Compress vcf when not compressed already

CHANGELOG.md

@@ -3,6 +3,22 @@
 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).
 
+## dev
+
+### Added
+
+- [72](https://github.com/nf-core/references/pull/72) - Compress vcf files when they are not already compressed
+
+### Changed
+
+### Fixed
+
+### Dependencies
+
+### Subworkflows
+
+### Deprecated
+
 ## [0.1](https://github.com/nf-core/references/releases/tag/0.1) - Tar Tarasque
 
 Initial pre-release of nf-core/references, created with the [nf-core](https://nf-co.re/) template.
@@ -60,6 +76,7 @@ Tar is a dark grey color ( #383838), and the Tarasque is a legendary dragon from
 - [64](https://github.com/nf-core/references/pull/64) - Improve documentation
 - [68](https://github.com/nf-core/references/pull/68) - Minor refactoring
 - [69](https://github.com/nf-core/references/pull/69) - Better comments
+- [70](https://github.com/nf-core/references/pull/70) - Prepare release 0.1
 
 ### Fixed
 

README.md

@@ -47,7 +47,7 @@ With an additional annotation file describing the genes (either GFF3 or GTF), it
 - STAR index
 - Transcript fasta (with RSEM)
 
-With a vcf file, it will tabix index it.
+With a vcf file, it will compress it, if it was not already compressed, and tabix index it.
 
 ## Assets
 

assets/schema_input.json

@@ -191,7 +191,7 @@
             "vcf": {
                 "meta": ["vcf"],
                 "type": "string",
-                "pattern": "^\\S+\\.vcf\\.gz$",
+                "pattern": "^\\S+\\.vcf(\\.gz)?$",
                 "errorMessage": "VCF file, cannot contain spaces"
             },
             "vcf_tbi": {

assets/test/default_extended.yml

@@ -25,3 +25,8 @@
   source_vcf: "GATK_BUNDLE"
   species: "Homo_sapiens"
   vcf: "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
+- genome: "GRCh38_MT"
+  source: "nf-core/references"
+  source_vcf: "genmod_compound"
+  species: "Homo_sapiens"
+  vcf: "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/vcf/genmod_compound.vcf"

modules.json

@@ -117,6 +117,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/star/genomegenerate/star-genomegenerate.diff"
                     },
+                    "tabix/bgziptabix": {
+                        "branch": "master",
+                        "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45",
+                        "installed_by": ["modules"]
+                    },
                     "tabix/tabix": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",