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fastp assigns incorrect datatypes to ouput files with enabled read merging #6606

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igormakunin2 opened this issue Dec 3, 2024 · 0 comments
Open

fastp assigns incorrect datatypes to ouput files with enabled read merging #6606

igormakunin2 opened this issue Dec 3, 2024 · 0 comments

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@igormakunin2
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I came across an issue with fastp in paired end mode, when inputs are GZipped fastq files. No problem with the default settings, but when Merge forward and reverse reads is set to Yes, the output files with reads are in plain text FASTQ format, while datatype is fatsqsanger.gz. I tried couple versions of the tool, got the same outcome. Here is my history in Galaxy Australia:
https://usegalaxy.org.au/u/igor/h/fastptest
bernt-matthias added a commit to bernt-matthias/tools-iuc that referenced this issue Dec 16, 2024
@bernt-matthias
for output types and produce paired output for paired input
8b54dcf 
fixes galaxyproject#6606

fastp seems to decide on the compression of the output by file
extension. So we need to write to temporary files and move to the
tool outputs at the end for `merged*`, `unmerged*`, and `unpaired*`
outputs.
@bernt-matthias bernt-matthias mentioned this issue Dec 16, 2024
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