diff --git a/CHANGELOG.md b/CHANGELOG.md index cc3c002b..204d7a6c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## v1.1.0 - [xxxx-xx-xx] +## v1.1.0 - Abu [xxxx-xx-xx] ### `Added` @@ -21,7 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Avoiding publishing uncompressed VCF-file from `HMTNOTE_ANNOTATE`. (The corresponding compressed VCF-file still gets published.) [#368](https://github.com/nf-core/raredisease/pull/368) -## v1.0.0 - [2023-06-01] +## v1.0.0 - Aladdin [2023-06-01] Initial release of nf-core/raredisease, created with the [nf-core](https://nf-co.re/) template. diff --git a/README.md b/README.md index 260cd05e..672230e6 100644 --- a/README.md +++ b/README.md @@ -143,7 +143,7 @@ For more details about the output files and reports, please refer to the nf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm. -Additional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma Västerviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Linköping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics Örebro); [Annick Renevey](https://github.com/rannick) and [Peter Pruisscher](https://github.com/peterpru) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); and [Lucas Taniguti](https://github.com/lmtani). +Additional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma Västerviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Linköping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics Örebro); [Annick Renevey](https://github.com/rannick) and [Peter Pruisscher](https://github.com/peterpru) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani). We thank the nf-core community for their extensive assistance in the development of this pipeline. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index a32647a3..8388320b 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/raredisease/ custom_logo_title: "nf-core/raredisease" report_comment: > - This report has been generated by the nf-core/raredisease + This report has been generated by the nf-core/raredisease analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-raredisease-methods-description": order: -1000 diff --git a/modules/local/create_bed_from_fai.nf b/modules/local/create_bed_from_fai.nf index ed2a35d2..6b96b6ae 100644 --- a/modules/local/create_bed_from_fai.nf +++ b/modules/local/create_bed_from_fai.nf @@ -5,7 +5,7 @@ process BUILD_BED { conda "anaconda::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : - 'quay.io/biocontainers/gawk:5.1.0' }" + 'biocontainers/gawk:5.1.0' }" input: tuple val(meta), path(fasta_fai) diff --git a/modules/local/get_chrom_sizes.nf b/modules/local/get_chrom_sizes.nf index d5dc0a76..4ab80ed1 100644 --- a/modules/local/get_chrom_sizes.nf +++ b/modules/local/get_chrom_sizes.nf @@ -5,7 +5,7 @@ process GET_CHROM_SIZES { conda "conda-forge::coreutils=8.31" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--0' : - 'quay.io/biocontainers/gnu-wget:1.18--0' }" + 'biocontainers/gnu-wget:1.18--0' }" input: tuple val(meta), path(fai) diff --git a/modules/local/mt_deletion_script.nf b/modules/local/mt_deletion_script.nf index df586191..02d55876 100644 --- a/modules/local/mt_deletion_script.nf +++ b/modules/local/mt_deletion_script.nf @@ -2,10 +2,10 @@ process MT_DELETION { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.16.1" + conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/nextflow.config b/nextflow.config index 9e3b3fa2..ef5688fb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -280,7 +280,7 @@ manifest { description = """call and score variants from WGS/WES of rare disease patients""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.1.0dev' + version = '1.1.0' doi = '' }