Bug #13247: Check CGF CWL takes up too much local disk space - Lightning - Arvados

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Bug #13247

closed

Check CGF CWL takes up too much local disk space

Added by Abram Connelly about 6 years ago. Updated about 6 years ago.

Status:

Closed

Priority:

Normal

Assigned To:

Abram Connelly

Target version:

Story points:

Description

When running the check-cgf, the current script makes a local copy of the gVCF file to index it if the index isn't located in the collection.

A workaround can be done by just processing 5-10 at a time but the whole point of batching was to load the large SGLF file only once for a large group.

Subtasks 1 (0 open — 1 closed)

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Updated by Abram Connelly about 6 years ago

One possible solution is to create a symbolic link to the underlying gVCF file instead of copying it over wholesale and then index the symbolic link.

I'm not sure there's a way to provide the index file separately from the source file so that's why we need to copy to a local directory (or create a symbolic link) and index there.

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