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snakemake-workflows / dna-seq-varlociraptor

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
MIT License
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fix: update mark_duplicates to newest wrapper syntax #217

Closed user-tq closed 1 year ago

user-tq commented 1 year ago

fix mark_duplicates according to the new wrapper

dlaehnemann commented 1 year ago

Thanks for the fix! We'll merge this once the tests pass.

dlaehnemann commented 1 year ago

Could you run snakefmt on the changed file? That should get the Formatting test to pass.

dlaehnemann commented 1 year ago

And just to cross-reference: This closes #215 , once merged.

user-tq commented 1 year ago

你能在更改的文件上运行吗？这应该使格式测试通过。snakefmt

I am happy to make changes to pass the test, which may take some time because I am not proficient in these

user-tq commented 1 year ago

只是为了交叉引用：一旦合并，这将关闭#215。

fatal: Invalid symmetric difference expression master...bcbf71daeceea3c2cb98882189a3a4fd9060933d
2023-03-11 20:35:54 [WARN]   No files were found in the GITHUB_WORKSPACE:[/github/workspace] to lint!
2023-03-11 20:35:54 [ERROR]   Failed to switch back to branch!
2023-03-11 20:35:54 [FATAL]   [fatal: reference is not a tree: bcbf71daeceea3c2cb98882189a3a4fd9060933d]

According to the erro information I got, it seems that this is not because of the format, but because of the branch problem of github. I submitted this branch through the website. I really have no clue about this problem. I don't know if there is any way you can do it. Sorry, it's just a small problem but it took you so much time. image

dlaehnemann commented 1 year ago

Ah, I see. Sorry, is misinterpreted the error. I think I found a solution and introduced it on a fork of your fork... If you merge the pull request there, I think this should pass. The respective pull request can be found here: https://github.com/user-tq/dna-seq-varlociraptor/pull/1

dlaehnemann commented 1 year ago

Thanks again for investigating, reporting and fixing this!