annotate config.yaml @ 12:38c66e401040 draft

Uploaded
author dereeper
date Thu, 30 May 2024 19:59:16 +0000
parents e42d30da7a74
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
1 #########################################################
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
2 # Complete one of the following input data
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
3 # Remove the other lines if not needed
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
4 #########################################################
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
5
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
6 # Genbank accessions of assembly accession (GCA, GCF)
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
7 ids:
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
8 - GCA_001042775.1
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
9 - GCA_001021915.1
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
10 - GCA_022406815.1
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
11
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
12 # Path of genbank files
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
13 input_genbanks:
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
14 - data/GCA_001518895.1.gb
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
15 - data/GCA_001746615.1.gb
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
16 - data/GCA_003382895.1.gb
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
17
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
18 # Input genomes as fasta and annotation files in GFF format
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
19 # Only applied when using Orthofinder or PGGB workflows, starting from fasta and GFF
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
20 # To be used preferentially for eukaryotes
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
21 input_genomes:
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
22 "MSU7":
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
23 "fasta": "/share/banks/Oryza/sativa/japonica/MSU7/all.con"
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
24 "gff3": "/share/banks/Oryza/sativa/japonica/MSU7/all.gff3"
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
25 "name": "MSU7"
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
26 "kitaake":
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
27 "fasta": "/share/banks/Oryza/sativa/japonica/kitaake/Oryza_sativa_japonica_Kitaake.assembly.fna"
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
28 "gff3": "/share/banks/Oryza/sativa/japonica/kitaake/Oryza_sativa_japonica_Kitaake.gff3"
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
29 "name": "kitaake"
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
30 "nivara":
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
31 "fasta": "/share/banks/Oryza/nivara/Oryza_nivara.assembly.fna"
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
32 "gff3": "/share/banks/Oryza/nivara/Oryza_nivara.gff3"
e42d30da7a74 Uploaded
dereeper
parents:
diff changeset
33 "name": "nivara"