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docs: update README.md
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thomas-bailly authored Sep 26, 2024
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Expand Up @@ -51,6 +51,8 @@ other_db:
- faa: "/home/user/other.faa" # amino acid sequences in fasta format
- fna: "/home/user/other.fna" # nucleic acid sequences in fasta format
strain_library: "/home/user/strain_library.tsv"
date:
- trembl: "2024_07_28"
candidate_selection:
- strain_library
- order # strain available in the ATCC or DSM collection
Expand All @@ -66,6 +68,8 @@ All the `name_db` key correspond to a database, the `dmnd` format is required to

The `strain_library` key just give the path of the strain_library.

The `date` key is used to indicate a publication or update date for a database. This key is optional; without it, the file creation date is written to the summary.out file.

The `candidate_selection` key list the priority order for the selection. In the above case, the sequences in organism/strain find in the strain_library have priority on organism only in external collection. The `other` can be used if you have access on the sequences inside the `other_db`.

The `slurm`, `parallel` and `module` key are optionnal.
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