diff PanExplorer_workflow/config.yaml @ 1:032f6b3806a3 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PanExplorer_workflow/config.yaml	Thu May 30 11:16:08 2024 +0000
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+#########################################################
+# Complete one of the following input data
+# Remove the other lines if not needed
+#########################################################
+
+# Genbank accessions of assembly accession (GCA, GCF)
+ids:
+  - GCA_001042775.1
+  - GCA_001021915.1
+  - GCA_022406815.1
+
+# Path of genbank files
+input_genbanks:
+  - data/GCA_001518895.1.gb
+  - data/GCA_001746615.1.gb
+  - data/GCA_003382895.1.gb
+
+# Input genomes as fasta and annotation files in GFF format
+# Only applied when using Orthofinder or PGGB workflows, starting from fasta and GFF
+# To be used preferentially for eukaryotes
+input_genomes:
+  "MSU7":
+    "fasta": "/share/banks/Oryza/sativa/japonica/MSU7/all.con"
+    "gff3": "/share/banks/Oryza/sativa/japonica/MSU7/all.gff3"
+    "name": "MSU7"
+  "kitaake":
+    "fasta": "/share/banks/Oryza/sativa/japonica/kitaake/Oryza_sativa_japonica_Kitaake.assembly.fna"
+    "gff3": "/share/banks/Oryza/sativa/japonica/kitaake/Oryza_sativa_japonica_Kitaake.gff3"
+    "name": "kitaake"
+  "nivara":
+    "fasta": "/share/banks/Oryza/nivara/Oryza_nivara.assembly.fna"
+    "gff3": "/share/banks/Oryza/nivara/Oryza_nivara.gff3"
+    "name": "nivara"