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Patch nf schema - include integer & string as type for sample #450

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merged 5 commits into from
Dec 12, 2024
Merged

Patch nf schema - include integer & string as type for sample #450

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e6b06c1
bump nf-schema & remove type for sample
Joon-Klaps Dec 12, 2024
681a3a5
allow both integer and string
Joon-Klaps Dec 12, 2024
88ca8af
update changelog
Joon-Klaps Dec 12, 2024
1e6d1ed
fix prettier
Joon-Klaps Dec 12, 2024
d382134
don't do freyja bootstrapping with nanopore
Joon-Klaps Dec 12, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -30,6 +30,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [[PR #439](https://github.com/nf-core/viralrecon/pull/439)] - Fix cardinality issue when using `--bowtie2_index`
- [[PR #435](https://github.com/nf-core/viralrecon/pull/435)] - Changed to a patched cutadapt from nf-core modules, added `skip_noninternal_primers` param to allow users to process primers inside the pipeline, and added `threeprime_adapters` to determine whether primers are 3' or 5' adapters.
- [[PR #446](https://github.com/nf-core/viralrecon/pull/446)] - Update nextclade & pangolin modules
- [[PR #450](https://github.com/nf-core/viralrecon/pull/450)] - Patch nf schema - include integer & string as type for sample

### Parameters

Expand Down Expand Up @@ -64,6 +65,7 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
| `multiqc` | 1.14 | 1.19 |
| `nextclade` | 2.12.0 | 3.8.2 |
| `pangolin` | 4.2 | 4.3 |
| `nf-schema` | | 2.2.1 |

> **NB:** Dependency has been **updated** if both old and new version information is present.
>
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2 changes: 1 addition & 1 deletion assets/schema_input.json
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Expand Up @@ -8,7 +8,7 @@
"type": "object",
"properties": {
"sample": {
"type": "string",
"type": ["string", "integer"],
"pattern": "^\\S+$",
"errorMessage": "Sample name must be provided and cannot contain spaces",
"meta": ["id"]
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4 changes: 3 additions & 1 deletion conf/test_nanopore.config
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Expand Up @@ -35,7 +35,9 @@ params {
primer_set_version = 3

// variant calling options
freyja_repeats = 10
freyja_repeats = 10
skip_freyja_boot = true


// Other parameters
artic_minion_medaka_model = 's3://ngi-igenomes/test-data/viralrecon/minion_test/r941_min_high_g360_model.hdf5'
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -313,7 +313,7 @@ manifest {

// Nextflow plugins
plugins {
id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
id 'nf-schema@2.2.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

validation {
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