Add sex check

CHANGELOG.md

@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - New parameters to skip fastqc and haplocheck (`--skip_fastqc` and `--skip_haplocheck`) [#438](https://github.com/nf-core/raredisease/pull/438)
 - CNVnator for copy number variant calling [#438](https://github.com/nf-core/raredisease/pull/434)
 - A new parameter `svdb_query_bedpedbs` to provide bedpe files as databases for SVDB query [#449](https://github.com/nf-core/raredisease/pull/449)
+- ngsbits samplegender to check sex
 
 ### `Changed`
 

CITATIONS.md

@@ -80,6 +80,8 @@
 
   > Pedersen BS, Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Hancock J, ed. Bioinformatics. 2018;34(5):867-868. doi:10.1093/bioinformatics/btx699
 
+- [ngs-bits-samplegender](https://github.com/imgag/ngs-bits/tree/master)
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

conf/modules/qc_bam.config

@@ -53,6 +53,16 @@ process {
         ext.prefix = { "${meta.id}_mosdepth" }
     }
 
+    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 }
+        publishDir = [
+            path: { "${params.outdir}/ngsbits_samplegender" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS' {
         ext.when = { params.analysis_type.equals("wgs") && params.aligner.equals("bwamem2") }
         ext.prefix = { "${meta.id}_wgsmetrics" }

modules.json

@@ -277,6 +277,11 @@
                         "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
                         "installed_by": ["modules"]
                     },
+                    "ngsbits/samplegender": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "peddy": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

subworkflows/local/qc_bam.nf

@@ -12,6 +12,7 @@ include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS   } from '../../m
 include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_Y } from '../../modules/nf-core/picard/collectwgsmetrics/main'
 include { SENTIEON_WGSMETRICS                                                        } from '../../modules/nf-core/sentieon/wgsmetrics/main'
 include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_Y           } from '../../modules/nf-core/sentieon/wgsmetrics/main'
+include { NGSBITS_SAMPLEGENDER                                   } from '../../modules/nf-core/ngsbits/samplegender/main'
 
 workflow QC_BAM {
 
@@ -59,6 +60,9 @@ workflow QC_BAM {
         SENTIEON_WGSMETRICS ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs.map{ interval -> [[:], interval]} )
         SENTIEON_WGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y.map{ interval -> [[:], interval]} )
 
+        // Check sex
+        NGSBITS_SAMPLEGENDER(ch_bam_bai, ch_genome_fasta, ch_genome_fai, "xy")
+
         ch_cov   = Channel.empty().mix(PICARD_COLLECTWGSMETRICS.out.metrics, SENTIEON_WGSMETRICS.out.wgs_metrics)
         ch_cov_y = Channel.empty().mix(PICARD_COLLECTWGSMETRICS_Y.out.metrics, SENTIEON_WGSMETRICS_Y.out.wgs_metrics)
 
@@ -67,6 +71,7 @@ workflow QC_BAM {
         ch_versions = ch_versions.mix(TIDDIT_COV.out.versions.first())
         ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions.first())
         ch_versions = ch_versions.mix(MOSDEPTH.out.versions.first())
+        ch_versions = ch_versions.mix(NGSBITS_SAMPLEGENDER.out.versions.first())
         ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first(), SENTIEON_WGSMETRICS.out.versions.first())
         ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS_Y.out.versions.first(), SENTIEON_WGSMETRICS_Y.out.versions.first())
 
@@ -78,6 +83,7 @@ workflow QC_BAM {
         bigwig           = UCSC_WIGTOBIGWIG.out.bw                   // channel: [ val(meta), path(bw) ]
         d4               = MOSDEPTH.out.per_base_d4                  // channel: [ val(meta), path(d4) ]
         global_dist      = MOSDEPTH.out.global_txt                   // channel: [ val(meta), path(txt) ]
+        sex_check        = NGSBITS_SAMPLEGENDER.out.tsv              // channel: [val(meta), path(tsv) ]
         cov              = ch_cov                                    // channel: [ val(meta), path(metrics) ]
         cov_y            = ch_cov_y                                  // channel: [ val(meta), path(metrics) ]
         versions         = ch_versions                               // channel: [ path(versions.yml) ]