feat: remove hacky INDEX

[maxulysse]

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[maxulysse]

ok, so first version f524d06 is what I would have preferred to do, and pass the path around.
second version 6316357 is I think a good compromise and require very little changes from the .tar.gz extractions process

[edmundmiller]

I love it! The only thing is how does this look in the work directory? Are all the index files in the root? Just wondering.

[maxulysse]

I love it! The only thing is how does this look in the work directory? Are all the index files in the root? Just wondering.

yes all files in the root folder, it how I use to do it in sarek before

[FriederikeHanssen]

How does it work with multiple bwa indices, so like for bwa and bwamem2?

I love it! The only thing is how does this look in the work directory? Are all the index files in the root? Just wondering.

[maxulysse]

How does it work with multiple bwa indices, so like for bwa and bwamem2?

I love it! The only thing is how does this look in the work directory? Are all the index files in the root? Just wondering.

Not sure I understood your question there

[drpatelh]

Hi Guys. Let's maybe discuss and vote for this on #modules before merging because this will have implications for other modules requiring a typical alignment index and will also mean we need to update the igenomes.config for all pipelines that use it.

Be great if you can summarise the advantages and disadvantages compared to the current method in #modules please @maxulysse ?

[FriederikeHanssen]

How does it work with multiple bwa indices, so like for bwa and bwamem2?

I love it! The only thing is how does this look in the work directory? Are all the index files in the root? Just wondering.

Not sure I understood your question there

Nevermind me, I half-way remembered this thread but didn't open it. Now I see that there is a long dicussion there. Will read through it there and comment

[maxulysse]

@mahesh-panchal any idea why the nf-core linting is failing?

[mahesh-panchal]

Looks like a parsing issue. I'll have a look.

[mahesh-panchal]

These lines need an update it seems:
https://github.com/nf-core/tools/blob/e563811adb292b07ec933a52611e937ce9ef5481/nf_core/modules/lint/main_nf.py#L55-L68
to account for the when. The linter thinks it's still in the output block.

[mahesh-panchal]

Updated linter in nf-core/tools#1397, but not sure what to do here.