Merge pull request #234 from nf-core/dev

Dev -> Master for 2.3.2 release
nf-core · Jun 7, 2023 · 06a85e8 · 06a85e8
2 parents 6cccb9d + cef9e13
commit 06a85e8
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Showing 13 changed files with 42 additions and 21 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,10 @@
 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).
 
+## v2.3.2 - 2023-06-07 Patched Yellow Strontium Pinscher
+
+- Move containers for pipeline to quay.io ([#233](https://github.com/nf-core/scrnaseq/pull/233))
+
 ## v2.3.1 - 2023-06-02 Yellow Strontium Pinscher
 
 - Add `public_aws_ecr` config for using the AWS mirror of containers where possible ([#225](https://github.com/nf-core/scrnaseq/pull/225))

diff --git a/conf/modules.config b/conf/modules.config
@@ -84,14 +84,14 @@ if(params.aligner == "universc") {
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
             ext.args = "--attribute=gene_biotype:protein_coding --attribute=gene_biotype:lncRNA --attribute=gene_biotype:pseudogene"
-            container = "docker.io/nfcore/universc:1.2.5.1"
+            container = "nf-core/universc:1.2.5.1"
         }
         withName: CELLRANGER_MKREF {
             publishDir = [
                 path: "${params.outdir}/cellranger/mkref",
                 mode: params.publish_dir_mode
             ]
-            container = "docker.io/nfcore/universc:1.2.5.1"
+            container = "nf-core/universc:1.2.5.1"
         }
         withName: UNIVERSC {
             publishDir = [

diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config
@@ -12,6 +12,15 @@ docker.registry = 'public.ecr.aws'
 podman.registry = 'public.ecr.aws'
 
 process {
+    withName: 'CELLRANGER_COUNT' {
+        container = 'quay.io/nf-core/cellranger:7.1.0'
+    }
+    withName: 'CELLRANGER_MKGTF' {
+        container = 'quay.io/nf-core/cellranger:7.1.0'
+    }
+    withName: 'CELLRANGER_MKREF' {
+        container = 'quay.io/nf-core/cellranger:7.1.0'
+    }
     withName: 'CONCAT_H5AD' {
         container = 'quay.io/biocontainers/scanpy:1.7.2--pyhdfd78af_0'
     }
@@ -27,10 +36,16 @@ process {
     withName: 'MTX_TO_H5AD' {
         container = 'quay.io/biocontainers/scanpy:1.7.2--pyhdfd78af_0'
     }
+    withName: 'MTX_TO_SEURAT' {
+        container = 'quay.io/nf-core/seurat:4.3.0'
+    }
     withName: 'SAMPLESHEET_CHECK' {
         container = 'quay.io/biocontainers/python:3.8.3'
     }
     withName: 'STAR_GENOMEGENERATE' {
         container = 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0'
     }
+    withName: 'UNIVERSC' {
+        container = 'quay.io/nf-core/universc:1.2.5.1'
+    }
 }
diff --git a/modules.json b/modules.json
@@ -7,17 +7,17 @@
                 "nf-core": {
                     "cellranger/count": {
                         "branch": "master",
-                        "git_sha": "d68b2e6526fcd22a2a6349e0859dbdc9924df93d",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkgtf": {
                         "branch": "master",
-                        "git_sha": "d68b2e6526fcd22a2a6349e0859dbdc9924df93d",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkref": {
                         "branch": "master",
-                        "git_sha": "d68b2e6526fcd22a2a6349e0859dbdc9924df93d",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
@@ -42,7 +42,7 @@
                     },
                     "kallistobustools/count": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "de204d3c950f091336539ad74f0e47ddffe69ed4",
                         "installed_by": ["modules"]
                     },
                     "kallistobustools/ref": {
@@ -62,7 +62,7 @@
                     },
                     "universc": {
                         "branch": "master",
-                        "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/local/mtx_to_seurat.nf b/modules/local/mtx_to_seurat.nf
@@ -3,7 +3,7 @@ process MTX_TO_SEURAT {
     label 'process_medium'
 
     conda "r-seurat"
-    container 'docker.io/satijalab/seurat:4.3.0'
+    container "nf-core/seurat:4.3.0"
 
     input:
     // inputs from cellranger nf-core module does not come in a single sample dir

diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf
diff --git a/modules/nf-core/cellranger/mkgtf/main.nf b/modules/nf-core/cellranger/mkgtf/main.nf
diff --git a/modules/nf-core/cellranger/mkref/main.nf b/modules/nf-core/cellranger/mkref/main.nf
diff --git a/modules/nf-core/cellranger/mkref/meta.yml b/modules/nf-core/cellranger/mkref/meta.yml
diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml
diff --git a/modules/nf-core/universc/README.md b/modules/nf-core/universc/README.md
diff --git a/modules/nf-core/universc/main.nf b/modules/nf-core/universc/main.nf
diff --git a/nextflow.config b/nextflow.config
@@ -257,7 +257,7 @@ manifest {
     description     = """Pipeline for processing 10x Genomics single cell rnaseq data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '2.3.1'
+    version         = '2.3.2'
     doi             = '10.5281/zenodo.3568187'
 }