Merge pull request nf-core#126 from nf-core/dev

Dev -> Master for 1.3.2 release
glichtenstein · Jun 7, 2023 · 67b8465 · 67b8465
2 parents 8f5d9ba + 4078074
commit 67b8465
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,12 @@
 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).
 
+## 1.3.2 - 2023-06-07
+
+### `Fixed`
+
+- [#125](https://github.com/nf-core/demultiplex/pull/125) Move containers for pipeline to quay.io
+
 ## 1.3.1 - 2023-06-05
 
 ### `Fixed`

diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config
@@ -13,18 +13,18 @@ podman.registry = 'public.ecr.aws'
 
 process {
     withName: 'BASES2FASTQ' {
-        container = 'docker.io/elembio/bases2fastq:1.1.0'
+        container = 'quay.io/nf-core/bases2fastq:1.1.0'
     }
     withName: 'BCL2FASTQ' {
-        container = 'docker.io/nfcore/bcl2fastq:2.20.0.422'
+        container = 'quay.io/nf-core/bcl2fastq:2.20.0.422'
     }
     withName: 'BCLCONVERT' {
-        container = 'docker.io/nfcore/bclconvert:4.0.3'
+        container = 'quay.io/nf-core/bclconvert:4.0.3'
     }
     withName: 'MD5SUM' {
-        container = 'docker.io/library/ubuntu:20.04'
+        container = 'quay.io/nf-core/ubuntu:20.04'
     }
     withName: 'UNTAR' {
-        container = 'docker.io/library/ubuntu:20.04'
+        container = 'quay.io/nf-core/ubuntu:20.04'
     }
 }
diff --git a/modules.json b/modules.json
@@ -7,17 +7,17 @@
                 "nf-core": {
                     "bases2fastq": {
                         "branch": "master",
-                        "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["modules"]
                     },
                     "bcl2fastq": {
                         "branch": "master",
-                        "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["bcl_demultiplex"]
                     },
                     "bclconvert": {
                         "branch": "master",
-                        "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["bcl_demultiplex"]
                     },
                     "custom/dumpsoftwareversions": {

diff --git a/modules/nf-core/bases2fastq/main.nf b/modules/nf-core/bases2fastq/main.nf
diff --git a/modules/nf-core/bcl2fastq/main.nf b/modules/nf-core/bcl2fastq/main.nf
diff --git a/modules/nf-core/bclconvert/main.nf b/modules/nf-core/bclconvert/main.nf
diff --git a/nextflow.config b/nextflow.config
@@ -227,7 +227,7 @@ manifest {
     description     = """Demultiplexing pipeline for Illumina sequencing data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.3.1'
+    version         = '1.3.2'
     doi             = '10.5281/zenodo.7153103'
 }
 

diff --git a/tests/pipeline/default/bclconvert.nf.test.snap b/tests/pipeline/default/bclconvert.nf.test.snap
@@ -13,11 +13,11 @@
                 "Quality_Metrics.csv:md5,6614accb1bb414fe312b17b81f5521f7",
                 "Quality_Tile_Metrics.csv:md5,cdc89fd2962bdd4a24f71e186112118a",
                 "RunInfo.xml:md5,03038959f4dd181c86bc97ae71fe270a",
-                "SampleSheet.csv:md5,ee5db2e12754e069998b0a96e535238c",
+                "SampleSheet.csv:md5,2df2e405991814571c021dc8749c2a89",
                 "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc",
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
             ]
         ],
-        "timestamp": "2023-01-18T23:51:44+0000"
+        "timestamp": "2023-06-07T17:53:57+0000"
     }
 }
diff --git a/tests/pipeline/default/skip_tools.nf.test.snap b/tests/pipeline/default/skip_tools.nf.test.snap
@@ -14,12 +14,12 @@
                 "Quality_Metrics.csv:md5,6614accb1bb414fe312b17b81f5521f7",
                 "Quality_Tile_Metrics.csv:md5,cdc89fd2962bdd4a24f71e186112118a",
                 "RunInfo.xml:md5,03038959f4dd181c86bc97ae71fe270a",
-                "SampleSheet.csv:md5,ee5db2e12754e069998b0a96e535238c",
+                "SampleSheet.csv:md5,2df2e405991814571c021dc8749c2a89",
                 "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc",
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
             ]
         ],
-        "timestamp": "2023-01-18T22:46:32+0000"
+        "timestamp": "2023-06-07T18:00:39+0000"
     },
     "Should skip trimming": {
         "content": [
@@ -36,12 +36,12 @@
                 "Quality_Metrics.csv:md5,6614accb1bb414fe312b17b81f5521f7",
                 "Quality_Tile_Metrics.csv:md5,cdc89fd2962bdd4a24f71e186112118a",
                 "RunInfo.xml:md5,03038959f4dd181c86bc97ae71fe270a",
-                "SampleSheet.csv:md5,ee5db2e12754e069998b0a96e535238c",
+                "SampleSheet.csv:md5,2df2e405991814571c021dc8749c2a89",
                 "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc",
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
             ]
         ],
-        "timestamp": "2023-01-18T22:42:00+0000"
+        "timestamp": "2023-06-07T18:00:39+0000"
     },
     "Should skip fastp": {
         "content": [
@@ -58,12 +58,12 @@
                 "Quality_Metrics.csv:md5,6614accb1bb414fe312b17b81f5521f7",
                 "Quality_Tile_Metrics.csv:md5,cdc89fd2962bdd4a24f71e186112118a",
                 "RunInfo.xml:md5,03038959f4dd181c86bc97ae71fe270a",
-                "SampleSheet.csv:md5,ee5db2e12754e069998b0a96e535238c",
+                "SampleSheet.csv:md5,2df2e405991814571c021dc8749c2a89",
                 "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc",
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
             ]
         ],
-        "timestamp": "2023-01-18T22:42:00+0000"
+        "timestamp": "2023-06-07T18:00:39+0000"
     },
     "Should skip fastqc": {
         "content": [
@@ -79,11 +79,11 @@
                 "Quality_Metrics.csv:md5,6614accb1bb414fe312b17b81f5521f7",
                 "Quality_Tile_Metrics.csv:md5,cdc89fd2962bdd4a24f71e186112118a",
                 "RunInfo.xml:md5,03038959f4dd181c86bc97ae71fe270a",
-                "SampleSheet.csv:md5,ee5db2e12754e069998b0a96e535238c",
+                "SampleSheet.csv:md5,2df2e405991814571c021dc8749c2a89",
                 "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc",
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
             ]
         ],
-        "timestamp": "2023-01-18T22:58:43+0000"
+        "timestamp": "2023-06-07T18:00:39+0000"
     }
 }