Merge pull request #1176 from GallVp/modules

Added gene models for actinidia_chinensis chr1
nf-core · May 28, 2024 · e72380e · e72380e
2 parents eb3b0b5 + ea31028
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diff --git a/README.md b/README.md
@@ -19,6 +19,7 @@ The `generic` folder contains generic files that currently cannot be associated
 
 The genomics folder contains subfolders for all organisms for which test data is available. At the moment, there are these organisms available in various places:
 
+- actinidia_chinensis
 - bacteroides_fragilis
 - candidatus_portiera_aleyrodidarum
 - deilephila_porcellus (mitochondrion)
@@ -646,6 +647,9 @@ The folder is structured in the following way: Any nonspecific-pangenome file is
     - genome
       - chr1
         - genome.fasta.gz: Chr1 bases 1 to 7 million acquired from [Zenodo/10.5281/zenodo.5717386](https://zenodo.org/doi/10.5281/zenodo.5717386)
+        - genome.gff3.gz: Gene models predicted by BRAKER3 pipeline on genome.fasta.gz and formatted by GenomeTools `gt gff3 -tidy -retainids` tool
+        - genome.gtf.gz: genome.gff3.gz converted to GTF format with `agat_convert_sp_gff2gtf.pl` script
+        - genome.hints.gff.gz: Hints file produced by BRAKER3 pipeline
 
 ### pangenomics
 

diff --git a/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.gff3.gz b/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.gff3.gz
diff --git a/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.gtf.gz b/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.gtf.gz
diff --git a/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.hints.gff.gz b/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.hints.gff.gz