remove profile aws_tower

.github/workflows/awsfulltest.yml

@@ -24,7 +24,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/crisprseq/results-${{ github.sha }}/targeted_test"
             }
-          profiles: test_full,aws_tower
+          profiles: test_full
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

.github/workflows/awsfulltest_screening.yml

@@ -24,7 +24,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/crisprseq/results-${{ github.sha }}/screening_test"
             }
-          profiles: test_screening_full,aws_tower
+          profiles: test_screening_full
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

.github/workflows/awstest.yml

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

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
         ANALYSIS:
           - "test_screening"

CHANGELOG.md

@@ -18,6 +18,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - Fix warning "module used more than once" ([#25](https://github.com/nf-core/crisprseq/pull/25))
+- Remove profile `aws_tower`, update from nf-core/tools v2.9 to make full tests pass ([#50](https://github.com/nf-core/crisprseq/pull/50))
+- Remove `quay.io` from all containers ([#50](https://github.com/nf-core/crisprseq/pull/50))
 
 ## [v1.0 - Salted Hypatia](https://github.com/nf-core/crisprseq/releases/tag/1.0) - [02.02.2023]
 

README.md

@@ -2,7 +2,7 @@
 
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/crisprseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7598497-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7598497)
 
-[![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/test_full.config

@@ -10,8 +10,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-cleanup = true
-
 params {
     config_profile_name        = 'Full test targeted profile'
     config_profile_description = 'Full test dataset to check pipeline function'

modules.json

@@ -99,7 +99,7 @@
                     },
                     "racon": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
@@ -119,13 +119,13 @@
                     },
                     "vsearch/cluster": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/vsearch/cluster/vsearch-cluster.diff"
                     },
                     "vsearch/sort": {
                         "branch": "master",
-                        "git_sha": "e7801603532df26b4bb4ef324ca2c39f7a4d0eee",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     }
                 }

nextflow.config

@@ -127,9 +127,7 @@ profiles {
     }
     docker {
         docker.enabled         = true
-        docker.registry        = 'quay.io'
         docker.userEmulation   = true
-        docker.registry        = 'quay.io'
         conda.enabled          = false
         singularity.enabled    = false
         podman.enabled         = false
@@ -152,7 +150,6 @@ profiles {
     }
     podman {
         podman.enabled         = true
-        podman.registry        = 'quay.io'
         conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
@@ -221,6 +218,13 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
+// 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'
+singularity.registry = 'quay.io'
+
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
@@ -245,7 +249,7 @@ manifest {
     homePage        = 'https://github.com/nf-core/crisprseq'
     description     = """Pipeline for the analysis of crispr data"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=22.10.1'
+    nextflowVersion = '!>=23.04.0'
     version         = '2.0.0'
     doi             = 'https://doi.org/10.5281/zenodo.7598497'
 }