nf-core / nf-core/fetchngs

Add ability to download more than 2 FastQ files via FTP and Aspera

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#260 3 comments 0 reactions 0 assignees View on GitHub

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enhancement
Dominant language
Nextflow
Stars
202
Forks
93
Avg merge
1d 18m
Merged PRs (30d)
15

Description

Description of feature

As raised in https://github.com/nf-core/fetchngs/pull/259#discussion_r1470946683 and https://github.com/nf-core/fetchngs/pull/259#discussion_r1470960788 we need to revisit why we restricted downloading a max of 2 FastQ files via FTP and Aspera.

I vaguely remember this was added because they may have been discrepancies in some files have 3 FastQ files but only 2 md5sum files which broke the pipeline. We need to find some examples of database ids that have 3 FastQ files and take a proper look to see if we can accommodate them in the pipeline.

If you do have more than 2 FastQ files e.g. single-cell data like in this issue https://github.com/nf-core/fetchngs/issues/144 then you should be able to retrieve these by using the --force_sratools_download parameter.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reviewing the linked discussion in pull request 259 and issue 144, then inspect the pipeline's restriction to two FastQ files for FTP and Aspera downloads. Find database IDs with three FastQ files and compare their FastQ and md5sum files. Done means the pipeline can accommodate valid cases with more than two FastQ files without breaking checksum handling.

Written by the indexing model from the issue text.

Assessment

Domain
data-engineering
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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