From 33e898da2ecc40ab9e4e8fa1a66c4c8a6008ae2b Mon Sep 17 00:00:00 2001
From: Samuel Ortion <samuel@ortion.fr>
Date: Sat, 18 Jan 2025 15:53:11 +0100
Subject: [PATCH] Update KaKs workflow config

---
 workflow/KaKs/nextflow.config | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 workflow/KaKs/nextflow.config

diff --git a/workflow/KaKs/nextflow.config b/workflow/KaKs/nextflow.config
new file mode 100644
index 0000000..757f79e
--- /dev/null
+++ b/workflow/KaKs/nextflow.config
@@ -0,0 +1,26 @@
+params {
+    families = "${baseDir}/../../tmp/Glycine_max_Blastp_filtered_coverage30_identity30.mcl.tsv"
+    proteome = "${baseDir}/../../tmp/proteome_filtered.fa"
+    cds = "${baseDir}/../../../data/Glycine_max.Glycine_max_v2.1.cds.all.fa.gz"
+    species = "Glycine_max"
+    results = "results"
+}
+
+profiles {
+
+    conda {
+        conda.enabled = true
+
+        process {
+            withLabel: paml {
+                conda = "$baseDir/conda/paml.yaml"
+            }
+            withLabel: pal2nal {
+                conda = "$baseDir/conda/pal2nal.yaml"
+            }
+            withLabel: clustalw {
+                conda = "$baseDir/conda/clustalw.yaml"
+            }
+        }
+    }
+}