Merge branch 'dev' into test-template-update-2.13.2dev

CHANGELOG.md

@@ -5,9 +5,27 @@ All notable changes to this project will be documented in this file.
 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).
 
+## dev
+
+### Added
+
+### Changed
+
+- [#1513](https://github.com/nf-core/sarek/pull/1513) - Back to dev
+
+### Fixed
+
+### Removed
+
+### Dependencies
+
+### Modules / Subworkflows
+
+### Parameters
+
 ## [3.4.2](https://github.com/nf-core/sarek/releases/tag/3.4.2) - Sájtáristjåhkkå
 
-Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is one of the few peak in Sweden that cannot be climbed without proper climbing equipments.
+Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is one of the few peaks in Sweden that cannot be climbed without proper climbing equipment.
 
 ### Added
 
@@ -22,6 +40,9 @@ Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is
 - [#1485](https://github.com/nf-core/sarek/pull/1485) - Update citation for publication
 - [#1487](https://github.com/nf-core/sarek/pull/1487) - Update sentieon-modules to Sentieon `202308.02`
 - [#1490](https://github.com/nf-core/sarek/pull/1490) - Update mosdepth to `0.3.8`
+- [#1505](https://github.com/nf-core/sarek/pull/1505) - Update CITATIONS.md
+- [#1506](https://github.com/nf-core/sarek/pull/1506) - Fixing typos (`index_alignement` -> `index_alignment`)
+- [#1509](https://github.com/nf-core/sarek/pull/1509) - Update contributors
 
 ### Fixed
 

CITATIONS.md

@@ -70,6 +70,8 @@
 
 - [FGBio](https://github.com/fulcrumgenomics/fgbio)
 
+  > doi: 10.5281/zenodo.10456900
+
 - [FreeBayes](https://arxiv.org/abs/1207.3907)
 
   > Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012. doi: 10.48550/arXiv.1207.3907

README.md

@@ -153,13 +153,15 @@ We thank the following people for their extensive assistance in the development
 - [Johannes Alneberg](https://github.com/alneberg)
 - [José Fernández Navarro](https://github.com/jfnavarro)
 - [Júlia Mir Pedrol](https://github.com/mirpedrol)
+- [Ken Brewer](https://github.com/kenibrewer)
 - [Lasse Westergaard Folkersen](https://github.com/lassefolkersen)
 - [Lucia Conde](https://github.com/lconde-ucl)
 - [Malin Larsson](https://github.com/malinlarsson)
 - [Marcel Martin](https://github.com/marcelm)
 - [Nick Smith](https://github.com/nickhsmith)
 - [Nicolas Schcolnicov](https://github.com/nschcolnicov)
 - [Nilesh Tawari](https://github.com/nilesh-tawari)
+- [Nils Homer](https://github.com/nh13)
 - [Olga Botvinnik](https://github.com/olgabot)
 - [Oskar Wacker](https://github.com/WackerO)
 - [pallolason](https://github.com/pallolason)
@@ -169,6 +171,7 @@ We thank the following people for their extensive assistance in the development
 - [Sam Minot](https://github.com/sminot)
 - [Sebastian-D](https://github.com/Sebastian-D)
 - [Silvia Morini](https://github.com/silviamorins)
+- [Simon Pearce](https://github.com/SPPearce)
 - [Solenne Correard](https://github.com/scorreard)
 - [Susanne Jodoin](https://github.com/SusiJo)
 - [Szilveszter Juhos](https://github.com/szilvajuhos)
@@ -193,7 +196,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 If you use `nf-core/sarek` for your analysis, please cite the `Sarek` article as follows:
 
-> Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven Nahnsen **Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery** _ NAR Genomics and Bioinformatics_ Volume 6, Issue 2, June 2024, lqae031, [doi: 10.1093/nargab/lqae031](https://doi.org/10.1093/nargab/lqae031).
+> Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven Nahnsen **Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery** _NAR Genomics and Bioinformatics_ Volume 6, Issue 2, June 2024, lqae031, [doi: 10.1093/nargab/lqae031](https://doi.org/10.1093/nargab/lqae031).
 
 > Garcia M, Juhos S, Larsson M et al. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved]** _F1000Research_ 2020, 9:63 [doi: 10.12688/f1000research.16665.2](http://dx.doi.org/10.12688/f1000research.16665.2).
 

main.nf

@@ -162,7 +162,7 @@ workflow NFCORE_SAREK {
                                     : PREPARE_GENOME.out.hashtable
 
     // Gather index for mapping given the chosen aligner
-    index_alignement = (aligner == "bwa-mem" || aligner == "sentieon-bwamem") ? bwa :
+    index_alignment = (aligner == "bwa-mem" || aligner == "sentieon-bwamem") ? bwa :
         aligner == "bwa-mem2" ? bwamem2 :
         dragmap
 
@@ -279,7 +279,7 @@ workflow NFCORE_SAREK {
         gc_file,
         germline_resource,
         germline_resource_tbi,
-        index_alignement,
+        index_alignment,
         intervals_and_num_intervals,
         intervals_bed_combined,
         intervals_bed_combined_for_variant_calling,

nextflow.config

@@ -397,7 +397,7 @@ manifest {
     description     = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '3.4.2'
+    version         = '3.5.0dev'
     doi             = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425'
 }
 

workflows/sarek/main.nf

@@ -106,7 +106,7 @@ workflow SAREK {
         gc_file
         germline_resource
         germline_resource_tbi
-        index_alignement
+        index_alignment
         intervals_and_num_intervals
         intervals_bed_combined
         intervals_bed_combined_for_variant_calling
@@ -188,7 +188,7 @@ workflow SAREK {
                 input_fastq,
                 fasta,
                 fasta_fai,
-                index_alignement,
+                index_alignment,
                 params.group_by_umi_strategy)
 
             bam_converted_from_fastq = FASTQ_CREATE_UMI_CONSENSUS_FGBIO.out.consensusbam.map{ meta, bam -> [ meta, bam, [] ] }
@@ -255,7 +255,7 @@ workflow SAREK {
 
         // reads will be sorted
         sort_bam = true
-        FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON(reads_for_alignment, index_alignement, sort_bam, fasta, fasta_fai)
+        FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON(reads_for_alignment, index_alignment, sort_bam, fasta, fasta_fai)
 
         // Grouping the bams from the same samples not to stall the workflow
         // Use groupKey to make sure that the correct group can advance as soon as it is complete