From bee2a1211b8f9454b2764489ff78dbebaa60c0e1 Mon Sep 17 00:00:00 2001
From: Guppy <30294975+glstott@users.noreply.github.com>
Date: Tue, 21 May 2024 12:59:59 -0400
Subject: [PATCH] Update generateLphyScripts process to use ReadFasta instead
 of readNexus #7

---
 nextflow/simulation.nf | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/nextflow/simulation.nf b/nextflow/simulation.nf
index 73d0dab..a49eca3 100644
--- a/nextflow/simulation.nf
+++ b/nextflow/simulation.nf
@@ -151,7 +151,7 @@ process generateLphyScripts {
     data {
     // Specify options for reading the date information from file
     options = {ageDirection="forward", ageRegex=".*_.*_(\d*\.\d+|\d+\.\d*)$"};
-    D = readNexus(file="!{seqs}", options=options);
+    D = ReadFasta(file="!{seqs}", options=options);
 
     // Retrieve number of sites in alignment and taxa names
     L = D.nchar();
@@ -234,4 +234,12 @@ workflow{
     simulateBiasedSampling(simulateSequences.out, seed, prefix, p)
 
     // Subsequence dataset using SRS, stratified, and LCUBE
+    n = 10
+    metadata = "metadata.csv"
+    runLCUBE(simulateSequences.out, seed, n, prefix, metadata)
+    runSimpleSampling(simulateSequences.out, seed, n, prefix, metadata)
+
+    // Generate LPHY scripts for BEAST 2
+    generateLphyScripts(simulateSequences.out, seed, prefix)
+    runBEAST(simulateSequences.out, seed, prefix)
 }