nf-core/deepvariant

Add CRAM support

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#26 opened on Feb 20, 2020

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feature-requestgood first issue

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Description

Currently, the pipeline uses "*.bam" to find input files. We have, for a while now, switched to CRAM since the space savings are significant (50%). Any chance that the pipeline could be updated to natively support cram (DV does, as far as I know)?

Contributor guide

Research direction
Investigate how the pipeline currently discovers BAM files and modify it to also handle CRAM files. Note that CRAM requires a reference genome for decompression, so check how to provide it in the pipeline configuration.
Tech stack
None
Domain
backend
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.
Half day
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
GitNextflow
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
65