Merge pull request #349 from nf-cmgg/dev

Release 1.13.5

Author: nvnieuwk

.nf-core.yml

@@ -41,4 +41,4 @@ template:
   skip_features:
     - fastqc
     - is_nfcore
-  version: 1.13.4
+  version: 1.13.5

CHANGELOG.md

@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.13.5
+
+- Set `outdir` type to `String` to avoid file existence checking
+
 ## v1.13.4
 
 - Fixes a small issue with the VEP config (`.split()` error) by replacing it with the `name` attribute.

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-cmgg/smallvariants/releases/tag/1.13.4" target="_blank">nf-cmgg/smallvariants</a> analysis pipeline.
+  This report has been generated by the <a href="https://github.com/nf-cmgg/smallvariants/releases/tag/1.13.5" target="_blank">nf-cmgg/smallvariants</a> analysis pipeline.
 report_section_order:
   "nf-cmgg-smallvariants-methods-description":
     order: -1000

main.nf

@@ -38,7 +38,7 @@ params {
     input: Path
 
     // The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
-    outdir: Path
+    outdir: String
 
     // Email address for completion summary.
     email: String?

nextflow.config

@@ -226,7 +226,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=26.04.0'
-    version         = '1.13.4'
+    version         = '1.13.5'
     doi             = ''
 }
 

ro-crate-metadata.json

@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2026-07-13T08:47:13+00:00",
+            "datePublished": "2026-07-22T12:51:01+00:00",
             "description": "# nf-cmgg/smallvariants\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-cmgg/smallvariants)\n[![GitHub Actions CI Status](https://github.com/nf-cmgg/smallvariants/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-cmgg/smallvariants/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-cmgg/smallvariants/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/smallvariants/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-cmgg/smallvariants)\n\n## Introduction\n\n**nf-cmgg/smallvariants** is a nextflow pipeline for calling and annotating small variants from short DNA reads for WES and WGS data.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nPlease have a look at the [documentation](https://nf-cmgg.github.io/smallvariants/latest/) on how to run the pipeline.\n\n## Development environment\n\nA [pixi](https://pixi.prefix.dev/latest/) development environment is available for this pipeline. Run the following command to install the environment:\n\n```\npixi install\n```\n\nThen run `pixi shell` to enter the environment and start developing.\n",
             "hasPart": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#02edf0b6-6333-43bb-be42-eae1d022add8"
+                    "@id": "#e6d7203f-a78f-4daa-a554-428a830bb448"
                 }
             ],
             "name": "nf-cmgg/smallvariants"
@@ -132,7 +132,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2026-07-13T10:47:13Z",
+            "dateModified": "2026-07-22T14:51:01Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -160,10 +160,10 @@
             },
             "url": [
                 "https://github.com/nf-cmgg/smallvariants",
-                "https://nf-co.re/nf-cmgg/smallvariants/1.13.4/"
+                "https://nf-co.re/nf-cmgg/smallvariants/1.13.5/"
             ],
             "version": [
-                "1.13.4"
+                "1.13.5"
             ]
         },
         {
@@ -179,11 +179,11 @@
             "version": "!>=26.04.0"
         },
         {
-            "@id": "#02edf0b6-6333-43bb-be42-eae1d022add8",
+            "@id": "#e6d7203f-a78f-4daa-a554-428a830bb448",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#a199ef34-c868-47f1-8c25-509e3dace0be"
+                    "@id": "#66262067-5e7f-452d-93e4-ca9008107954"
                 }
             ],
             "mainEntity": {
@@ -192,7 +192,7 @@
             "name": "Test suite for nf-cmgg/smallvariants"
         },
         {
-            "@id": "#a199ef34-c868-47f1-8c25-509e3dace0be",
+            "@id": "#66262067-5e7f-452d-93e4-ca9008107954",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-cmgg/smallvariants",
             "resource": "repos/nf-cmgg/smallvariants/actions/workflows/nf-test.yml",