Merge pull request #376 from genomic-medicine-sweden/release_prep

Release prep v1.1.0

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.
 

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.
 

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 <a href="https://github.com/nf-core/raredisease/1.1.0dev" target="_blank">nf-core/raredisease</a>
+  This report has been generated by the <a href="https://github.com/nf-core/raredisease/1.1.0" target="_blank">nf-core/raredisease</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/raredisease/1.1.0dev/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/raredisease/1.1.0/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-raredisease-methods-description":
     order: -1000

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)

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)

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)

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             = ''
 }