Merge branch 'master' of github.com:nf-core/demultiplex

adamrtalbot · Jun 5, 2023 · 81241a9 · 81241a9
2 parents cb01e68 + 8709f05
commit 81241a9
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Showing 9 changed files with 55 additions and 13 deletions.
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -27,7 +27,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/demultiplex/results-${{ github.sha }}"
             }
-          profiles: test_full,aws_tower
+          profiles: test_full,public_aws_ecr,aws_tower
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -22,7 +22,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/demultiplex/results-test-${{ github.sha }}"
             }
-          profiles: test,aws_tower
+          profiles: test,public_aws_ecr,aws_tower
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,13 +3,16 @@
 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).
 
-## dev
+## 1.3.0 - 2023-05-31
 
 ### `Added`
 
+- Add `public_aws_ecr` profile for using ECR containers.
+- Bump `fastp` module to v0.23.4
+
 ### `Changed`
 
-- [#113](https://github.com/nf-core/demultiplex/pull/113) Back to dev
+- [#115](https://github.com/nf-core/demultiplex/pull/115/files) Add public_aws_ecr profile
 
 ### `Fixed`
 

diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config
@@ -0,0 +1,30 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    AWS ECR Config
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config to set public AWS ECR images wherever possible
+    This improves speed when running on AWS infrastructure.
+    Use this as an example template when using your own private registry.
+----------------------------------------------------------------------------------------
+*/
+
+docker.registry = 'public.ecr.aws'
+podman.registry = 'public.ecr.aws'
+
+process {
+    withName: 'BASES2FASTQ' {
+        container = 'docker.io/elembio/bases2fastq:1.1.0'
+    }
+    withName: 'BCL2FASTQ' {
+        container = 'docker.io/nfcore/bcl2fastq:2.20.0.422'
+    }
+    withName: 'BCLCONVERT' {
+        container = 'docker.io/nfcore/bclconvert:4.0.3'
+    }
+    withName: 'MD5SUM' {
+        container = 'docker.io/library/ubuntu:20.04'
+    }
+    withName: 'UNTAR' {
+        container = 'docker.io/library/ubuntu:20.04'
+    }
+}
diff --git a/modules.json b/modules.json
@@ -32,7 +32,7 @@
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
                         "installed_by": ["modules"]
                     },
                     "fqtk": {
@@ -42,7 +42,7 @@
                     },
                     "md5sum": {
                         "branch": "master",
-                        "git_sha": "38b16706fa3a9d4ee2bf46fa5805e7397e275cdd",
+                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -57,7 +57,7 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "38b16706fa3a9d4ee2bf46fa5805e7397e275cdd",
+                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
                         "installed_by": ["modules", "bcl_demultiplex"]
                     }
                 }

diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
diff --git a/modules/nf-core/md5sum/main.nf b/modules/nf-core/md5sum/main.nf
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
diff --git a/nextflow.config b/nextflow.config
@@ -170,6 +170,9 @@ profiles {
         executor.cpus          = 16
         executor.memory        = 60.GB
     }
+    public_aws_ecr {
+        includeConfig 'conf/public_aws_ecr.config'
+    }
     test             { includeConfig 'conf/test.config'             }
     test_bases2fastq { includeConfig 'conf/test_bases2fastq.config' }
     test_bcl2fastq   { includeConfig 'conf/test_bcl2fastq.config'   }
@@ -193,6 +196,12 @@ 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 to your registry if you have a mirror of containers
+docker.registry = 'quay.io'
+podman.registry = 'quay.io'
+
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
@@ -218,7 +227,7 @@ manifest {
     description     = """Demultiplexing pipeline for Illumina sequencing data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.3.0dev'
+    version         = '1.3.0'
     doi             = '10.5281/zenodo.7153103'
 }