Merge branch 'dev' into targetbedtodeepvariant

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - Change the regions used by deepavariant for WES samples from bait interval files to target bed files [#636](https://github.com/nf-core/raredisease/pull/636)
+- Merge output from germlinecnvcaller [#635](https://github.com/nf-core/raredisease/pull/635)
 - Update tools [#623](https://github.com/nf-core/raredisease/pull/623)
 - Update output file name prefix for upd and chromograph to sample-based [#620](https://github.com/nf-core/raredisease/pull/620)
 - Update tools [#619](https://github.com/nf-core/raredisease/pull/619)

assets/multiqc_config.yml

@@ -18,6 +18,7 @@ export_plots: true
 
 run_modules:
   - fastqc
+  - fastp
   - qualimap
   - picard
   - mosdepth
@@ -33,6 +34,8 @@ module_order:
       name: "Picard"
   - qualimap:
       name: "Qualimap"
+  - fastp:
+      name: "fastp"
   - mosdepth:
       name: "Mosdepth"
   - peddy:

conf/modules/call_sv_germlinecnvcaller.config

@@ -34,4 +34,9 @@ process {
         ext.prefix = { "${meta.id}_gatkcnv_segments_refiltered" }
         ext.args = { '--output-type z --exclude "N_ALT = 0" ' }
     }
+
+    withName: '.*CALL_STRUCTURAL_VARIANTS:CALL_SV_GERMLINECNVCALLER:SVDB_MERGE_GCNVCALLER' {
+        ext.args   = '--notag --pass_only'
+        ext.prefix = { "${meta.id}_gcnvcaller" }
+    }
 }

nextflow.config

@@ -283,11 +283,6 @@ podman.registry       = 'quay.io'
 singularity.registry  = 'quay.io'
 charliecloud.registry = 'quay.io'
 
-// Load wes.config if --analysis_type='wes'
-if (params.analysis_type == 'wes') {
-    includeConfig 'conf/wes.config'
-}
-
 // Load igenomes.config if required
 includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
 

subworkflows/local/call_structural_variants.nf

@@ -58,7 +58,7 @@ workflow CALL_STRUCTURAL_VARIANTS {
         }
 
         if (!params.skip_germlinecnvcaller) {
-            CALL_SV_GERMLINECNVCALLER (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_readcount_intervals, ch_genome_dictionary, ch_ploidy_model, ch_gcnvcaller_model)
+            CALL_SV_GERMLINECNVCALLER (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_readcount_intervals, ch_genome_dictionary, ch_ploidy_model, ch_gcnvcaller_model, ch_case_info)
                 .genotyped_filtered_segments_vcf
                 .collect{it[1]}
                 .set { gcnvcaller_vcf }

subworkflows/local/variant_calling/call_sv_cnvnator.nf

@@ -44,6 +44,7 @@ workflow CALL_SV_CNVNATOR {
         ch_versions = ch_versions.mix(CNVNATOR_PARTITION.out.versions)
         ch_versions = ch_versions.mix(CNVNATOR_CALL.out.versions)
         ch_versions = ch_versions.mix(CNVNATOR_CONVERT2VCF.out.versions)
+        ch_versions = ch_versions.mix(SVDB_MERGE_CNVNATOR.out.versions)
 
     emit:
         vcf        = SVDB_MERGE_CNVNATOR.out.vcf  // channel: [ val(meta), path(*.tar.gz) ]

subworkflows/local/variant_calling/call_sv_germlinecnvcaller.nf

@@ -8,6 +8,7 @@ include { GATK4_GERMLINECNVCALLER             } from '../../../modules/nf-core/g
 include { GATK4_POSTPROCESSGERMLINECNVCALLS   } from '../../../modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf'
 include { BCFTOOLS_VIEW                       } from '../../../modules/nf-core/bcftools/view/main'
 include { TABIX_TABIX                         } from '../../../modules/nf-core/tabix/tabix/main'
+include { SVDB_MERGE as SVDB_MERGE_GCNVCALLER } from '../../../modules/nf-core/svdb/merge/main'
 
 workflow CALL_SV_GERMLINECNVCALLER {
     take:
@@ -18,6 +19,7 @@ workflow CALL_SV_GERMLINECNVCALLER {
         ch_genome_dictionary   // channel: [mandatory][ val(meta), path(ch_dict) ]
         ch_ploidy_model        // channel: [mandatory][ path(ch_ploidy_model) ]
         ch_gcnvcaller_model    // channel: [mandatory][ path(ch_gcnvcaller_model) ]
+        ch_case_info           // channel: [mandatory] [ val(case_info) ]
 
     main:
         ch_versions = Channel.empty()
@@ -56,17 +58,29 @@ workflow CALL_SV_GERMLINECNVCALLER {
         // Filter out reference only (0/0) segments
         BCFTOOLS_VIEW (ch_segments_in , [], [], [] )
 
+        BCFTOOLS_VIEW.out.vcf
+            .collect{it[1]}
+            .toList()
+            .set { vcf_file_list }
+
+        ch_case_info
+            .combine(vcf_file_list)
+            .set { merge_input_vcfs }
+
+        SVDB_MERGE_GCNVCALLER ( merge_input_vcfs, [] )
+
         ch_versions = ch_versions.mix(GATK4_COLLECTREADCOUNTS.out.versions)
         ch_versions = ch_versions.mix(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.versions)
         ch_versions = ch_versions.mix(GATK4_GERMLINECNVCALLER.out.versions)
         ch_versions = ch_versions.mix(GATK4_POSTPROCESSGERMLINECNVCALLS.out.versions)
         ch_versions = ch_versions.mix(TABIX_TABIX.out.versions)
         ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions)
+        ch_versions = ch_versions.mix(SVDB_MERGE_GCNVCALLER.out.versions)
 
     emit:
         genotyped_intervals_vcf          = GATK4_POSTPROCESSGERMLINECNVCALLS.out.intervals  // channel: [ val(meta), path(*.vcf.gz) ]
         genotyped_segments_vcf           = GATK4_POSTPROCESSGERMLINECNVCALLS.out.segments   // channel: [ val(meta), path(*.vcf.gz) ]
-        genotyped_filtered_segments_vcf  = BCFTOOLS_VIEW.out.vcf                            // channel: [ val(meta), path(*.vcf.gz) ]
+        genotyped_filtered_segments_vcf  = SVDB_MERGE_GCNVCALLER.out.vcf                    // channel: [ val(meta), path(*.vcf.gz) ]
         denoised_vcf                     = GATK4_POSTPROCESSGERMLINECNVCALLS.out.denoised   // channel: [ val(meta), path(*.vcf.gz) ]
         versions                         = ch_versions                                      // channel: [ versions.yml ]
 }