Propr propr #4817
Propr propr #4817
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out.matrix).match("Test propr/propr using default options") }, |
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Why only snapshotting the matrix?
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The FDR file is calculated based on a random sampling, so I don´t think we can snapshot.
Then the rds is the R object including the matrix, and the fdr, and more stuff that could be useful to run propr again if the user wants. So, same problem cannot be snapshot and have the same md5
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Can you use set.seed() to make the FDR reproducible? You're right on the rds of course
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That would require to change the package code and rebuild container and so on...
It is really a test that shuffles the input data and run multiple times the function used to create the matrix output, so I think if the matrix output is consistent, this step should not have problem too
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You need to check this file in some way I think.
One thing you could do is e.g. extract the last line of the file, and check that the first value matches a test value to a limited number of decimal places (hopefully the FDR is stable to a limited extent). You could adapt from https://nf-co.re/docs/contributing/tutorials/nf-test_assertions#file-contains-check
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@pinin4fjords now it should be fine. I added a way to fix the seed for fdr reproducibility
tests/config/pytest_modules.yml
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| adapterremovalfixprefix: | |||
| - modules/nf-core/adapterremovalfixprefix/** | |||
| - tests/modules/nf-core/adapterremovalfixprefix/** | |||
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Don't think you need to be changing this file- probably just something funny on your branch.
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Cuz it always give me merging conflicts with the master... what should I do then?
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Probably something funny in your git history. Try literally copying in the file from master in a new commit?
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out.matrix).match("Test propr/propr using default options - matrix") }, | ||
| { assert snapshot(process.out.versions).match("versions") } |
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hey there! fdr is an optional output actually. Here in the default test, I did not ask to compute fdr.
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Ahh, my bad, thanks for explanation
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out.matrix).match("Test propr/propr while running clr+pcor.bshrink explicitly - matrix")}, | ||
| { assert snapshot(process.out.fdr).match("Test propr/propr while running clr+pcor.bshrink explicitly - fdr")} |
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Conventionally, we have a version check in every test. But I won't insist.
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@pinin4fjords Thank you for the review! |
* modified affy/justrma to allow the user get the unlog data when --keep.log2 FALSE * after prettier * trailing whitespace * added final newline * fix issue * updated snapshot * corrected md5sum issues with inconsistent decimals * corrected round matrix method * . * copied pytest_modules.yml * . * updated container version and added reproducible test for fdr
* modified affy/justrma to allow the user get the unlog data when --keep.log2 FALSE * after prettier * trailing whitespace * added final newline * fix issue * updated snapshot * corrected md5sum issues with inconsistent decimals * corrected round matrix method * . * copied pytest_modules.yml * . * updated container version and added reproducible test for fdr
Add propr/propr module to perform compositional data analysis on rna-seq data
PR checklist
Closes #XXX
versions.ymlfile.labelPROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware