NBISweden / pipelines-nextflow

A set of workflows written in Nextflow for Genome Annotation.

GNU General Public License v3.0

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Update AGAT to version 0.4.0 #42

Closed Juke34 closed 4 years ago

Juke34 commented 4 years ago

AGAT can be updated. For each pipeline we need to change the version in:

label_agat.yml
software_packages.config

For pipeline using the script agat_sp_split_by_level2_feature.pl it must be replaced by agat_sp_separate_by_record_type.pl. (name changed in version > 0.2.3)

I don't know if any pipeline use agat_sp_gxf_to_gff3.pl but is has been removed in new AGAT version (version > 0.2.3). It successor is agat_convert_sp_gxf2gxf.pl.

royfrancis commented 4 years ago

agat version updated to 0.4.0
agat_sp_split_by_level2_feature.pl replaced with agat_sp_feature_by_record_type.pl
no instances of agat_sp_gxf_to_gff3.pl found. Changes are on branch agat_0.4.0

NBISweden / pipelines-nextflow

Update AGAT to version 0.4.0 #42

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