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Update hyphy samplesheets with control_file field
1 parent bda2f97 commit e1a38a7

11 files changed

Lines changed: 32 additions & 31 deletions

‎samplesheet/test_absrel_samplesheet.csv‎

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gene_name,alignment,tree,suite,tool
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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
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gene_name,alignment,tree,suite,tool,control_file
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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,

‎samplesheet/test_bgm_samplesheet.csv‎

Lines changed: 2 additions & 2 deletions
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gene_name,alignment,tree,suite,tool
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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
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gene_name,alignment,tree,suite,tool,control_file
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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,

‎samplesheet/test_busted_samplesheet.csv‎

Lines changed: 2 additions & 2 deletions
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gene_name,alignment,tree,suite,tool
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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
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gene_name,alignment,tree,suite,tool,control_file
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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,

‎samplesheet/test_fade_samplesheet.csv‎

Lines changed: 2 additions & 2 deletions
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gene_name,alignment,tree,suite,tool
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KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.faa,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,fade
1+
gene_name,alignment,tree,suite,tool,control_file
2+
KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.faa,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,fade,

‎samplesheet/test_fel_samplesheet.csv‎

Lines changed: 2 additions & 2 deletions
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gene_name,alignment,tree,suite,tool
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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
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gene_name,alignment,tree,suite,tool,control_file
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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,

‎samplesheet/test_fubar_samplesheet.csv‎

Lines changed: 2 additions & 2 deletions
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gene_name,alignment,tree,suite,tool
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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
1+
gene_name,alignment,tree,suite,tool,control_file
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,fubar,

‎samplesheet/test_gard_samplesheet.csv‎

Lines changed: 2 additions & 2 deletions
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gene_name,alignment,tree,suite,tool
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KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2_subset.fna,,hyphy,gard
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gene_name,alignment,tree,suite,tool,control_file
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KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2_subset.fna,,hyphy,gard,

‎samplesheet/test_meme_samplesheet.csv‎

Lines changed: 2 additions & 2 deletions
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gene_name,alignment,tree,suite,tool
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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
1+
gene_name,alignment,tree,suite,tool,control_file
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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,

‎samplesheet/test_relax_samplesheet.csv‎

Lines changed: 2 additions & 2 deletions
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gene_name,alignment,tree,suite,tool
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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
1+
gene_name,alignment,tree,suite,tool,control_file
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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,

‎samplesheet/test_samplesheet.csv‎

Lines changed: 12 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,12 @@
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gene_name,alignment,tree,suite,tool
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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
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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
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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
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KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.faa,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,fade
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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
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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
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KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2_subset.fna,,hyphy,gard
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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
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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
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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
1+
gene_name,alignment,tree,suite,tool,control_file
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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,
3+
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,
4+
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,
5+
KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.faa,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,fade,
6+
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,
7+
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,
8+
KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2_subset.fna,,hyphy,gard,
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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,
10+
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,
11+
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,
12+
Mx,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/Mx_aln.phy,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/Mx_unroot.tree,paml,codeml,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/codeml-sites.ctl

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