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Update cutadapt v.3.4 #3704

Merged
merged 20 commits into from
Jun 2, 2021
Merged

Update cutadapt v.3.4 #3704

merged 20 commits into from
Jun 2, 2021

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gallardoalba
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@gallardoalba gallardoalba commented Jun 1, 2021 •
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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)

This PR updates cutadapt to version 3.4. It includes the following modifications:

  • Include option --cut: info
  • Include option --rename: info
  • Include option --action: info
  • Include option --revcomp: info
  • Include the possibility of setting minimum and maximum length in R2 in paired reads: info
  • Remove the options --prefix and --suffix, since are considered outdated: info
  • Update the --pair-filteroption (include first): info
  • Include the Disallow internal adaptor ocurrences option: info
  • Include the option --max-expected-errors: info
  • Reorganize output options section.

@gallardoalba gallardoalba marked this pull request as ready for review June 1, 2021 15:13
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#2585

bgruening
bgruening approved these changes Jun 1, 2021
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bgruening
bgruening reviewed Jun 1, 2021
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@bgruening bgruening left a comment

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Very nice, final comment. Thanks for the bunch of tests.

@bgruening bgruening enabled auto-merge (squash) June 2, 2021 22:14
@bgruening bgruening merged commit b26a2d9 into galaxyproject:master Jun 2, 2021
@gallardoalba gallardoalba deleted the update_cutadapt branch June 2, 2021 22:43
bernt-matthias added a commit to bernt-matthias/tools-iuc that referenced this pull request Nov 22, 2021
@bernt-matthias
add missing arguments to command
4c208a0 
--strip-suffix seems absent from the beginning
--discard-cassava was apparently forgotten in galaxyproject#3704

xref galaxyproject#4095
bernt-matthias added a commit to bernt-matthias/tools-iuc that referenced this pull request Nov 22, 2021
@bernt-matthias
add missing arguments to command
540beea 
--strip-suffix seems absent from the beginning
--discard-cassava was apparently forgotten in galaxyproject#3704

xref galaxyproject#4095
bernt-matthias added a commit to bernt-matthias/tools-iuc that referenced this pull request Nov 23, 2021
@bernt-matthias
add missing arguments to command
7ccb4d4 
--strip-suffix seems absent from the beginning
--discard-cassava was apparently forgotten in galaxyproject#3704

xref galaxyproject#4095
bgruening pushed a commit that referenced this pull request Nov 27, 2021
@bernt-matthias
cutadapt: add missing arguments and remove unsued test params (#4195)
9ec830a 
* cutadapt: remove absent read_modification

this was once the select of a conditional which was removed in
9a3d1b1

* same for output_filtering

* add missing arguments to command

--strip-suffix seems absent from the beginning
--discard-cassava was apparently forgotten in #3704

xref #4095
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@bgruening bgruening bgruening approved these changes

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@gallardoalba @bgruening