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Add agat sp compare two annotations #127

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Add agat sp compare two annotations #127

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d5fcc60
add help
Leila011 Aug 7, 2024
14fff01
add config
Leila011 Aug 7, 2024
9274bd6
add run script
Leila011 Aug 7, 2024
8b7b2fa
add test data & expected output + script to fetch them
Leila011 Aug 7, 2024
a1b45ad
config: remove required tag for a boolean type
Leila011 Aug 7, 2024
5c91b02
config: update keywords
Leila011 Aug 7, 2024
4d098c1
fix config
Leila011 Aug 7, 2024
c2212de
config: replace `-output` by `output_dir`
Leila011 Aug 7, 2024
96318fe
add test
Leila011 Aug 7, 2024
eba7eca
add extra test data & expected outputs
Leila011 Aug 7, 2024
5e62c75
DEBUG: check if output_dir is set if not stop
Leila011 Aug 7, 2024
7ced2ee
Merge main into add-agat_sp_compare_two_annotations
rcannood Aug 13, 2024
ca67df9
add set -eo pipefail to test and script files
Leila011 Aug 19, 2024
a10f6d2
create temporary directory and clean up on exit
Leila011 Aug 19, 2024
d4e0718
update config: add keywords, add requirements, fix --output_dir type,…
Leila011 Aug 19, 2024
d435a85
update changelog
Leila011 Aug 19, 2024
a4b3c20
Merge branch 'main' into add-agat_sp_compare_two_annotations
Leila011 Aug 19, 2024
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config: update keywords
@Leila011
Leila011 committed Aug 7, 2024

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Learn about vigilant mode
commit 5c91b02ca3ac2bff14449fa41e5d7673f0ee2417
2 changes: 1 addition & 1 deletion src/agat/agat_sp_compare_two_annotations/config.vsh.yaml
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Original file line number Diff line number Diff line change
@@ -21,7 +21,7 @@ description: |
The script output a folder containing a report of number of different
cases as well as a file per case type listing per line the gene
feature's ID involved in each case.
keywords: [gene annotations, GTF conversion]
keywords: [gene annotations]
links:
homepage: https://github.com/NBISweden/AGAT
documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_compare_two_annotations.html