diff --git a/CHANGELOG.md b/CHANGELOG.md index 113692a9..95cafcd5 100644 --- 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 index 253c25e6..b9d907cf 100644 --- 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 index 4ebc067f..0f4a7163 100644 --- 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 index 3e01672d..76e69565 100644 --- 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 index b55008bb..cc74e906 100644 --- 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 index 7c481d6e..6aacdbc3 100644 --- a/modules/nf-core/cellranger/count/main.nf +++ b/modules/nf-core/cellranger/count/main.nf @@ -2,7 +2,7 @@ process CELLRANGER_COUNT { tag "$meta.id" label 'process_high' - container "docker.io/nfcore/cellranger:7.1.0" + container "nf-core/cellranger:7.1.0" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/nf-core/cellranger/mkgtf/main.nf b/modules/nf-core/cellranger/mkgtf/main.nf index 40a27a31..5411b0fd 100644 --- a/modules/nf-core/cellranger/mkgtf/main.nf +++ b/modules/nf-core/cellranger/mkgtf/main.nf @@ -2,7 +2,7 @@ process CELLRANGER_MKGTF { tag "$gtf" label 'process_low' - container "docker.io/nfcore/cellranger:7.1.0" + container "nf-core/cellranger:7.1.0" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/nf-core/cellranger/mkref/main.nf b/modules/nf-core/cellranger/mkref/main.nf index d3826f97..b4b9c547 100644 --- a/modules/nf-core/cellranger/mkref/main.nf +++ b/modules/nf-core/cellranger/mkref/main.nf @@ -2,7 +2,7 @@ process CELLRANGER_MKREF { tag "$fasta" label 'process_high' - container "docker.io/nfcore/cellranger:7.1.0" + container "nf-core/cellranger:7.1.0" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/nf-core/cellranger/mkref/meta.yml b/modules/nf-core/cellranger/mkref/meta.yml index 34bdaf9d..1ad5d6e3 100644 --- a/modules/nf-core/cellranger/mkref/meta.yml +++ b/modules/nf-core/cellranger/mkref/meta.yml @@ -22,7 +22,7 @@ input: description: Reference transcriptome GTF file pattern: "*.gtf" - reference_name: - type: val + type: string description: The name to give the new reference folder pattern: str output: diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml index 81c1d1c0..f25b7bc4 100644 --- a/modules/nf-core/kallistobustools/count/meta.yml +++ b/modules/nf-core/kallistobustools/count/meta.yml @@ -3,13 +3,15 @@ description: quantifies scRNA-seq data from fastq files using kb-python. keywords: - scRNA-seq - count + - single-cell + - kallisto + - bustools tools: - kb: description: kallisto and bustools are wrapped in an easy-to-use program called kb homepage: https://www.kallistobus.tools/ documentation: https://kb-python.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/pachterlab/kb_python - licence: MIT License input: @@ -40,11 +42,11 @@ input: description: kb ref's c2 unspliced_t2c file pattern: "*.{introns_t2c.txt}" - workflow_mode: - type: value + type: string description: String value defining workflow to use, can be one of "standard", "lamanno", "nucleus" pattern: "{standard,lamanno,nucleus,kite}" - technology: - type: value + type: string description: String value defining the sequencing technology used. pattern: "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}" diff --git a/modules/nf-core/universc/README.md b/modules/nf-core/universc/README.md index 30b6b65e..e5da6f3b 100644 --- a/modules/nf-core/universc/README.md +++ b/modules/nf-core/universc/README.md @@ -45,10 +45,10 @@ process { ... withName: CELLRANGER_MKGTF { - container = "docker.io/nfcore/universc:1.2.5.1" + container = "nf-core/universc:1.2.5.1" } withName: CELLRANGER_MKREF{ - container = "docker.io/nfcore/universc:1.2.5.1" + container = "nf-core/universc:1.2.5.1" } ... } @@ -66,7 +66,7 @@ and for singularity use the `--writeable` parameter. These are set as default in universc/main.nf: ``` - container "docker.io/nfcore/universc:1.2.5.1" + container "nf-core/universc:1.2.5.1" if (workflow.containerEngine == 'docker'){ containerOptions = "--privileged" } @@ -104,7 +104,7 @@ modify this code provided that they also contain this license. The tomkellygenetics/universc: container is automatically updated with tomkellygenetics/universc:latest. -A stable release is mirrored at nfcore/universc:1.2.5.1 and will be updated as needed. +A stable release is mirrored at nf-core/universc:1.2.5.1 and will be updated as needed. To build an updated container use the Dockerfile provided here: diff --git a/modules/nf-core/universc/main.nf b/modules/nf-core/universc/main.nf index 2108624d..6d6cc020 100644 --- a/modules/nf-core/universc/main.nf +++ b/modules/nf-core/universc/main.nf @@ -6,7 +6,7 @@ process UNIVERSC { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { exit 1, "UNIVERSC module does not support Conda. Please use Docker / Singularity / Podman instead." } - container "docker.io/nfcore/universc:1.2.5.1" + container "nf-core/universc:1.2.5.1" if (workflow.containerEngine == 'docker'){ containerOptions = "--privileged" } diff --git a/nextflow.config b/nextflow.config index d583913f..76a0d4a2 100644 --- 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' }