Mercurial > repos > dereeper > pangenome_explorer
comparison config.yaml @ 3:e42d30da7a74 draft
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author | dereeper |
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date | Thu, 30 May 2024 11:52:25 +0000 |
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comparison
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2:97e4e3e818b6 | 3:e42d30da7a74 |
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1 ######################################################### | |
2 # Complete one of the following input data | |
3 # Remove the other lines if not needed | |
4 ######################################################### | |
5 | |
6 # Genbank accessions of assembly accession (GCA, GCF) | |
7 ids: | |
8 - GCA_001042775.1 | |
9 - GCA_001021915.1 | |
10 - GCA_022406815.1 | |
11 | |
12 # Path of genbank files | |
13 input_genbanks: | |
14 - data/GCA_001518895.1.gb | |
15 - data/GCA_001746615.1.gb | |
16 - data/GCA_003382895.1.gb | |
17 | |
18 # Input genomes as fasta and annotation files in GFF format | |
19 # Only applied when using Orthofinder or PGGB workflows, starting from fasta and GFF | |
20 # To be used preferentially for eukaryotes | |
21 input_genomes: | |
22 "MSU7": | |
23 "fasta": "/share/banks/Oryza/sativa/japonica/MSU7/all.con" | |
24 "gff3": "/share/banks/Oryza/sativa/japonica/MSU7/all.gff3" | |
25 "name": "MSU7" | |
26 "kitaake": | |
27 "fasta": "/share/banks/Oryza/sativa/japonica/kitaake/Oryza_sativa_japonica_Kitaake.assembly.fna" | |
28 "gff3": "/share/banks/Oryza/sativa/japonica/kitaake/Oryza_sativa_japonica_Kitaake.gff3" | |
29 "name": "kitaake" | |
30 "nivara": | |
31 "fasta": "/share/banks/Oryza/nivara/Oryza_nivara.assembly.fna" | |
32 "gff3": "/share/banks/Oryza/nivara/Oryza_nivara.gff3" | |
33 "name": "nivara" |