Change phyloanalysis to genephylomodeler

ninaxiong11 · ninaxiong11 · commit 81f96aa05dea · 2026-03-12T11:23:07.000-04:00
diff --git a/samplesheet/test_absrel_samplesheet.csv b/samplesheet/test_absrel_samplesheet.csv
@@ -1,2 +1,2 @@
 gene_name,alignment,tree,suite,tool
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/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,absrel
diff --git a/samplesheet/test_bgm_samplesheet.csv b/samplesheet/test_bgm_samplesheet.csv
@@ -1,2 +1,2 @@
 gene_name,alignment,tree,suite,tool
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/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,absrel
diff --git a/samplesheet/test_busted_samplesheet.csv b/samplesheet/test_busted_samplesheet.csv
@@ -1,2 +1,2 @@
 gene_name,alignment,tree,suite,tool
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/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,busted
diff --git a/samplesheet/test_fel_samplesheet.csv b/samplesheet/test_fel_samplesheet.csv
@@ -1,2 +1,2 @@
 gene_name,alignment,tree,suite,tool                                                                    
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.tree,hyphy,fel
+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
diff --git a/samplesheet/test_meme_samplesheet.csv b/samplesheet/test_meme_samplesheet.csv
@@ -1,2 +1,2 @@
 gene_name,alignment,tree,suite,tool
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.tree,hyphy,meme
+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,meme
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/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/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_test_reference.tree,hyphy,relax
diff --git a/samplesheet/test_samplesheet.csv b/samplesheet/test_samplesheet.csv
@@ -1,8 +1,8 @@
 gene_name,alignment,tree,suite,tool
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.tree,hyphy,absrel
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.tree,hyphy,bgm
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.tree,hyphy,busted
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.tree,hyphy,fel 
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.tree,hyphy,meme
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2_labeled_test_reference.tree,hyphy,relax
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.tree,hyphy,slac
+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,fel 
+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,meme
+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.tree,hyphy,slac
diff --git a/samplesheet/test_slac_samplesheet.csv b/samplesheet/test_slac_samplesheet.csv
@@ -1,2 +1,2 @@
 gene_name,alignment,tree,suite,tool
-KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.tree,hyphy,slac
+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,slac

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/phyloanalysis/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phyloanalysis/data/ksr2.tree,hyphy,absrel`
	`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,absrel`