Update output paths to match spec

[edmundmiller]

s3://nf-core-references
species/source/build/patch/tool/tool_version/annotation

annotation/
databases/
indices/
sequences/

[maxulysse]

This is what we set up

aws s3 ls --recursive s3://nf-core-references/

2024-02-07 10:16:04          0 genomes/
2024-02-07 10:17:57          0 genomes/homo_sapiens/
2024-02-07 10:18:58          0 genomes/homo_sapiens/ensembl/
2024-02-07 10:20:52          0 genomes/homo_sapiens/ensembl/grch38/
2024-02-07 10:30:57          0 genomes/homo_sapiens/ensembl/grch38/111/
2024-02-07 10:34:26          0 genomes/homo_sapiens/ensembl/grch38/111/annotation/
2024-02-07 10:41:09          0 genomes/homo_sapiens/ensembl/grch38/111/annotation/genes/
2024-02-07 10:41:27          0 genomes/homo_sapiens/ensembl/grch38/111/annotation/smallrna/
2024-02-07 10:36:13          0 genomes/homo_sapiens/ensembl/grch38/111/databases/
2024-02-07 10:48:22          0 genomes/homo_sapiens/ensembl/grch38/111/databases/snpeff/
2024-02-07 10:48:03          0 genomes/homo_sapiens/ensembl/grch38/111/databases/vep/
2024-02-07 10:34:31          0 genomes/homo_sapiens/ensembl/grch38/111/indices/
2024-02-07 10:44:56          0 genomes/homo_sapiens/ensembl/grch38/111/indices/star/
2024-02-07 10:45:24          0 genomes/homo_sapiens/ensembl/grch38/111/indices/star/2.7.11b/
2024-02-07 10:35:14          0 genomes/homo_sapiens/ensembl/grch38/111/sequences/
2024-02-07 10:38:00          0 genomes/homo_sapiens/ensembl/grch38/111/sequences/chromosomes/
2024-02-07 10:40:02          0 genomes/homo_sapiens/ensembl/grch38/111/sequences/genome/