't be able to check with -p command since it'll try to grab the old-version wrapper.py which won't have the out_unmapped command and will fail. I guess since the test/Snakefile is updated with unmapped files as output and if they are passing, it should be working.

Your pursuit to make unmapped as list is unwavering and it does make it very clean, thanks for review and great suggestions.