Detach vcfanno from the --annotate parameter (#108)

* split annotation subwf to make vcfanno runnable without --annotate

* update tests

* prettier

* update changelog

* make sure new tests do run

.github/workflows/ci.yml

@@ -47,7 +47,8 @@ jobs:
           - "bam_variant_calling_qdnaseq"
           - "bam_variant_calling_smoove"
           - "bam_variant_calling_wisecondorx"
-          - "vcf_annotate_vep_annotsv_vcfanno"
+          - "vcf_annotate_vep_annotsv"
+          - "vcf_annotate_vcfanno"
           - "vcf_concat_bcftools"
           - "vcf_merge_callers_jasmine"
           - "vcf_merge_family_jasmine"

CHANGELOG.md

@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 5. Fixed language server errors
 6. Removed the old output publishing code and used the new workflow output definitions instead
 7. Bumped the minimal nextflow version to 24.10.0
+8. VCFanno will now run when `--vcfanno_toml` has been given and `--annotate` has not been given. You still need to supply `--annotate` to get the full annotation, but this can be used check for common variants without having to perform full annotation.
 
 ### `Fixed`
 

conf/modules.config

@@ -197,12 +197,12 @@ process {
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     */
 
-    withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:BCFTOOLS_FILTER\$" {
+    withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV:BCFTOOLS_FILTER\$" {
         ext.prefix = {"${meta.id}.filter"}
         ext.args = "-e 'GT=\"ref\"' --output-type z"
     }
 
-    withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:ANNOTSV_ANNOTSV\$" {
+    withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV:ANNOTSV_ANNOTSV\$" {
         ext.args = {[
             "-SVminSize 20",
             "-vcf 1",
@@ -211,12 +211,12 @@ process {
         ext.prefix = {"${meta.id}.annot"}
     }
 
-    withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:BCFTOOLS_CONCAT\$" {
+    withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV:BCFTOOLS_CONCAT\$" {
         ext.prefix = "annotsv_annotated"
         ext.args = "--output-type z --naive-force"
     }
 
-    withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:ENSEMBLVEP_VEP\$" {
+    withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV:ENSEMBLVEP_VEP\$" {
         ext.prefix = {"${meta.id}.vep"}
         ext.args = {[
             // specify we use VCF files
@@ -240,17 +240,14 @@ process {
         ].join(' ').trim()}
     }
 
-    withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:VCFANNO\$" {
+    withName: "^.*VCF_ANNOTATE_VCFANNO:VCFANNO\$" {
+        ext.prefix = {"${meta.id}.${meta.variant_type}.vcfanno"}
         ext.args = "-permissive-overlap -ends"
     }
 
-    withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:TABIX_ANNOTATED\$" {
-        ext.prefix = { "${meta.id}.${meta.variant_type}.annotated" }
-    }
-
-    withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:BCFTOOLS_FILTER_COMMON\$" {
-        ext.prefix = {"${meta.id}.${meta.variant_type}.annotated"}
-        ext.args = "${params.annotations_filter} --output-type z"
+    withName: "^.*VCF_ANNOTATE_VCFANNO:BCFTOOLS_FILTER\$" {
+        ext.prefix = {"${meta.id}.${meta.variant_type}.filtered"}
+        ext.args = "${params.annotations_filter} --output-type z --write-index=tbi"
     }
 
     /*

modules.json

@@ -28,9 +28,8 @@
                     },
                     "bcftools/filter": {
                         "branch": "master",
-                        "git_sha": "a3893076a76e91b3ff152faddf872f00778fb224",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/bcftools/filter/bcftools-filter.diff"
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "installed_by": ["modules"]
                     },
                     "bcftools/sort": {
                         "branch": "master",
@@ -152,8 +151,9 @@
                     },
                     "vcfanno": {
                         "branch": "master",
-                        "git_sha": "b558cd24f8751dcda51f957391f5f9cb83e28586",
-                        "installed_by": ["modules"]
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/vcfanno/vcfanno.diff"
                     },
                     "wisecondorx/convert": {
                         "branch": "master",