Merge pull request #1081 from nf-core/dev

Release candidate 3.2.1

.github/workflows/awsfulltest.yml

@@ -25,7 +25,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/somatic_test"
             }
-          profiles: test_full,public_aws_tower
+          profiles: test_full,public_aws_ecr
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

.github/workflows/awsfulltest_germline.yml

@@ -8,7 +8,7 @@ on:
     types: [published]
   workflow_dispatch:
 jobs:
-  run-tower-germline:
+  run-tower:
     name: Run AWS full tests
     if: github.repository == 'nf-core/sarek'
     runs-on: ubuntu-latest
@@ -25,7 +25,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/germline_test"
             }
-          profiles: test_full_germline,aws_tower
+          profiles: test_full_germline,public_aws_ecr
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

.github/workflows/awstest.yml

@@ -22,7 +22,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-test-${{ github.sha }}"
             }
-          profiles: test,public_aws_tower
+          profiles: test,public_aws_ecr
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

.github/workflows/ci.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
         test:
           - "default"

.github/workflows/pytest-workflow.yml

@@ -37,7 +37,7 @@ jobs:
         TEST_DATA_BASE:
           - "test-datasets/data"
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
         exclude:
           # - profile: "conda"

CHANGELOG.md

@@ -5,6 +5,24 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.2.1](https://github.com/nf-core/sarek/releases/tag/3.2.1) - Pierikjaure
+
+Pierikjaure is a previous spelling of Bierikjávrre.
+
+### Changed
+
+- [#1073](https://github.com/nf-core/sarek/pull/1073) - Back to dev
+- [#1080](https://github.com/nf-core/sarek/pull/1080) - Prepare release `3.2.1`
+- [#1082](https://github.com/nf-core/sarek/pull/1082) - Bump minimal Nextflow version to 23.04.0
+
+### Fixed
+
+- [#1078](https://github.com/nf-core/sarek/pull/1078) - Update tabix/bgziptabix module to fix typo
+- [#1079](https://github.com/nf-core/sarek/pull/1079) - Fixed typo in profile name for tower aws megatests
+- [#1082](https://github.com/nf-core/sarek/pull/1082) - Patch more modules to use quay.io registry
+- [#1082](https://github.com/nf-core/sarek/pull/1082) - Update `public_aws_ecr` profile
+- [#1082](https://github.com/nf-core/sarek/pull/1082) - Add quay.io as singularity default registry
+
 ## [3.2.0](https://github.com/nf-core/sarek/releases/tag/3.2.0) - Bierikjávrre
 
 Bierikjávrre is one of the largest lake in Sarek.
@@ -21,7 +39,7 @@ Bierikjávrre is one of the largest lake in Sarek.
 - [#978](https://github.com/nf-core/sarek/pull/978) - Validate that patient/sample does not contain spaces
 - [#981](https://github.com/nf-core/sarek/pull/981) - Added documentation on generating ASCAT resources for exome and targeted sequencing
 - [#1041](https://github.com/nf-core/sarek/pull/1041) - Add params `vep_custom_args` to let user specify custom params more easily for `VEP`
-- [#1045](https://github.com/nf-core/sarek/pull/1045) - Add `public_aws_ecr` for using ECR hosted containers.
+- [#1045](https://github.com/nf-core/sarek/pull/1045) - Add `public_aws_ecr` for using ECR hosted containers
 
 ### Changed
 

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%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.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/)

conf/public_aws_ecr.config

@@ -39,9 +39,24 @@ process {
     withName: 'CREATE_INTERVALS_BED' {
         container = 'quay.io/biocontainers/gawk:5.1.0'
     }
+    withName: 'DEEPVARIANT' {
+        container = 'quay.io/nf-core/deepvariant:1.5.0'
+    }
     withName: 'DRAGMAP_ALIGN' {
         container = 'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0'
     }
+    withName: 'GATK4_APPLYBQSR_SPARK' {
+        container = 'quay.io/nf-core/gatk:4.4.0.0'
+    }
+    withName: 'GATK4_BASERECALIBRATOR_SPARK' {
+        container = 'quay.io/nf-core/gatk:4.4.0.0'
+    }
+    withName: 'GATK4_CNNSCOREVARIANTS' {
+        container = 'quay.io/nf-core/gatk:4.4.0.0'
+    }
+    withName: 'GATK4_MARKDUPLICATES_SPARK' {
+        container = 'quay.io/nf-core/gatk:4.4.0.0'
+    }
     withName: 'SAMBLASTER' {
         container = 'quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:cee56b506ceb753d4bbef7e05b81e1bfc25d937f-0'
     }

modules.json

@@ -107,7 +107,7 @@
                     },
                     "deepvariant": {
                         "branch": "master",
-                        "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["modules"]
                     },
                     "dragmap/align": {
@@ -168,7 +168,7 @@
                     },
                     "gatk4/applybqsrspark": {
                         "branch": "master",
-                        "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["modules"]
                     },
                     "gatk4/applyvqsr": {
@@ -183,7 +183,7 @@
                     },
                     "gatk4/baserecalibratorspark": {
                         "branch": "master",
-                        "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["modules"]
                     },
                     "gatk4/calculatecontamination": {
@@ -193,7 +193,7 @@
                     },
                     "gatk4/cnnscorevariants": {
                         "branch": "master",
-                        "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["modules"]
                     },
                     "gatk4/createsequencedictionary": {
@@ -263,7 +263,7 @@
                     },
                     "gatk4/markduplicatesspark": {
                         "branch": "master",
-                        "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mergemutectstats": {
@@ -398,7 +398,7 @@
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
-                        "git_sha": "01b3b2509d76625b6d6cd613b349fb4777712a15",
+                        "git_sha": "591b71642820933dcb3c954c934b397bd00d8e5e",
                         "installed_by": ["vcf_annotate_snpeff", "modules"]
                     },
                     "tabix/tabix": {

nextflow.config

@@ -291,11 +291,12 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-// Set default registry for Docker and Podman independent of -profile
-// Will not be used unless Docker / Podman are enabled
+// Set default registry for Docker, Singularity and Podman independent of -profile
+// Will not be used unless Docker, Singularity and Podman are enabled
 // Set to your registry if you have a mirror of containers
-docker.registry = 'quay.io'
-podman.registry = 'quay.io'
+docker.registry      = 'quay.io'
+podman.registry      = 'quay.io'
+singularity.registry = 'quay.io'
 
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
@@ -321,8 +322,8 @@ manifest {
     homePage        = 'https://github.com/nf-core/sarek'
     description     = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=22.10.1'
-    version         = '3.2.0'
+    nextflowVersion = '!>=23.04.0'
+    version         = '3.2.1'
     doi             = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683'
 }