Add qualimap to pipeline

[lpantano]

Added qualimap to the main pipeline, with option to skip it, labeled as low-memory step. Updated the docs and readme mentioning the tools.

Related issue: #202

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md

[apeltzer]

Minor comments

[lpantano]

I forgot to add the qualimap version, and I realized that it doesn't have a way to do it without output with an error. get_software_versions will break if a tool exit with error?

[apeltzer]

Typically, you just add each tool that is in the pipeline to the get_software_versions process for the sake of completeness yes :-)

You can redirect the output of qualimap to a file in that process, e.g. also redirecting stderr to the same file which you can then parse in the scrape_software_versions.py script in /bin/. Redirecting can be done like this:

https://www.brianstorti.com/understanding-shell-script-idiom-redirect/

[lpantano]

Thanks. The || 1 made the trick to avoid the error in the process. But now the file is not parsed, for some reason is not in the final software_versions.csv, where is scrape_software_versions.py code?

[apeltzer]

Always in bin of the pipeline !

[lpantano]

ok! that was helpful. Now is part of the version file.

[apeltzer]

Looking good now 👍 Thanks a bunch!