galaxyproject / galaxyproject/tools-iuc

File extension causes error when extracting reads from SRA archive in current history

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Description

The following line directly store the file name as `acc`.
https://github.com/galaxyproject/tools-iuc/blob/86211daa63a6f39524df8759364795b782324303/tools/sra-tools/fasterq_dump.xml#L14

This works fine when the uploaded SRA file has no extension aka '.sra'. However, with extension the following line would fail at capturing the output files. Because `fasterq-dump` tends to only include the sra id in its output files and only generates files like `SRR000000_1.fastq` and `SRR000000_2.fastq`.

https://github.com/galaxyproject/tools-iuc/blob/86211daa63a6f39524df8759364795b782324303/tools/sra-tools/fasterq_dump.xml#L45-L46

Maybe the upstream code could remove the file extension for `acc`, so the symlink down here won't have the '.sra' (tried to tweak the code by myself but ended up getting strange errors)
https://github.com/galaxyproject/tools-iuc/blob/86211daa63a6f39524df8759364795b782324303/tools/sra-tools/fasterq_dump.xml#L15

Contributor guide

Open the contributing guide

Research direction

Open tools/sra-tools/fasterq_dump.xml at lines 14-15 and 45-46, then reproduce the extraction with an uploaded .sra file. Compare the archive name with the fasterq-dump outputs SRR000000_1.fastq and SRR000000_2.fastq; done means the wrapper captures those files when the input has an extension.

Written by the indexing model from the issue text.

Assessment

Tech stack
xml
Domain
tooling
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Clearly specified
Newbie friendliness
52/100

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