nextflow-io/nextflow

Add an option to the file method to check for md5sum

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#2,491 opened on Dec 14, 2021

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 (9 comments) (0 reactions) (1 assignee)Groovy (784 forks)batch import
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.

Contributor guide

Research direction
Find the File class implementation in Nextflow, locate where staging occurs, and add a checksum option that validates MD5 hash against provided value. Raise an exception if mismatch.
Tech stack
groovy
Domain
backenddevopstooling
Issue type
Feature
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
3
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-2 days
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
GroovyNextflow
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
50