git pull upstream

Author: emmadizdarevic

CHANGELOG.md

@@ -45,6 +45,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#789](https://github.com/nf-core/raredisease/pull/789)
 - Remove redundant TABIX processes, and update configs for nf-test [#790](https://github.com/nf-core/raredisease/pull/790)
 - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#791](https://github.com/nf-core/raredisease/pull/791)
+- Remove Qualimap and Haplogrep3 as they were made redundant by Picard and VerifyBamID2 [#801](https://github.com/nf-core/raredisease/pull/801)
 
 ### `Fixed`
 
@@ -80,6 +81,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | gens-preproc          | 1.0.11      |             |
 | gens/preparecovandbaf |             | 1.1.5       |
 | haplocheck            | 1.3.3       |             |
+| haplogrep3            | 3.2.2       |             |
 | hmtnote               | 0.7.2       |             |
 | htslib                | 1.20        | 1.21        |
 | MitoSalt              |             | 1.1.1       |
@@ -88,6 +90,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | ngsbits               | 202411      | 202512      |
 | picard                | 3.3.0       | 3.4.0       |
 | pigz                  | 2.3.4       | 2.8         |
+| qualimap              | 2.3         |             |
 | sambamba              |             | 1.0.1       |
 | samtools              | 1.21        | 1.22.1      |
 | sentieon              | 202503      | 202503.02   |

CITATIONS.md

@@ -74,10 +74,6 @@
 
   > Yun T, Li H, Chang PC, Lin MF, Carroll A, McLean CY. Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Robinson P, ed. Bioinformatics. 2021;36(24):5582-5589. doi:10.1093/bioinformatics/btaa1081
 
-- [HaploGrep 3](https://academic.oup.com/nar/article/51/W1/W263/7177898)
-
-  > Schönherr S, Weissensteiner H, Kronenberg F, Forer L. Haplogrep 3 an interactive haplogroup classification and analysis platform. Nucleic Acids Res. 2023;51(W1):W263-W268. doi:10.1093/nar/gkad284
-
 - [Manta](https://academic.oup.com/bioinformatics/article/32/8/1220/1743909?login=true)
 
   > Chen X, Schulz-Trieglaff O, Shaw R, et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016;32(8):1220-1222. doi:10.1093/bioinformatics/btv710
@@ -98,10 +94,6 @@
 
 - [Picard](https://broadinstitute.github.io/picard/)
 
-- [Qualimap](https://academic.oup.com/bioinformatics/article/32/2/292/1744356?login=true)
-
-  > Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 2016;32(2):292-294. doi:10.1093/bioinformatics/btv566
-
 - [RetroSeq](https://academic.oup.com/bioinformatics/article/29/3/389/257479)
 
   > Thomas M. Keane, Kim Wong, David J. Adams, RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics.2013 Feb 1;29(3):389-90. doi: 10.1093/bioinformatics/bts697

README.md

@@ -66,7 +66,6 @@ On release, automated continuous integration tests run the pipeline on a full-si
 - [Mosdepth](https://github.com/brentp/mosdepth)
 - [MultiQC](http://multiqc.info/)
 - [Picard's CollectMultipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)
-- [Qualimap](http://qualimap.conesalab.org/)
 - [Sambamba](https://github.com/biod/sambamba)
 - [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)
 - [TIDDIT's cov](https://github.com/J35P312/)
@@ -109,7 +108,6 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 - [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)
 - Annotation:
-  - [HaploGrep3](https://github.com/genepi/haplogrep3)
   - [vcfanno](https://github.com/brentp/vcfanno)
   - [CADD](https://cadd.gs.washington.edu/)
   - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)

assets/multiqc_config.yml

@@ -20,7 +20,6 @@ export_plots: true
 run_modules:
   - fastqc
   - fastp
-  - qualimap
   - picard
   - mosdepth
   - ngsbits
@@ -35,8 +34,6 @@ module_order:
         - "*.zip"
   - picard:
       name: "Picard"
-  - qualimap:
-      name: "Qualimap"
   - fastp:
       name: "fastp"
   - mosdepth:

conf/modules/annotate_mt_snvs.config

@@ -52,9 +52,4 @@ process {
         ext.args   = "--output-type z --write-index=tbi"
         ext.args2  = { "-i 'FMT/AF>=${params.homoplasmy_af_threshold} && FMT/DP>=100'" }
     }
-
-    withName: '.*ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT' {
-        ext.args   = '--tree phylotree-rsrs@17.1'
-        ext.prefix = { "${meta.prefix}_haplogrep" }
-    }
 }

conf/modules/qc_bam.config

@@ -26,10 +26,6 @@ process {
         ext.prefix = { "${meta.id}_hsmetrics" }
     }
 
-    withName: '.*QC_BAM:QUALIMAP_BAMQC' {
-        ext.prefix = { "${meta.id}_qualimap" }
-    }
-
     withName: '.*QC_BAM:TIDDIT_COV' {
         ext.args = '-z 500 -w'
         ext.prefix = { "${meta.id}_tidditcov" }

conf/test.config

@@ -32,7 +32,7 @@ params {
     mito_name                       = 'MT'
     pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
 
-    skip_tools                      = 'fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,ngsbits'
+    skip_tools                      = 'fastp,gens,peddy,germlinecnvcaller,ngsbits'
 
     input                           = params.pipelines_testdata_base_path + '/testdata/samplesheet_fq_spring.csv'
     fasta                           = params.pipelines_testdata_base_path + '/reference/reference.fasta'

conf/test_bam.config

@@ -30,7 +30,7 @@ params {
     mito_name                       = 'MT'
     pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/'
 
-    skip_tools                      = "fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits"
+    skip_tools                      = "fastp,gens,peddy,germlinecnvcaller,eklipse,ngsbits"
 
     input                           = params.pipelines_testdata_base_path + 'testdata/samplesheet_bam.csv'
 

conf/test_sentieon.config

@@ -29,7 +29,7 @@ params {
     igenomes_ignore                 = true
     mito_name                       = 'MT'
 
-    skip_tools                      = "fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits"
+    skip_tools                      = "fastp,gens,peddy,germlinecnvcaller,eklipse,ngsbits"
 
     // Input data
     pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/'

conf/test_singleton.config

@@ -30,7 +30,7 @@ params {
     mito_name                       = 'MT'
     pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/'
 
-    skip_tools                      = "fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits"
+    skip_tools                      = "fastp,gens,peddy,germlinecnvcaller,eklipse,ngsbits"
 
     input                           = params.pipelines_testdata_base_path + 'testdata/samplesheet_single.csv'
     fasta                           = params.pipelines_testdata_base_path + 'reference/reference.fasta'