FIX: patch more modules

.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

@@ -13,11 +13,15 @@ Pierikjaure is a previous spelling of Bierikjávrre.
 
 - [#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
 

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": {

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 {
@@ -321,7 +322,7 @@ 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'
+    nextflowVersion = '!>=23.04.0'
     version         = '3.2.1'
     doi             = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683'
 }