nf-core · ramprasadn · Jan 17, 2025 · Jan 17, 2025 · Jan 17, 2025 · Jan 17, 2025
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -45,7 +45,6 @@ jobs:
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -18,4 +18,4 @@ template:
   name: raredisease
   org: nf-core
   outdir: .
-  version: 2.3.0dev
+  version: 2.3.0
diff --git 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).
 
-## 2.3.0dev - Getafix [xxxx-xx-xx]
+## 2.3.0 - Getafix [xxxx-xx-xx]
 
 ### `Added`
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -3,9 +3,10 @@ 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/tree/dev" 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/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/raredisease/releases/tag/2.3.0"
+  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/2.3.0/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   "nf-core-raredisease-methods-description":
     order: -1000

diff --git a/conf/modules/annotate_cadd.config b/conf/modules/annotate_cadd.config
@@ -17,7 +17,7 @@
 
 process {
     withName: '.*:ANNOTATE_CADD.*' {
-        ext.when = { ( !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun) }
+        ext.when = { ( !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun) }
     }
 
     withName: '.*:ANNOTATE_CADD:BCFTOOLS_VIEW' {

diff --git a/conf/modules/annotate_genome_snvs.config b/conf/modules/annotate_genome_snvs.config
@@ -42,13 +42,13 @@ process {
     withName: '.*ANNOTATE_GENOME_SNVS:UPD_SITES' {
         ext.prefix = { "${meta.upd_child}_upd_sites" }
         ext.args = {"--af-tag GNOMADAF --proband ${meta.upd_child} --mother ${meta.mother} --father ${meta.father} sites"}
-        ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun }
+        ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun }
     }
 
     withName: '.*ANNOTATE_GENOME_SNVS:UPD_REGIONS' {
         ext.prefix = { "${meta.upd_child}_upd_regions" }
         ext.args = {"--af-tag GNOMADAF --proband ${meta.upd_child} --mother ${meta.mother} --father ${meta.father} regions --min-size 5 --min-sites 1"}
-        ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun }
+        ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun }
     }
 
     withName: '.*ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES' {
@@ -65,7 +65,7 @@ process {
     withName: '.*ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS' {
         ext.prefix = { "${meta6.upd_child}_chromograph_regions" }
         ext.args = { '--euploid' }
-        ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon']).size() >= 1) || workflow.stubRun }
+        ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun }
         tag =  {"${meta6.upd_child}"}
         publishDir = [
             path: { "${params.outdir}/annotate_snv/genome" },

diff --git a/conf/modules/annotate_rhocallviz.config b/conf/modules/annotate_rhocallviz.config
@@ -45,7 +45,7 @@ process {
     withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG' {
         ext.prefix = { "${autozyg.simpleName}_autozyg_chromograph" }
         ext.args = { "--euploid" }
-        ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun }
+        ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun }
         publishDir = [
             path: { "${params.outdir}/annotate_snv/genome/" },
             mode: params.publish_dir_mode,

diff --git a/conf/modules/call_snv_MT.config b/conf/modules/call_snv_MT.config
@@ -50,7 +50,7 @@ process {
     }
 
     withName: '.*CALL_SNV_MT_SHIFT:HAPLOCHECK_MT' {
        ext.when = null
+        ext.when = false
     }
 
 }
diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config
@@ -60,7 +60,7 @@ process {
 
     withName: '.*QC_BAM:NGSBITS_SAMPLEGENDER' {
         //  NGSBITS_SAMPLEGENDER needs a chrX and chrY in order to run so we skip it for the two test profiles
-        ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon']).size() >= 1) || workflow.stubRun }
+        ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun }
         ext.prefix = { "${meta.id}_ngsbits_sex" }
         publishDir = [
             path: { "${params.outdir}/ngsbits_samplegender" },

diff --git a/docs/output.md b/docs/output.md
@@ -58,6 +58,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
       - [SVDB query](#svdb-query)
       - [VEP](#vep-1)
     - [Mitochondrial analysis](#mitochondrial-analysis)
+      - [Haplocheck](#haplocheck)
       - [Alignment and variant calling](#alignment-and-variant-calling)
         - [MT deletion script](#mt-deletion-script)
         - [eKLIPse](#eklipse)

diff --git a/nextflow.config b/nextflow.config
@@ -279,8 +279,7 @@ profiles {
 includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
 // Load nf-core/raredisease custom profiles from different institutions.
-// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/raredisease.config" : "/dev/null"
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/raredisease.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -339,23 +338,105 @@ manifest {
     name            = 'nf-core/raredisease'
     author          = """Clinical Genomics Stockholm""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
     contributors    = [
-        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
         [
-            name: 'Clinical Genomics Stockholm',
-            affiliation: '',
+            name: 'Ramprasad Neethiraj',
+            affiliation: 'School of Engineering sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden',
+            email: 'rne@kth.se',
+            github: 'https://github.com/ramprasadn',
+            contribution: ['author', 'maintainer'],
+            orcid: 'https://orcid.org/0000-0001-7313-3734'
+        ],
+        [
+            name: 'Anders Jemt',
+            affiliation: 'Genomics Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden',
+            email: 'anders.jemt@scilifelab.se',
+            github: 'https://github.com/jemten',
+            contribution: ['author', 'maintainer'],
+            orcid: 'https://orcid.org/0000-0002-2219-0197'
+        ],
+        [
+            name: 'Mei Wu',
+            github: 'https://github.com/projectoriented',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Lucía Peña-Pérez',
+            affiliation: 'Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden',
+            email: 'lucia.pena.perez@scilifelab.se',
+            github: 'https://github.com/Lucpen',
+            contribution: ['contributor'],
+            orcid: 'https://orcid.org/0000-0002-5044-7754'
+        ],
+        [
+            name: 'Peter Pruisscher',
+            affiliation: 'Genomics Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden',
+            email: 'peter.pruisscher@scilifelab.se',
+            github: 'https://github.com/peterpru',
+            contribution: ['contributor'],
+            orcid: 'https://orcid.org/0000-0002-6987-5839'
+        ],
+        [
+            name: 'Anders Sune Pedersen',
+            affiliation: 'Danish National Genome Center',
+            email: 'aspe@clin.au.dk',
+            github: 'https://github.com/asp8200',
+            contribution: ['contributor'],
+            orcid: 'https://orcid.org/0009-0008-1112-841X'
+        ],
+        [
+            name: 'Gwenna Breton',
+            affiliation: 'Clinical Genomics Gothenburg, Sahlgrenska University Hospital and University of Gothenburg',
+            email: 'gwenna.breton@gu.se',
+            github: 'https://github.com/Gwennid',
+            contribution: ['contributor'],
+            orcid: 'https://orcid.org/0000-0002-4100-9963'
+        ],
+        [
+            name: 'Sima Rahimi',
+            affiliation: 'Clinical Genomics Lund, Lund University',
+            email: 'sima.rahimi@med.lu.se',
+            github: 'https://github.com/sima-r',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Felix Lenner',
+            affiliation: 'Department of Immunology, Genetics and Pathology, Uppsala University, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden',
+            email: 'felix.lenner@scilifelab.se',
+            github: 'https://github.com/fellen31',
+            contribution: ['contributor'],
+            orcid: 'https://orcid.org/0000-0002-9594-0710'
+        ],
+        [
+            name: 'Maxime U Garcia',
+            affiliation: 'Seqera',
+            email: 'maxime.garcia@seqera.io',
+            github: 'https://github.com/maxulysse',
+            contribution: ['contributor'],
+            orcid: 'https://orcid.org/0000-0003-2827-9261'
+        ],
+        [
+            name: 'Eva Caceres',
+            affiliation: 'Clinical Genomics Stockholm',
+            email: 'eva.caceres@scilifelab.se',
+            github: 'https://github.com/fevac',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'and the nf-core/raredisease team',
+            affiliation: 'nf-core community',
             email: '',
-            github: '',
-            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            github: 'https://github.com/nf-core',
+            contribution: ['contributor'],
             orcid: ''
-        ],
+        ]
     ]
     homePage        = 'https://github.com/nf-core/raredisease'
     description     = """call and score variants from WGS/WES of rare disease patients"""
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
-    version         = '2.3.0dev'
-    doi             = ''
+    version         = '2.3.0'
+    doi             = '10.5281/zenodo.7995798'
 }
 
 // Load DSL2 module options from config files, where each file contains the options for modules used in the eponymous subworkflow.

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json