Alfa qc

Added rules for generating ALFA output, for each sample separately and for all samples together. Closes #18 (closed).

changed milestone to %v0.1.0 release

Since all rules rely on singularity we also need to add a container for ALFA and remove the conda dependecy. @kanitz If you have time, can you please build a container for ALFA? Otherwise I will do it later today.

I run the ALFA rules already with a singularity image. I guess I forgot to remove --use-conda in the tests.

Then we could also remove env_alfa.yaml

Yes, please. So I can close #88 (closed)

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See comment below regarding conda

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Please move this import on the beginning of the Snakefile, where all imports are performed

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mentioned in issue #88 (closed)

added Blocked label

We need to fix #88 (closed) first

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• 54656531 - removed conda dependence, moved import statement.

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@burri0000: Do you maybe want to rebase your branch and group some of your commits together logically? This is a huge branch and probably warrants more than a simple squash into one commit. But you will definitely not get the whole 45 either

So what I would recommend you is to locally create a new branch from this one, then do an interactive rebase (see for example here) on the master branch and merge your commits together into a couple of sensible informative commits (e.g., one for ALFA rule & wiring, one for ALFA test, dunno what else...). Then you can push that new branch (with a rewritten history basically) and file a merge request for that one instead of this.

If you create a new branch locally from the latest commit of this branch, you don't have to worry about messing anything up. All is safe here in the remote. If you mess up rewriting history, go back to this branch, no problem. ;-)

I will try to do this, but I never did this before. So I will go through the example and create a local branch as you described.

It's a good exercise. You'll find it won't be that hard. If the tutorial isn't clear, find another one, I just picked the first I found. Just search for interactive rebase

I managed to do it. I basically skipped all commits previous of the STAR RPM integration and then squashed some commits together. The new branch is called alfa

And before you do that, two minor things:

• I think you should probably remove the following dir from version control: tests/test_alfa/results. Or perhaps I am missing a point here? Is there some need to keep these files? If not, it might be best might be to also simplify the cleanup () function in your tests/test_alfa/test.sh so that it says rm -rfv results/ instead of 4 different calls to remove specific files from the results. If yes, could you please explain what you need them for?
• To be consistent with other tests, it might be better to place your input files in tests/input_files. Perhaps other people/rules have use for them as well later on.

I need the .bam & .bam.bai in the results/ directory as input, because I want to test STAR RPM and ALFA alone. That is why I remove all files generated by these rules but not my input. I would therefore like to keep it that way.

The input_files I can actually move to tests/input_files. But then I need to rename config.yaml and samples.tsv, correct?

Okay, got it. Forget about the results then. As for the input files that would probably be good, yes. And yes, you'd need to change the paths in these files, but should be easy enough

Btw, this looks really nice. Hell of a job! :)

closed