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Tidy up 'skipping tools' and 'alignment' options #1090

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adamrtalbot opened this issue Oct 10, 2023 · 1 comment
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Tidy up 'skipping tools' and 'alignment' options #1090

adamrtalbot opened this issue Oct 10, 2023 · 1 comment
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enhancement
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3.13.0

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@adamrtalbot
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Description of feature

In the parameters, we have some skipping flags in 'Alignment options' and some in the 'Process skipping options'. I feel like these should be resolved into a simpler interface. Either they should all go in skipping, or each skip should go with the relevant options. Ideally somewhere near the top for easier discovery.

Aim is to make it more accessible for new users.

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adamrtalbot added a commit to adamrtalbot/rnaseq that referenced this issue Oct 10, 2023
@adamrtalbot
Reorganise arguments for clearer syntax
b6f2d69 
Changes:
 - Grouped arguments into sections based on _what they do_
 - Reordered slightly to go in chronological order of the pipeline and set up
 - I think it's clearer for a new user

Fixes nf-core#1090
@adamrtalbot adamrtalbot mentioned this issue Oct 10, 2023
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@drpatelh
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Fixed in #1091

@drpatelh drpatelh added this to the 3.12.1 milestone Oct 15, 2023
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