nextflow-io / nextflow-io/nextflow

Add an option to the file method to check for md5sum

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#2,491 9 comments 0 reactions 1 assignee View on GitHub

@jordeu is already working on this.

Since Oct 16, 2023.

  • #5807 by @edmundmiller — closed without merging
good first issue
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Description

After discussion on the nf-core slack, we (@ewels, @mahesh-panchal) think that it would be useful to add a native option to the file method to check the integrity of the files that are staged.
Using the example shown in the documentation here, an option that might be named checksum should allow providing the hash in a similar manner to the code below:

pdb = file('http://files.rcsb.org/header/5FID.pdb', checksum: 'ba45addcc599af2ac71492f0f55da866')

The idea will be that the hash of the file is calculated either if the file is staged or if it is already present in the cage by a previous execution and that if the hash does not match the provided by the user an exception is raised, similarly to what happens when checkIfExists option is set to true and the file is not found in the system.

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