Fix pipeline not running without --vep_cache

.github/workflows/ci_master.yml

@@ -18,9 +18,6 @@ on:
       - synchronize
     branches:
       - master
-  pull_request_target:
-    branches:
-      - master
 
 env:
   NXF_ANSI_LOG: false

.nf-core.yml

@@ -1,4 +1,4 @@
-bump_version: null
+bump_version:
 lint:
   files_exist:
     - CITATIONS.md
@@ -28,7 +28,7 @@ lint:
     - manifest.name
     - manifest.homePage
 nf_core_version: 3.0.2
-org_path: null
+org_path:
 repository_type: pipeline
 template:
   author: Felix Lenner
@@ -39,5 +39,5 @@ template:
   org: genomic-medicine-sweden
   outdir: .
   skip_features: []
-  version: 0.4.0dev
-update: null
+  version: 0.4.1dev
+update:

CHANGELOG.md

@@ -3,6 +3,13 @@
 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).
 
+## 0.4.1 - [2025-02-17]
+
+### `Fixed`
+
+- [#553](https://github.com/genomic-medicine-sweden/nallo/pull/553) - Fixed pipeline always requiring `--vep_cache` to run, and clarified documentation
+- [#553](https://github.com/genomic-medicine-sweden/nallo/pull/553) - Fixed `process.shell` in `nextflow.config` causing CI runners to fail
+
 ## 0.4.0 - [2025-01-15]
 
 ### `Added`

assets/multiqc_config.yml

@@ -1,6 +1,6 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/nallo/releases/tag/0.4.0" target="_blank">genomic-medicine-sweden/nallo</a>
-  analysis pipeline.
+  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/nallo/releases/tag/0.4.1"
+  target="_blank">genomic-medicine-sweden/nallo</a> analysis pipeline.
 report_section_order:
   "genomic-medicine-sweden-nallo-methods-description":
     order: -1000

docs/usage.md

@@ -276,9 +276,12 @@ Turned off with `--skip_rank_variants`.
 
 This subworkflow relies on the alignment subworkflow, and requires the following additional files:
 
-| Parameter                        | Description                                                           |
-| -------------------------------- | --------------------------------------------------------------------- |
-| `svdb_sv_databases` <sup>1</sup> | Csv file with databases (VCFs) used for structural variant annotation |
+| Parameter                        | Description                                                                                                                                                                                                                                                                                                                                        |
+| -------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `svdb_sv_databases` <sup>1</sup> | Csv file with databases (VCFs) used for structural variant annotation                                                                                                                                                                                                                                                                              |
+| `vep_cache`                      | VEP cache matching your reference genome, either as a `.tar.gz` archive or path to a directory (e.g. [homo_sapiens_vep_110_GRCh38.tar.gz](https://ftp.ensembl.org/pub/release-110/variation/vep/homo_sapiens_vep_110_GRCh38.tar.gz))                                                                                                               |
+| `vep_plugin_files` <sup>2</sup>  | A csv file with VEP plugin files, pLI and LoFtool are required. Example provided below.                                                                                                                                                                                                                                                            |
+| `variant_consequences_svs`       | A list of SO terms listed in the order of severity from most severe to lease severe for annotating SVs. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/variant_consequences_v2.txt). You can learn more about these terms [here](https://ensembl.org/info/genome/variation/prediction/predicted_data.html) |
 
 <sup>1</sup> Example file for input with `--svdb_sv_databases`:
 
@@ -289,6 +292,17 @@ https://github.com/genomic-medicine-sweden/test-datasets/raw/b9ff54b59cdd39df5b6
 
 These databases could for example come from [CoLoRSdb](https://zenodo.org/records/13145123).
 
+<sup>2</sup> Example file for input with `--vep_plugin_files`
+
+```
+vep_files
+https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/spliceai_21_scores_raw_indel_-v1.3-.vcf.gz.tbi
+https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/spliceai_21_scores_raw_indel_-v1.3-.vcf.gz
+https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/spliceai_21_scores_raw_snv_-v1.3-.vcf.gz.tbi
+https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/pLI_values.txt
+https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/LoFtool_scores.txt
+```
+
 Turned off with `--skip_sv_annotation`.
 
 ### Rank SVs

modules.json

@@ -13,7 +13,7 @@
                     },
                     "bcftools/concat": {
                         "branch": "master",
-                        "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "bcftools/index": {