Merge pull request #1925 from ninaxiong11/genephylomodeler

ninaxiong11 · web-flow · commit e24a4bd7e839 · 2026-03-13T12:30:37.000-04:00
Update FADE and RELAX samplesheets, rename labeled tree
diff --git a/data/ksr2_labeled.tree b/data/ksr2_labeled.tree
diff --git a/samplesheet/test_fade_samplesheet.csv b/samplesheet/test_fade_samplesheet.csv
@@ -0,0 +1,2 @@
+gene_name,alignment,tree,suite,tool
+KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,fade
diff --git a/samplesheet/test_relax_samplesheet.csv b/samplesheet/test_relax_samplesheet.csv
@@ -1,2 +1,2 @@
 gene_name,alignment,tree,suite,tool
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2_labeled_test_reference.tree,hyphy,relax
+KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2_labeled.tree,hyphy,relax
diff --git a/samplesheet/test_samplesheet.csv b/samplesheet/test_samplesheet.csv
@@ -2,6 +2,7 @@ gene_name,alignment,tree,suite,tool
 KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,absrel
 KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,bgm
 KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,busted
+KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,fade
 KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,fubar
 KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,fel
 KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2_subset.fna,,hyphy,gard

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+gene_name,alignment,tree,suite,tool`
	`2`	`+KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,fade`
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`gene_name,alignment,tree,suite,tool`
`2`		`-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2_labeled_test_reference.tree,hyphy,relax`
	`2`	`+KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2_labeled.tree,hyphy,relax`