replace local subworkflow with nf-core version - vcf_annotate_ensemblvep

CHANGELOG.md

@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [#859](https://github.com/nf-core/sarek/pull/859) - Back to dev
+- [#860](https://github.com/nf-core/sarek/pull/860) - replace local subworkflow with nf-core version - vcf_annotate_snpeff
+- [#865](https://github.com/nf-core/sarek/pull/865) - replace local subworkflow with nf-core version - vcf_annotate_ensemblvep
 
 ### Fixed
 

modules.json

@@ -12,7 +12,8 @@
                     },
                     "bcftools/mpileup": {
                         "branch": "master",
-                        "git_sha": "6301e29d77e7ec7ce98b55b8a361b316a9a91bfe"
+                        "git_sha": "6301e29d77e7ec7ce98b55b8a361b316a9a91bfe",
+                        "installed_by": ["modules"]
                     },
                     "bcftools/sort": {
                         "branch": "master",
@@ -119,7 +120,7 @@
                     "ensemblvep": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules", "vcf_annotate_ensemblvep"]
                     },
                     "fastp": {
                         "branch": "master",
@@ -386,7 +387,7 @@
                     "tabix/bgziptabix": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": ["modules", "vcf_annotate_snpeff"]
+                        "installed_by": ["modules", "vcf_annotate_snpeff", "vcf_annotate_ensemblvep"]
                     },
                     "tabix/tabix": {
                         "branch": "master",
@@ -417,6 +418,11 @@
             },
             "subworkflows": {
                 "nf-core": {
+                    "vcf_annotate_ensemblvep": {
+                        "branch": "master",
+                        "git_sha": "8c343b3c8a0925949783dc547666007c245c235b",
+                        "installed_by": ["subworkflows"]
+                    },
                     "vcf_annotate_snpeff": {
                         "branch": "master",
                         "git_sha": "df47164506202e7b994825a9bcd38d2ca5954e1a",

subworkflows/local/vcf_annotate_all/main.nf

@@ -2,9 +2,9 @@
 // ANNOTATION
 //
 
-include { VCF_ANNOTATE_ENSEMBLVEP                       } from '../vcf_annotate_ensemblvep/main'
-include { VCF_ANNOTATE_ENSEMBLVEP as VCF_ANNOTATE_MERGE } from '../vcf_annotate_ensemblvep/main'
-include { VCF_ANNOTATE_SNPEFF                           } from '../../nf-core/vcf_annotate_snpeff/main'
+include { VCF_ANNOTATE_ENSEMBLVEP                       } from '../../nf-core/vcf_annotate_ensemblvep/main.nf'
+include { VCF_ANNOTATE_ENSEMBLVEP as VCF_ANNOTATE_MERGE } from '../../nf-core/vcf_annotate_ensemblvep/main.nf'
+include { VCF_ANNOTATE_SNPEFF                           } from '../../nf-core/vcf_annotate_snpeff/main.nf'
 
 workflow VCF_ANNOTATE_ALL {
     take:

tests/config/pytest_tags.yml

@@ -244,7 +244,7 @@ merge:
   - modules/nf-core/snpeff/main.nf
   - modules/nf-core/tabix/bgziptabix/main.nf
   - subworkflows/local/vcf_annotate_all/main.nf
-  - subworkflows/local/vcf_annotate_ensemblvep/main.nf
+  - subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf
   - subworkflows/nf-core/vcf_annotate_snpeff/main.nf
 
 ## snpeff
@@ -259,4 +259,4 @@ vep:
   - conf/modules/annotate.config
   - modules/nf-core/ensemblvep/main.nf
   - modules/nf-core/tabix/bgziptabix/main.nf
-  - subworkflows/local/vcf_annotate_ensemblvep/main.nf
+  - subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf