From e6b06c10985e0aad12e5efe3f61516a5739f1abd Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Thu, 12 Dec 2024 10:27:11 +0000 Subject: [PATCH 1/5] bump nf-schema & remove type for sample --- CHANGELOG.md | 1 + assets/schema_input.json | 2 +- nextflow.config | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index eb3990ba..cad9e65c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -64,6 +64,7 @@ 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. > diff --git a/assets/schema_input.json b/assets/schema_input.json index 55c9333c..dd699a1c 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -8,7 +8,7 @@ "type": "object", "properties": { "sample": { - "type": "string", + "pattern": "^\\S+$", "errorMessage": "Sample name must be provided and cannot contain spaces", "meta": ["id"] diff --git a/nextflow.config b/nextflow.config index e577ae62..48762495 100644 --- a/nextflow.config +++ b/nextflow.config @@ -313,7 +313,7 @@ manifest { // Nextflow plugins plugins { - id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.2.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { From 681a3a5275a6c77999ca984b131f40818d843222 Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Thu, 12 Dec 2024 10:32:18 +0000 Subject: [PATCH 2/5] allow both integer and string --- assets/schema_input.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index dd699a1c..1411f46c 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -8,7 +8,7 @@ "type": "object", "properties": { "sample": { - + "type": ["string", "integer"], "pattern": "^\\S+$", "errorMessage": "Sample name must be provided and cannot contain spaces", "meta": ["id"] From 88ca8af21cebbc0c2b9b694d9b771563d6dce652 Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Thu, 12 Dec 2024 10:46:02 +0000 Subject: [PATCH 3/5] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index cad9e65c..fb9fcc73 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 From 1e6d1eda7515c7631e7c0d086e62fa59c1da794a Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Thu, 12 Dec 2024 10:51:29 +0000 Subject: [PATCH 4/5] fix prettier --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fb9fcc73..f35e4d78 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,7 +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 +- [[PR #450](https://github.com/nf-core/viralrecon/pull/450)] - Patch nf schema - include integer & string as type for sample ### Parameters From d382134977644178573078bd960827a9c80ef7a6 Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Thu, 12 Dec 2024 11:40:14 +0000 Subject: [PATCH 5/5] don't do freyja bootstrapping with nanopore --- conf/test_nanopore.config | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/conf/test_nanopore.config b/conf/test_nanopore.config index 13009cee..72b44828 100644 --- a/conf/test_nanopore.config +++ b/conf/test_nanopore.config @@ -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'