From 596b3dc89c74f19d4e6fd1ebf580bdc9c72212a5 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 21 Jun 2022 14:53:46 +0200 Subject: [PATCH 1/3] remove TODO in awsfulltest --- .github/workflows/awsfulltest.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index e27d804a17..8fef331d76 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.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 }} From 58b532473a59c211e87f67eceef2676d34395339 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 21 Jun 2022 14:54:08 +0200 Subject: [PATCH 2/3] add description in schema --- nextflow_schema.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index 5c9020e4de..d0f6147dd9 100644 --- a/nextflow_schema.json +++ b/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 } } From a002fe3024c08cc1695d86033dfc65b93f50c209 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 21 Jun 2022 14:56:37 +0200 Subject: [PATCH 3/3] update CHANGELOG --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 996256a3ad..b742742047 100644 --- a/CHANGELOG.md +++ b/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