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Update schema #205

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merged 5 commits into from
Oct 28, 2024
Merged

Update schema #205

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ed0e422
change schema
luisas Oct 25, 2024
6b2271c
update usage
luisas Oct 25, 2024
be2bf18
fix
luisas Oct 25, 2024
bb1aa85
update changelog
luisas Oct 28, 2024
a006829
Update CHANGELOG.md
JoseEspinosa Oct 28, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -72,6 +72,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [[PR ##163](https://github.com/nf-core/proteinfold/pull/163)] - Fix full test CI.
- [[#150]](https://github.com/nf-core/proteinfold/issues/150)] - Add thanks to the AWS Open Data Sponsorship program in `README.md`.
- [[PR ##166](https://github.com/nf-core/proteinfold/pull/166)] - Create 2 different parameters for Colabfold and ESMfold number of recycles.
- [[PR ##205](https://github.com/nf-core/proteinfold/pull/205)] - Change input schema from `sequence,fasta` to `id,fasta`.

### Parameters

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4 changes: 2 additions & 2 deletions assets/schema_input.json
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Expand Up @@ -7,7 +7,7 @@
"items": {
"type": "object",
"properties": {
"sequence": {
"id": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Sequence name must be provided and cannot contain spaces",
Expand All @@ -21,6 +21,6 @@
"errorMessage": "Fasta file must be provided, cannot contain spaces and must have extension '.fa' or '.fasta'"
}
},
"required": ["sequence", "fasta"]
"required": ["id", "fasta"]
}
}
8 changes: 4 additions & 4 deletions docs/usage.md
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Expand Up @@ -28,10 +28,10 @@ T1026,https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testda

The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 2 columns to match those defined in the table below:

| Column | Description |
| ---------- | --------------------------------------------------------------------------------------------------- |
| `sequence` | Custom sequence name. Spaces in sequence names are automatically converted to underscores (`_`). |
| `fasta` | Full path to fasta file for the provided sequence. File has to have the extension ".fasta" or "fa". |
| Column | Description |
| ------- | --------------------------------------------------------------------------------------------------- |
| `id` | Custom sequence name. Spaces in sequence names are automatically converted to underscores (`_`). |
| `fasta` | Full path to fasta file for the provided sequence. File has to have the extension ".fasta" or "fa". |

An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.

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