Merge pull request #600 from maxulysse/dev_tools_lint_warning

Remove tools lint warning

.github/workflows/awsfulltest.yml

@@ -13,11 +13,9 @@ jobs:
     if: github.repository == 'nf-core/sarek'
     runs-on: ubuntu-latest
     steps:
+      # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v3
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

CHANGELOG.md

@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#557](https://github.com/nf-core/sarek/pull/557) - Add `Haplotypecaller` single sample mode together with `CNNScoreVariants` and `FilterVariantTranches`
 - [#576](https://github.com/nf-core/sarek/pull/576) - Add modules and subworkflows for `cnvkit` germline mode
 - [#582](https://github.com/nf-core/sarek/pull/582) - Added option `--vep_out_format` for setting the format of the output-file from VEP to `json`, `tab` or `vcf` (default)
+- [#600](https://github.com/nf-core/sarek/pull/600) - Added description for UMI related params in schema
 
 ### Changed
 
@@ -65,6 +66,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#585](https://github.com/nf-core/sarek/pull/585) - Remove explicit BAM to CRAM conversion after MarkduplicatesSpark; tool does it internally
 - [#581](https://github.com/nf-core/sarek/pull/581) - `TIDDIT` is updated to `3.1.0`
 - [#593](https://github.com/nf-core/sarek/pull/593) - update `ensembl-vep` cache version and module
+- [#600](https://github.com/nf-core/sarek/pull/600) - Remove `TODO` in awsfulltest
 
 ### Fixed
 
@@ -96,6 +98,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#590](https://github.com/nf-core/sarek/pull/590) - Fix empty folders during scatter/gather
 - [#592](https://github.com/nf-core/sarek/pull/592) - Fix optional resources for Mutect2, GetPileupSummaries, and HaplotypeCaller: issue [#299](https://github.com/nf-core/sarek/issues/299), [#359](https://github.com/nf-core/sarek/issues/359), [#367](https://github.com/nf-core/sarek/issues/367)
 - [#598](https://github.com/nf-core/sarek/pull/598) - Remove WARNING message for config selector not matching
+- [#600](https://github.com/nf-core/sarek/pull/600) - Remove `nf-core lint` warnings
 
 ### Deprecated
 

nextflow_schema.json

@@ -171,11 +171,13 @@
                 "umi_read_structure": {
                     "type": "string",
                     "fa_icon": "fas fa-tape",
+                    "description": "Specify UMI read structure.",
                     "hidden": true
                 },
                 "group_by_umi_strategy": {
                     "type": "string",
                     "default": "Adjacency",
+                    "description": "Default strategy with UMI.",
                     "hidden": true
                 }
             }