Add in path to all files in index directory to copy on Azure correctly.

[vsmalladi]

PR checklist

Closes #627

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[drpatelh]

Yo! Why doesn't the current behaviour of copying a directory work here? This would have been tested already on Azure?

[vsmalladi]

Never tested making the bwa index and saving them. I had just upload the index files already or just made them for the test.

[drpatelh]

Merging this in will need some thought because this will change the way we are dealing with indices in pipelines quite a bit and how they are defined by users. What error do you see when using the current behaviour on Azure?

[vsmalladi]

The error is that nextflow can't find the file to copy over.

[drpatelh]

But it should just be a directory no? This should then affect any directory defined as output on Azure?

[vsmalladi]

That would be my assumption, but i wonder if its just the way the directory contents are referred to. If you add directory/* vs just directory. I think this will require some more investigation.

[adamrtalbot]

Does type: dir help?

[vsmalladi]

@adamrtalbot can you take a look?

[adamrtalbot]

I'm still a bit confused, what happens? I've been using BWA on Azure quite a bit and never seen this error, could you provide some steps to reproduce it?

[vsmalladi]

@adamrtalbot might not be an issue anymore. Maybe we can hold off until it becomes an issue again.

[SPPearce]

Closing this until someone flags it as an issue again.

[FriederikeHanssen]

Someone flagged the index publishing here: https://github.com/nf-core/sarek/issues/1905