Fastp - Format_source to ensure WF usability and remove non-sanger input formats #6499
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RZ9082
changed the title
mvdbeek
reviewed
Oct 30, 2024
mvdbeek
reviewed
Oct 30, 2024
| @@ -379,10 +335,10 @@ $read_mod_options.base_correction_options.correction | |||
| </inputs> | |||
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| <outputs> | |||
| <data name="out1" format="auto" label="${tool.name} on ${on_string}: Read 1 output"> | |||
| <data name="out1" format_source="in1" label="${tool.name} on ${on_string}: Read 1 output"> | |||
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Does fastp compress the output if the input is compressed ?
I would assume all output is uncompressed ?
Suggested change
| <data name="out1" format_source="in1" label="${tool.name} on ${on_string}: Read 1 output"> | |
| <data name="out1" format="fastqsanger" label="${tool.name} on ${on_string}: Read 1 output"> |
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The tool itself produces a compressed output if the output name has the ext .gz regardless whether the input is compressed or not.
Actually i had it this way at the beginning, but changed to format_source to be able to connect the output to fastqsanger.gz inputs..
Co-authored-by: Marius van den Beek <[email protected]>
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If there any other suggestions, please let me know. |
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Fixes #6560 |
mvdbeek
approved these changes
Nov 15, 2024
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FOR CONTRIBUTOR:
format_sourceto ensure WF usability. However 'paired' and 'paired_collection' useformat_source="in1"orformat_source="in2"which is not affecting functionality, but it is still wrong!('paired_collection' should useformat_source="paired_input['forward']"orformat_source="paired_input['reverse']"). I still didn't figure out how to solve that rather than creating distinct outputs for each 'paired' and 'paired_collection, Any Ideas, before I do this?@mvdbeek, @wm75 Could you review this please?