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Fastp fixes #6642

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Fastp fixes #6642

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bernt-matthias
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FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • License permits unrestricted use (educational + commercial)
  • This PR adds a new tool or tool collection
  • This PR updates an existing tool or tool collection
  • This PR does something else (explain below)

@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
fix TestsCaseValidation linter errors
e9435f2
@bernt-matthias
fully qualify format_source references
8adf006
@bernt-matthias
remove unpaired paired input
b837c17 
much cleaner
@bernt-matthias
fix filter
1a3bc54
@bgruening
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Thanks @bernt-matthias! This also needs a bump.

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@bernt-matthias @bgruening