Merge remote-tracking branch 'upstream/dev' into multiple-entry-points

CHANGELOG.md

@@ -3,12 +3,17 @@
 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 - Abu [xxxx-xx-xx]
+## v1.2.0 - Genie [xxxx-xx-xx]
+
+### `Added`
+
+### `Fixed`
+
+## v1.1.0 - Abu [2023-07-21]
 
 ### `Added`
 
 - Add GATK's cnv calling pipeline [#362](https://github.com/nf-core/raredisease/pull/362)
-- Add `public_aws_ecr` profile for using AWS ECR public gallery images [#360](https://github.com/nf-core/raredisease/pull/360)
 - GATK's ShiftFasta to generate all the files required for mitochondrial analysis [#354](https://github.com/nf-core/raredisease/pull/354)
 - Feature to calculate CADD scores for indels [#325](https://github.com/nf-core/raredisease/pull/325)
 - HmtNote to annotate mitochondria [#355](https://github.com/nf-core/raredisease/pull/355)

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/1.1.0" target="_blank">nf-core/raredisease</a>
+  This report has been generated by the <a href="https://github.com/nf-core/raredisease/1.2.0dev" 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/1.1.0/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/raredisease/1.2.0dev/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-raredisease-methods-description":
     order: -1000

docs/output.md

@@ -54,6 +54,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   - [Annotation:](#annotation-)
     - [HaploGrep2](#haplogrep2)
     - [vcfanno](#vcfanno-1)
+    - [CADD](#cadd-1)
     - [VEP](#vep-2)
     - [HmtNote](#hmtnote)
 - [Rank variants and filtering](#rank-variants-and-filtering)
@@ -247,15 +248,15 @@ The pipeline performs variant calling using [Sentieon DNAscope](https://support.
 
 #### Manta
 
-[Manta](https://github.com/Illumina/manta) calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It combines paired and split-read evidence during SV discovery and scoring to improve accuracy, but does not require split-reads or successful breakpoint assemblies to report a variant in cases where there is strong evidence otherwise. Output vcf files are treated as intermediates and are not placed in the output folder by default.
+[Manta](https://github.com/Illumina/manta) calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It combines paired and split-read evidence during SV discovery and scoring to improve accuracy, but does not require split-reads or successful breakpoint assemblies to report a variant in cases where there is strong evidence otherwise. Output vcf files are treated as intermediates and are not placed in the output folder.
 
 #### TIDDIT sv
 
-[TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT) is used to identify chromosomal rearrangements using sequencing data. TIDDIT identifies intra and inter-chromosomal translocations, deletions, tandem-duplications and inversions, using supplementary alignments as well as discordant pairs. TIDDIT searches for discordant reads and split reads (supplementary alignments). Output vcf files are treated as intermediates and are not placed in the output folder by default.
+[TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT) is used to identify chromosomal rearrangements using sequencing data. TIDDIT identifies intra and inter-chromosomal translocations, deletions, tandem-duplications and inversions, using supplementary alignments as well as discordant pairs. TIDDIT searches for discordant reads and split reads (supplementary alignments). Output vcf files are treated as intermediates and are not placed in the output folder.
 
 #### GATK GermlineCNVCaller - CNV calling
 
-[GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk) is used to identify copy number variants in germline samples given their read counts and a model describing a sample's ploidy. Output vcf files are treated as intermediates and are not placed in the output folder by default.
+[GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk) is used to identify copy number variants in germline samples given their read counts and a model describing a sample's ploidy. Output vcf files are treated as intermediates and are not placed in the output folder.
 
 #### SVDB merge
 
@@ -302,17 +303,17 @@ The pipeline performs variant calling using [Sentieon DNAscope](https://support.
 
 #### bcftools roh
 
-[bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh) is a program for detecting runs of homo/autozygosity.from only bi-allelic sites. The output files are not published in the output folder by default, and is passed to vcfanno for further annotation.
+[bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh) is a program for detecting runs of homo/autozygosity.from only bi-allelic sites. The output files are not published in the output folder, and is passed to vcfanno for further annotation.
 
 #### vcfanno
 
-[vcfanno](https://github.com/brentp/vcfanno) allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF. Values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns. The output files are not published in the output folder by default, and is passed to CADD and/or VEP for further annotation.
+[vcfanno](https://github.com/brentp/vcfanno) allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs. It uses a simple configuration file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF. Values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns. The output files are not published in the output folder, and is passed to CADD and/or VEP for further annotation.
 
 We recommend using vcfanno to annotate SNVs with precomputed CADD scores (files can be downloaded from [here](https://cadd.gs.washington.edu/download)).
 
 #### CADD
 
-[CADD](https://cadd.gs.washington.edu/) is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. In nf-core/raredisease, SNVs can be annotated with precomputed CADD scores using vcfanno. However, for small indels they will be calculated on the fly by CADD. The output files are not published in the output folder by default, and is passed to VEP for further annotation.
+[CADD](https://cadd.gs.washington.edu/) is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. In nf-core/raredisease, SNVs can be annotated with precomputed CADD scores using vcfanno. However, for small indels they will be calculated on the fly by CADD. The output files are not published in the output folder, and is passed to VEP for further annotation.
 
 #### VEP
 
@@ -360,7 +361,7 @@ Based on VEP annotations, custom scripts used by the pipeline further annotate e
 
 #### SVDB query
 
-[SVDB query](https://github.com/J35P312/SVDB#Query) allows you to quickly annotate your VCF with data from one or more structural variant databases. The output files are not published in the output folder by default, and is passed to vep for further annotation.
+[SVDB query](https://github.com/J35P312/SVDB#Query) allows you to quickly annotate your VCF with data from one or more structural variant databases. The output files are not published in the output folder, and is passed to vep for further annotation.
 
 #### VEP
 
@@ -407,17 +408,17 @@ The pipeline for mitochondrial variant discovery, using Mutect2, uses a high sen
 
 ##### vcfanno
 
-[vcfanno](https://github.com/brentp/vcfanno) allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF. Values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns. The output files are not published in the output folder by default, and is passed to vep for further annotation.
+[vcfanno](https://github.com/brentp/vcfanno) allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF. Values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns. The output files are not published in the output folder, and is passed to vep for further annotation.
 
 We recommend using vcfanno to annotate SNVs with precomputed CADD scores (files can be downloaded from [here](https://cadd.gs.washington.edu/download)).
 
-#### CADD
+##### CADD
 
-[CADD](https://cadd.gs.washington.edu/) is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. In nf-core/raredisease, SNVs can be annotated with precomputed CADD scores using vcfanno. However, for small indels they will be calculated on the fly by CADD. The output files are not published in the output folder by default, and is passed to VEP for further annotation.
+[CADD](https://cadd.gs.washington.edu/) is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. In nf-core/raredisease, SNVs can be annotated with precomputed CADD scores using vcfanno. However, for small indels they will be calculated on the fly by CADD. The output files are not published in the output folder, and is passed to VEP for further annotation.
 
 ##### Hmtnote
 
-[HmtNote](https://github.com/robertopreste/HmtNote) annotates vcf containing human mitochondrial variants with HmtVar. It will run offline by default wiht a database within the container.
+[HmtNote](https://github.com/robertopreste/HmtNote) annotates vcf containing human mitochondrial variants with HmtVar. It will run offline by default with a database within the container.
 
 ##### VEP
 

lib/WorkflowRaredisease.groovy

@@ -14,10 +14,6 @@ class WorkflowRaredisease {
 
         genomeExistsError(params, log)
 
-
-        if (!params.fasta) {
-            Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
-        }
     }
 
     //

nextflow.config

@@ -273,7 +273,7 @@ manifest {
     description     = """call and score variants from WGS/WES of rare disease patients"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.1.0'
+    version         = '1.2.0dev'
     doi             = ''
 }