Merge branch 'dev' into pl_goleft

.github/workflows/ci.yml

@@ -247,6 +247,7 @@ jobs:
           - tags: "gatk4spark/applybqsr"
           - tags: "gatk4spark/markduplicates"
           - tags: "gawk"
+          - tags: "lofreq/callparallel"
           - tags: "mosdepth"
           - tags: "multiqc"
           - tags: "ngscheckmate/ncm"

CHANGELOG.md

@@ -5,6 +5,54 @@ 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
+
+- [1640](https://github.com/nf-core/sarek/pull/1620) - Add `lofreq` as a tumor-only variant caller.
+- [1642](https://github.com/nf-core/sarek/pull/1642) - Back to dev
+
+### Changed
+
+### Fixed
+
+### Removed
+
+### Dependencies
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `lofreq`   |             | 2.1.5       |
+
+### Parameters
+
+## [3.4.4](https://github.com/nf-core/sarek/releases/tag/3.4.4) - Ruopsokjåkhå
+
+Ruopsokjåkhå is another peak of the Pårte massif.
+
+### Added
+
+- [1614](https://github.com/nf-core/sarek/pull/1614) - Back to dev
+- [1639](https://github.com/nf-core/sarek/pull/1639) - Bump version to prepare release
+
+### Changed
+
+- [1627](https://github.com/nf-core/sarek/pull/1627) - Correct tower reports/snpeff format
+
+### Fixed
+
+- [1623](https://github.com/nf-core/sarek/pull/1623) - Update docs to clarify vep cache folder organisation
+- [1628](https://github.com/nf-core/sarek/pull/1628) - Fix dbsnp channel mapping in germline variant calling subworkflow
+
+### Removed
+
+### Dependencies
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+
+### Parameters
+
 ## [3.4.3](https://github.com/nf-core/sarek/releases/tag/3.4.3) - Loametjåhkkå
 
 Loametjåhkkå is another one of the main peaks of the Pårte massif.

CITATIONS.md

@@ -146,6 +146,10 @@
 
   > Danecek P, Auton A, Abecasis G, et al.: The variant call format and VCFtools. Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. PubMed PMID: 21653522; PubMed Central PMCID: PMC3137218.
 
+- [Lofreq](https://pubmed.ncbi.nlm.nih.gov/23066108/)
+
+  > Wilm et al. LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 2012; 40(22):11189-201.
+
 ## R packages
 
 - [R](https://www.R-project.org/)

README.md

@@ -61,6 +61,7 @@ Depending on the options and samples provided, the pipeline can currently perfor
   - `Sentieon Haplotyper`
   - `Strelka2`
   - `TIDDIT`
+  - `Lofreq`
 - Variant filtering and annotation (`SnpEff`, `Ensembl VEP`, `BCFtools annotate`)
 - Summarise and represent QC (`MultiQC`)
 
@@ -132,6 +133,7 @@ We thank the following people for their extensive assistance in the development
 - [Abhinav Sharma](https://github.com/abhi18av)
 - [Adam Talbot](https://github.com/adamrtalbot)
 - [Adrian Lärkeryd](https://github.com/adrlar)
+- [Àitor Olivares](https://github.com/AitorPeseta)
 - [Alexander Peltzer](https://github.com/apeltzer)
 - [Alison Meynert](https://github.com/ameynert)
 - [Anders Sune Pedersen](https://github.com/asp8200)
@@ -145,6 +147,7 @@ We thank the following people for their extensive assistance in the development
 - [Edmund Miller](https://github.com/edmundmiller)
 - [Famke Bäuerle](https://github.com/famosab)
 - [Francesco Lescai](https://github.com/lescai)
+- [Francisco Martínez](https://github.com/nevinwu)
 - [Gavin Mackenzie](https://github.com/GCJMackenzie)
 - [Gisela Gabernet](https://github.com/ggabernet)
 - [Grant Neilson](https://github.com/grantn5)

assets/multiqc_config.yml

@@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/sarek/
 custom_logo_title: "nf-core/sarek"
 
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/sarek/releases/tag/3.4.3" target="_blank">nf-core/sarek</a>
+  This report has been generated by the <a href="https://github.com/nf-core/sarek/tree/dev" target="_blank">nf-core/sarek</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/sarek/3.4.3/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/sarek/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-sarek-methods-description":
     order: -1000

conf/modules/lofreq.config

@@ -0,0 +1,45 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+        ext.when   = When to run the module.
+----------------------------------------------------------------------------------------
+*/
+
+//LOFREQ
+
+process {
+    if (params.tools && params.tools.split(',').contains('lofreq')) {
+
+        withName: "LOFREQ_CALLPARALLEL" {
+            ext.args = { "--call-indels" }
+            ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.lofreq" : "${meta.id}.lofreq.${intervals.baseName}" }
+            ext.when   = { params.tools && params.tools.split(',').contains('lofreq') }
+            publishDir = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/" },
+                pattern: "*{vcf.gz,vcf.gz.tbi}",
+                saveAs: { meta.num_intervals > 1 ? null : "lofreq/${meta.id}/${it}" }
+            ]
+        }
+
+        withName:'VCFTOOLS_TSTV_COUNT'{
+            errorStrategy = 'ignore'
+        }
+
+        withName: 'MERGE_LOFREQ.*' {
+            ext.prefix = { "${meta.id}.lofreq" }
+            publishDir = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/lofreq/${meta.id}" },
+                pattern: "*{vcf.gz,vcf.gz.tbi}"
+            ]
+        }
+    }
+
+}