20364489032
57%

Ran 19 Dec 2025 08:54AM UTC

Jobs 1

Files 91

Run time 397min

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Committed 19 Dec 2025 08:35AM UTC coverage: 75.07% (-0.02%) from 75.09%

Build # 20364489032

Build Type

push

github

Committed by

web-flow

Commit Message

556 (#575)

* fix #556 - avoid glue of empty attribute to the ID in GFF3 parsing
* fix #250  url_escaped. Keep escaped characters in in the output
* add url_encode_out parameter to decode GFF3 url escaped chraracter (is it useful?)
* homogenize usage output: output|out|o (remove outfile)
* homogenize POD (type describe in the options line: -o, --out, --output <file>)
* Add --force parameter to overwrite output if already exists 
* Add nextflow pipeline to assess performance 
* homogenize usage of boolean: --bolean_option activate the option. In order to deactivate a boolean (e.g. in agat.pl because other scripts suggest only boolean activation) use the --no-bolean_option syntax.

Run Details

13126 of 17485 relevant lines covered (75.07%)

2539.46 hits per line

Uncovered Existing Lines

Lines	Coverage	∆	File
2	98.06	0.0%	/home/runner/work/AGAT/AGAT/bin/agat_convert_genscan2gff.pl
2	97.14	-0.04%	/home/runner/work/AGAT/AGAT/bin/agat_sp_flag_short_introns.pl
3	80.0	0.0%	/home/runner/work/AGAT/AGAT/bin/agat
5	89.87	-0.13%	/home/runner/work/AGAT/AGAT/bin/agat_sp_flag_short_introns_ebi.pl
5	91.38	-0.15%	/home/runner/work/AGAT/AGAT/bin/agat_sq_manage_IDs.pl
8	80.0	0.0%	/home/runner/work/AGAT/AGAT/lib/AGAT/Utilities.pm
10	78.95	0.0%	/home/runner/work/AGAT/AGAT/bin/agat_convert_embl2gff.pl
14	86.98	0.0%	/home/runner/work/AGAT/AGAT/bin/agat_convert_bed2gff.pl
29	30.14	0.0%	/home/runner/work/AGAT/AGAT/bin/agat_sp_filter_by_mrnaBlastValue.pl
47	72.67	0.0%	/home/runner/work/AGAT/AGAT/bin/agat_sp_kraken_assess_liftover.pl
54	20.87	-0.68%	/home/runner/work/AGAT/AGAT/bin/agat_sp_fix_small_exon_from_extremities.pl
58	60.08	-0.16%	/home/runner/work/AGAT/AGAT/bin/agat_sp_fix_features_locations_duplicated.pl
73	69.39	-0.79%	/home/runner/work/AGAT/AGAT/lib/AGAT/AGAT.pm
76	50.57	-0.03%	/home/runner/work/AGAT/AGAT/lib/AGAT/Config.pm
101	61.93	0.56%	/home/runner/work/AGAT/AGAT/lib/AGAT/BioperlGFF.pm
121	54.52	0.22%	/home/runner/work/AGAT/AGAT/lib/AGAT/OmniscientO.pm

Jobs

ID	Job ID	Ran	Files	Coverage
1	20364489032.1	19 Dec 2025 08:54AM UTC	91	75.07	GitHub Action Run

NBISweden / AGAT / 20364489032
57%

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NBISweden / AGAT / 20364489032 57%

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NBISweden / AGAT / 20364489032
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