Adding module for cram-size command of samtools

[limrp]

A new module for the cram-size command of the samtools tool has been added.

[nvnieuwk]

Very good job already! Here are some comments to make this module adhere to the guidelines set up by nf-core. Feel free to ping me if you have any questions

[nvnieuwk]

Hi some tests are still failing, can you fix these before I do a final review? Also it's easier to get reviews when you have one module per PR (don't worry about it for now, just some advice for the future :wink:)

[limrp]

Hi some tests are still failing, can you fix these before I do a final review? Also it's easier to get reviews when you have one module per PR (don't worry about it for now, just some advice for the future wink)

Thank you for checking! I'll review the test that are failing :smiley: Sorry for the 2 modules in one PR. I'll be more careful in the future :smiling_face_with_tear: :smiley_cat:

[limrp]

Tests for plasflow are still failing if you fixed those I'll give you a ✔️ :p

Hi @nvnieuwk ! The only tests that are failing are the ones related to Plasflow from Conda. There is no issue with Plasflow from Docker and Singularity. There is also no problem with Samtools' cramsize.

I attempted to fix Plasflow's recipe in the Bioconda repository. I needed to specify the required Python version (3.5) for Plasflow to function.

Here is the link: https://github.com/bioconda/bioconda-recipes/pull/42697

However, I was given the following message:

DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality. ERROR: tensorflow-0.10.0rc0-cp35-cp35m-linux_x86_64.whl is not a supported wheel on this platform.

It seems that it will not be possible to make Plasflow work with conda because conda will not support Python 3.5 soon. But everything else works fine. Do you think that in a case like this is it possible to accept the PR?

[nvnieuwk]

Can you add the tool to be excluded from the conda tests in .github/workflows/test.yml? You'll see it in the pytest clause. This way conda won't be tested (this should only be used for tools that absolutely don't work with conda though). After that all tests should pass and you'll be ready to go. Thanks for all the effort in trying to fix it

[limrp]

Can you add the tool to be excluded from the conda tests in .github/workflows/test.yml? You'll see it in the pytest clause. This way conda won't be tested (this should only be used for tools that absolutely don't work with conda though). After that all tests should pass and you'll be ready to go. Thanks for all the effort in trying to fix it

Hi @nvnieuwk ! Thanks for your reply!

Are you refering to this section of the test.yml file?

Should I add Plasflow to that list?

Thanks a lot for all you advice!

[nvnieuwk]

Yes, that's it!

[SPPearce]

I'm going to close this for now, as there seems to be no response from @limrp . I moved the samtools cramsize module out into a separate PR and merged that, but I can't immediately see a way to get plasflow to work properly