Merge pull request #898 from maxulysse/sync_template

merge TEMPLATE

.github/workflows/ci.yml

@@ -23,14 +23,11 @@ jobs:
       fail-fast: false
       matrix:
         NXF_VER:
-          - "21.10.3"
+          - "22.10.1"
           - "latest-everything"
         test:
           - "default"
         profile: ["docker", "singularity", "conda"]
-        exclude:
-          - NXF_VER: "latest-everything"
-            profile: "conda"
     env:
       NXF_ANSI_LOG: false
     steps:

.github/workflows/fix-linting.yml

@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "name=result::pass" >> $GITHUB_OUTPUT
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "name=result::fail" >> $GITHUB_OUTPUT
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'

.github/workflows/linting_comment.yml

@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2

.github/workflows/pytest-workflow.yml

@@ -34,11 +34,9 @@ jobs:
         tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
         profile: ["docker", "singularity", "conda"]
         NXF_VER:
-          - "21.10.3"
+          - "22.10.1"
           - "latest-everything"
         exclude:
-          - profile: "conda"
-            NXF_VER: "latest-everything"
           - profile: "conda"
             tags: umi
           - profile: "conda"

CHANGELOG.md

@@ -10,33 +10,41 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - [#864](https://github.com/nf-core/sarek/pull/864) - Added possibilities to export assembled haplotypes and locally realigned reads
-- [#792](https://github.com/nf-core/sarek/pull/792) - Added the option `--concatenate_vcfs` for concatenating the germline vcf-files. Per default, the resulting vcf-files will be placed under `<outDir>/variant_calling/concat`.
+- [#792](https://github.com/nf-core/sarek/pull/792) - Added the option `--concatenate_vcfs` for concatenating the germline VCF files. Per default, the resulting vcf-files will be placed under `<outDir>/variant_calling/concat`
 - [#889](https://github.com/nf-core/sarek/pull/889) - Added possibilities to skip variant filtering after Haplotypecaller
 
 ### 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
+- [#890](https://github.com/nf-core/sarek/pull/890) - Sync `TEMPLATE` with `tools` `2.7.1`
+- [#898](https://github.com/nf-core/sarek/pull/898) - Sync `TEMPLATE` with `tools` `2.7.2`
+- [#898](https://github.com/nf-core/sarek/pull/898) - Nextflow minimal version is now `22.10.1`
 
 ### 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`
 - [#893](https://github.com/nf-core/sarek/pull/893) - Fix logic of when to execute tabix on dbsnp
-- [#894](https://github.com/nf-core/sarek/pull/894) - Add description to --cnvkit_reference
+- [#894](https://github.com/nf-core/sarek/pull/894) - Add description to `--cnvkit_reference`
 - [#894](https://github.com/nf-core/sarek/pull/894) - Remove methods description TODO prompt
 
 ### Deprecated
 
 ### Removed
 
+- [#898](https://github.com/nf-core/sarek/pull/898) - Params `enable_conda` was removed
+
 ### Dependencies
 
-| Dependency | Old version | New version |
-| ---------- | ----------- | ----------- |
-| `svdb`     | 2.6.1       | 2.8.1       |
+| Dependency    | Old version | New version |
+| ------------- | ----------- | ----------- |
+| `bcftools`    | 1.15.1      | 1.16        |
+| `ensembl-vep` | 106.1       | 108.2       |
+| `multiqc`     | 1.13a       | 1.13        |
+| `svdb`        | 2.6.1       | 2.8.1       |
 
 ## [3.1.1](https://github.com/nf-core/sarek/releases/tag/3.1.1) - Lilla Luleälven
 

README.md

@@ -7,7 +7,7 @@
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/sarek/results)
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3476426-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3476425)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -49,7 +49,7 @@ By default, the pipeline currently performs the following:
 
 ## Quick Start
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
 

conf/test/test.config

@@ -93,20 +93,22 @@ process {
 if (System.getenv('PROFILE')) {
     if ("$PROFILE" == "conda") {
         conda.createTimeout                      = "120 min"
-        params.enable_conda                      = true
+        conda.enabled                            = true
         charliecloud.enabled                     = false
         docker.enabled                           = false
         podman.enabled                           = false
         shifter.enabled                          = false
         singularity.enabled                      = false
     } else if ("$PROFILE" == "docker") {
+        conda.enabled                            = false
         docker.enabled                           = true
         docker.userEmulation                     = { params.use_gatk_spark ? false : true }.call()
         charliecloud.enabled                     = false
         podman.enabled                           = false
         shifter.enabled                          = false
         singularity.enabled                      = false
     } else if ("$PROFILE" == "singularity") {
+        conda.enabled                            = false
         params.singularity_pull_docker_container = false
         singularity.autoMounts                   = true
         singularity.enabled                      = true

lib/WorkflowMain.groovy

@@ -72,7 +72,7 @@ class WorkflowMain {
         NfcoreTemplate.checkConfigProvided(workflow, log)
 
         // Check that conda channels are set-up correctly
-        if (params.enable_conda) {
+        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
             Utils.checkCondaChannels(log)
         }