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Add subread featurecounts #11

Merged
merged 29 commits into from
Jan 31, 2024
Merged

Add subread featurecounts #11

merged 29 commits into from
Jan 31, 2024

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sainirmayi
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@sainirmayi sainirmayi commented Jan 29, 2024 •
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Description

Add featurecounts component

Issue ticket number

Closes #xxxx

Checklist before requesting a review

  • I have performed a self-review of my code

  • Conforms to the Contributing guidelines

  • Proposed changes are described in the CHANGELOG.md

  • I have tested my code with viash ns test --parallel -q <name or namespace>

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Documentation
    • Bug fixes

@sainirmayi sainirmayi marked this pull request as ready for review January 29, 2024 16:33
@sainirmayi sainirmayi requested a review from rcannood January 29, 2024 16:33
rcannood
rcannood requested changes Jan 30, 2024
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@rcannood rcannood left a comment

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Thanks for creating this PR! ☺️

I didn't quite make it through the whole PR yet, but here are already some minor comments.

CHANGELOG.md Outdated Show resolved Hide resolved
src/featurecounts/config.vsh.yaml Outdated Show resolved Hide resolved
src/featurecounts/config.vsh.yaml Outdated Show resolved Hide resolved
src/featurecounts/script.sh Outdated Show resolved Hide resolved
rcannood
rcannood requested changes Jan 31, 2024
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@rcannood rcannood left a comment

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Didn't fully make it through the whole PR yet

src/featurecounts/config.vsh.yaml Outdated Show resolved Hide resolved
src/featurecounts/config.vsh.yaml Outdated Show resolved Hide resolved
src/featurecounts/config.vsh.yaml Show resolved Hide resolved
src/featurecounts/config.vsh.yaml Outdated Show resolved Hide resolved
src/featurecounts/config.vsh.yaml Outdated Show resolved Hide resolved
src/featurecounts/config.vsh.yaml Outdated Show resolved Hide resolved
src/featurecounts/script.sh Outdated Show resolved Hide resolved
src/featurecounts/script.sh Outdated Show resolved Hide resolved
src/featurecounts/script.sh Show resolved Hide resolved
sainirmayi and others added 13 commits January 31, 2024 09:12
@sainirmayi @rcannood
Update output arguments
53c72e7 
Co-authored-by: Robrecht Cannoodt <[email protected]>
@sainirmayi @rcannood
remove tmpdir argument
14fc14c 
Co-authored-by: Robrecht Cannoodt <[email protected]>
@sainirmayi @rcannood
use $meta_tmp_dir
aedb01d 
Co-authored-by: Robrecht Cannoodt <[email protected]>
@sainirmayi @rcannood
add quotes
0812ec9 
Co-authored-by: Robrecht Cannoodt <[email protected]>
@sainirmayi
rename r_path to results_path
09b1a3b
@sainirmayi
modified arguments
af58534
@sainirmayi
fix incorrect argument in description
829fa49
@sainirmayi
fix --output_counts argument
0b5a1d4
@sainirmayi @rcannood
use multiple_sep
2cbf8aa 
Co-authored-by: Robrecht Cannoodt <[email protected]>
@sainirmayi @rcannood
Update src/featurecounts/config.vsh.yaml
3dbc8c4 
Co-authored-by: Robrecht Cannoodt <[email protected]>
@sainirmayi
use example instead of default
09433d2
@rcannood
minor edits
dc3e8b9
@rcannood
rename files to verify that parameters work as intended
69c2b45
rcannood
rcannood approved these changes Jan 31, 2024
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LGTM!

@rcannood rcannood merged commit 3e0926c into main Jan 31, 2024
6 checks passed
@rcannood rcannood deleted the add_subread_featurecounts branch January 31, 2024 11:40
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Thanks Nirmayi!

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@rcannood rcannood rcannood approved these changes

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@sainirmayi @rcannood