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Rename phyloanalysis to genephylomodeller #1902

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Merged
jfy133 merged 10 commits into from
Mar 12, 2026
Merged

Rename phyloanalysis to genephylomodeller #1902

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6c269e1
Added test data for phyloanalysis
ninaxiong11 Mar 11, 2026
d79dbdf
Merge pull request #1896 from ninaxiong11/phyloanalysis
ninaxiong11 Mar 11, 2026
46bf204
Update filepaths in samplesheet
ninaxiong11 Mar 11, 2026
9012096
Merge pull request #1897 from ninaxiong11/phyloanalysis
ninaxiong11 Mar 11, 2026
e770b58
Add FEL test samplesheet
rrari84 Mar 11, 2026
18a6424
Add SLAC test
ninaxiong11 Mar 11, 2026
bffabd6
Merge pull request #1899 from ninaxiong11/phyloanalysis
ninaxiong11 Mar 11, 2026
62db922
Add FEL to main test samplesheet
rrari84 Mar 11, 2026
b235a59
Update test_samplesheet.csv
ninaxiong11 Mar 12, 2026
6221aea
Merge pull request #1901 from ninaxiong11/phyloanalysis
ninaxiong11 Mar 12, 2026
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18 changes: 18 additions & 0 deletions data/ksr2.fna
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1 change: 1 addition & 0 deletions data/ksr2.tree
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(((((((HUM, PAN), GOR), PON), GIB), (MAC, BAB)), MAR), BUS);
1 change: 1 addition & 0 deletions data/ksr2_labeled_test_reference.tree
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(((((((HUM{test}, PAN{reference}), GOR), PON), GIB), (MAC, BAB)), MAR), BUS);
2 changes: 2 additions & 0 deletions samplesheet/test_absrel_samplesheet.csv
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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
2 changes: 2 additions & 0 deletions samplesheet/test_busted_samplesheet.csv
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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
2 changes: 2 additions & 0 deletions samplesheet/test_fel_samplesheet.csv
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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
2 changes: 2 additions & 0 deletions samplesheet/test_meme_samplesheet.csv
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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
2 changes: 2 additions & 0 deletions samplesheet/test_relax_samplesheet.csv
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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
7 changes: 7 additions & 0 deletions samplesheet/test_samplesheet.csv
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@@ -0,0 +1,7 @@
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,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
2 changes: 2 additions & 0 deletions samplesheet/test_slac_samplesheet.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +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
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