Merge pull request #874 from maxulysse/dev_update_modules

nf-core modules update -a
nf-core · Dec 1, 2022 · fe24ecb · fe24ecb
2 parents ae76448 + 4715c67
commit fe24ecb
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,19 +14,25 @@ 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
+- [#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
+- [#874](https://github.com/nf-core/sarek/pull/874) - Update all modules
 
 ### Fixed
 
 - [#870](https://github.com/nf-core/sarek/pull/870) - Fix output for locally realigned reads from haplotypecaller
+- [#874](https://github.com/nf-core/sarek/pull/874) - Remove `CITATION.cff`
 
 ### Deprecated
 
 ### Removed
 
 ### Dependencies
 
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `svdb`     | 2.6.1       | 2.8.1       |
+
 ## [3.1.1](https://github.com/nf-core/sarek/releases/tag/3.1.1) - Lilla Luleälven
 
 Lilla Luleälven river's main affluent is Rapaätno.

diff --git a/CITATION.cff b/CITATION.cff
diff --git a/modules.json b/modules.json
@@ -32,7 +32,7 @@
                     },
                     "bwa/mem": {
                         "branch": "master",
-                        "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
+                        "git_sha": "653588be2a4aadab487b530643dbc9baf7a485c4",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
@@ -42,7 +42,7 @@
                     },
                     "bwamem2/mem": {
                         "branch": "master",
-                        "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
+                        "git_sha": "653588be2a4aadab487b530643dbc9baf7a485c4",
                         "installed_by": ["modules"]
                     },
                     "cat/cat": {
@@ -119,8 +119,8 @@
                     },
                     "ensemblvep": {
                         "branch": "master",
-                        "git_sha": "69f158610f25a3bff40b3eadfedd3ac67a3cfc23",
-                        "installed_by": ["modules", "vcf_annotate_ensemblvep"]
+                        "git_sha": "1ec0d59beb1e794a7a4a4351e15138ffa213aa20",
+                        "installed_by": ["vcf_annotate_ensemblvep", "modules"]
                     },
                     "fastp": {
                         "branch": "master",
@@ -129,7 +129,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "3dd73937b084b547f9272bc901e0f120a7913fd8",
+                        "git_sha": "810e8f2603ec38401d49a4aaed06f6d058745552",
                         "installed_by": ["modules"]
                     },
                     "fgbio/callmolecularconsensusreads": {
@@ -265,7 +265,7 @@
                     },
                     "gatk4/mergevcfs": {
                         "branch": "master",
-                        "git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67",
+                        "git_sha": "c25943553f62be5f907e3c12c42eaf0a1b40746d",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mutect2": {
@@ -381,7 +381,7 @@
                     },
                     "svdb/merge": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "4a8a2caf44b87734b41ea4c67f508c14f0745ee7",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgziptabix": {

diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf
diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
diff --git a/modules/nf-core/ensemblvep/main.nf b/modules/nf-core/ensemblvep/main.nf
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf
diff --git a/modules/nf-core/gatk4/mergevcfs/meta.yml b/modules/nf-core/gatk4/mergevcfs/meta.yml
diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf