fix: wrong stub output files

[matq007]

PR checklist

StarSolo module was generating incorrect test files. The stub now matches the output wildcards.

[SPPearce]

Hi @matq007,
Are you able to address #5863 while you are updating this module?
And this module could also do with swapping to nf-test rather than the pytest as well.

[matq007]

Hi @matq007, Are you able to address #5863 while you are updating this module? And this module could also do with swapping to nf-test rather than the pytest as well.

Sure, I can fix the whitelist. Can you point me to a direction about the nf-test? I am not familiar with it.

[mashehu]

Hi @matq007, Are you able to address #5863 while you are updating this module? And this module could also do with swapping to nf-test rather than the pytest as well.

Sure, I can fix the whitelist. Can you point me to a direction about the nf-test? I am not familiar with it.

https://nf-co.re/docs/tutorials/tests_and_test_data/nf-test_writing_tests but nf-core modules create --migrate-pytest should get you already a long way

[matq007]

╭───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── nf-test output ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                                                                                                                                           │
│ 🚀 nf-test 0.9.0                                                                                                                                                                                                                                                                                          │
│ https://www.nf-test.com                                                                                                                                                                                                                                                                                   │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr                                                                                                                                                                                                                                                      │
│                                                                                                                                                                                                                                                                                                           │
│ Load .nf-test/plugins/nft-bam/0.3.0/nft-bam-0.3.0.jar                                                                                                                                                                                                                                                     │
│ Warning: Module /Users/fdb589/GitHub/matq007/modules/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test: Dependency '/Users/fdb589/GitHub/matq007/modules/modules/nf-core/ltrretriever/ltrretriever/tests/../../../gunzip/main' not found.                                                      │
│ Warning: Module /Users/fdb589/GitHub/matq007/modules/modules/nf-core/ltrfinder/tests/main.nf.test: Dependency '/Users/fdb589/GitHub/matq007/modules/modules/nf-core/ltrfinder/tests/../../gunzip/main' not found.                                                                                         │
│                                                                                                                                                                                                                                                                                                           │
│ Test Process STAR_STARSOLO                                                                                                                                                                                                                                                                                │
│                                                                                                                                                                                                                                                                                                           │
│   Test [6c67d245] 'homo_sapiens - CB_UMI_Simple' PASSED (17.699s)                                                                                                                                                                                                                                         │
│   Test [d209817d] 'homo_sapiens - CB_UMI_Simple - stub' PASSED (5.373s)                                                                                                                                                                                                                                   │
│                                                                                                                                                                                                                                                                                                           │
│                                                                                                                                                                                                                                                                                                           │
│ SUCCESS: Executed 2 tests in 23.166s                                                                                                                                                                                                                                                                      │
│                                                                                                                                                                                                                                                                                                           │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
INFO     All tests passed!

Ok, the stuff is working for me locally, soo can we merge?

[SPPearce]

Hmm,
I'm not quite sure what is going on.
Opening on gitpod, we get a very consistent md5sum of 84d031c3083ae44cfa1984733b4875b7, with the content of the file:

Number of Reads,10000
Reads With Valid Barcodes,1
Sequencing Saturation,0.111111
Q30 Bases in CB+UMI,-nan
Q30 Bases in RNA read,0.951199
Reads Mapped to Genome: Unique+Multiple,0.0089
Reads Mapped to Genome: Unique,0.0047
Reads Mapped to Gene: Unique+Multiple Gene,NoMulti
Reads Mapped to Gene: Unique Gene,0.0009
Estimated Number of Cells,8
Unique Reads in Cells Mapped to Gene,9
Fraction of Unique Reads in Cells,1
Mean Reads per Cell,1
Median Reads per Cell,1
UMIs in Cells,8
Mean UMI per Cell,1
Median UMI per Cell,1
Mean Gene per Cell,1
Median Gene per Cell,1
Total Gene Detected,2

But you seem to be getting a different md5sum that is consistent for you? No obvious reason that this file would vary, no timestamps or file paths.
I've just pushed this md5sum, will see what the tests do, but would be interested to see what is different.

[SPPearce]

So that seems consistent on here/gitpod, what does the Summary.csv file look like for you locally?

[matq007]

So that seems consistent on here/gitpod, what does the Summary.csv file look like for you locally?

For me the summary is "Summary.csv:md5,8b43bfcfcfdfb48d0cd70e78429d0311"

[SPPearce]

So that seems consistent on here/gitpod, what does the Summary.csv file look like for you locally?

For me the summary is "Summary.csv:md5,8b43bfcfcfdfb48d0cd70e78429d0311"

Can you find the file itself inside the .nf-test/tests/ folder; when you run the test it gives you the hash of the folder where the files are being made.

[matq007]

I have two hashes 6c67d245768281b8b832913e3b7505e and d209817de1f4e6d6dc9b1887c94db9fc