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Merged
mirpedrol merged 2 commits into from
Dec 1, 2025
Merged

Add ontologies to tcoffee/regressive and upp/align modules #9484

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8515780
add ontologies to tcoffee regressive
mirpedrol Dec 1, 2025
d71ee06
add ontologies to upp align
mirpedrol Dec 1, 2025
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20 changes: 13 additions & 7 deletions modules/nf-core/tcoffee/regressive/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,9 @@ input:
type: file
description: Input sequences in FASTA format
pattern: "*.{fa,fasta}"
ontologies: []
ontologies:
- edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
- edam: http://edamontology.org/format_1929 # FASTA
- - meta2:
type: map
description: |
Expand All @@ -40,7 +42,8 @@ input:
type: file
description: Input guide tree in Newick format
pattern: "*.{dnd}"
ontologies: []
ontologies:
- edam: http://edamontology.org/format_2006 # PHYLOGENETIC TREE
- - meta3:
type: map
description: |
Expand All @@ -50,14 +53,14 @@ input:
type: file
description: T_coffee template file that maps sequences to the accessory information
files to be used.
pattern: "*"
ontologies: []
ontologies:
- edam: http://edamontology.org/format_1476 # PDB
- accessory_information:
type: file
description: Accessory files to be used in the alignment. For example, it could
be protein structures or secondary structures.
pattern: "*"
ontologies: []
ontologies:
- edam: http://edamontology.org/format_1476 # PDB
- compress:
type: boolean
description: Flag representing whether the output MSA should be compressed. Set
Expand All @@ -74,7 +77,10 @@ output:
type: file
description: Alignment file in FASTA format. May be gzipped.
pattern: "*.aln{.gz,}"
ontologies: []
ontologies:
- edam: http://edamontology.org/format_2554 # ALIGNMENT FORMAT TXT
- edam: http://edamontology.org/format_1921 # ALIGNMENT FORMAT
- edam: http://edamontology.org/format_1984 # FASTA-ALN
versions:
- versions.yml:
type: file
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12 changes: 9 additions & 3 deletions modules/nf-core/upp/align/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,9 @@ input:
type: file
description: Input sequences in FASTA format
pattern: "*.{fa,fasta}"
ontologies: []
ontologies:
- edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
- edam: http://edamontology.org/format_1929 # FASTA
- - meta2:
type: map
description: |
Expand All @@ -35,7 +37,8 @@ input:
type: file
description: Input guide tree in Newick format
pattern: "*.{dnd}"
ontologies: []
ontologies:
- edam: http://edamontology.org/format_2006 # PHYLOGENETIC TREE
- compress:
type: boolean
description: Flag representing whether the output MSA should be compressed. Set
Expand All @@ -52,7 +55,10 @@ output:
description: Alignment file, in FASTA format. May be gzipped or uncompressed,
depending on if compress is set to true or false
pattern: "*.aln{.gz,}"
ontologies: []
ontologies:
- edam: http://edamontology.org/format_2554 # ALIGNMENT FORMAT TXT
- edam: http://edamontology.org/format_1921 # ALIGNMENT FORMAT
- edam: http://edamontology.org/format_1984 # FASTA-ALN
versions:
- versions.yml:
type: file
Expand Down
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