Merge pull request #1227 from maxulysse/container_customdump_software

FIX: update modules
nf-core · Sep 12, 2023 · 0a3abcc · 0a3abcc
2 parents 767e4af + 7bebb39
commit 0a3abcc
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Showing 7 changed files with 28 additions and 19 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -2,6 +2,7 @@ repository_type: pipeline
 lint:
   actions_ci: False
   files_exist:
+    - .github/workflows/awsfulltest.yml
     - conf/modules.config
   files_unchanged:
     - assets/nf-core-sarek_logo_light.png

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -36,6 +36,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas
 - [#1200](https://github.com/nf-core/sarek/pull/1200) - Streamline Github Actions workflows
 - [#1212](https://github.com/nf-core/sarek/pull/1212) - Use matrix for AWS megatests
 - [#1218](https://github.com/nf-core/sarek/pull/1218) - Remove Singularity tests for GHA
+- [#1227](https://github.com/nf-core/sarek/pull/1227) - Update modules
 
 ### Fixed
 
@@ -67,6 +68,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas
 - [#1222](https://github.com/nf-core/sarek/pull/1222) - Better documentation for annotation cache
 - [#1224](https://github.com/nf-core/sarek/pull/1224) - Update BCFTOOLS_SORT module with `--temp-dir .` added as option, which was required for Singularity
 - [#1225](https://github.com/nf-core/sarek/pull/1225) - Better test coverage for all tests
+- [#1227](https://github.com/nf-core/sarek/pull/1227) - Lint warning fix
 
 ### Dependencies
 

diff --git a/modules.json b/modules.json
@@ -32,7 +32,7 @@
                     },
                     "bwa/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "bfed129da5134b4439b1821c917972570d44d39c",
                         "installed_by": ["modules"]
                     },
                     "bwa/mem": {
@@ -42,7 +42,7 @@
                     },
                     "bwamem2/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "bfed129da5134b4439b1821c917972570d44d39c",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/mem": {
@@ -102,7 +102,7 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
                         "installed_by": ["modules"]
                     },
                     "deepvariant": {

diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf
diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -34,6 +34,7 @@
                 },
                 "input_restart": {
                     "type": "string",
+                    "description": "Automatic retrieval for restart",
                     "format": "file-path",
                     "exists": true,
                     "mimetype": "text/csv",