Tiddit subworkflow

CHANGELOG.md

@@ -89,10 +89,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#630](https://github.com/nf-core/sarek/pull/630) - Update citations file
 - [#632](https://github.com/nf-core/sarek/pull/632) - Update `snpEff` version to `5.1` and cache up to `105`
 - [#632](https://github.com/nf-core/sarek/pull/632) - Update `VEP` version to `106.1` and cache up to `106`
+- [#618](https://github.com/nf-core/sarek/pull/618) - Update `multiqc` module update test yml files
+- [#618](https://github.com/nf-core/sarek/pull/618) - Update test yml files
 - [#633](https://github.com/nf-core/sarek/pull/633) - Update `BCFTOOLS` version to `1.15.1`
 - [#644](https://github.com/nf-core/sarek/pull/644) - Use `-Y` for `bwa-mem(2)` and remove `-M`
 - [#645](https://github.com/nf-core/sarek/pull/645) - Merge `tests/nextflow.config` in `conf/test.config`
 - [#646](https://github.com/nf-core/sarek/pull/646) - Update `nextflow_schema.json` to reflect new parameters and functions, removes `--annotation_cache`, removes `--ascat_chromosomes`
+- [#651](https://github.com/nf-core/sarek/pull/651) - Added TIDDIT_SOMATIC subworkflow
 - [#653](https://github.com/nf-core/sarek/pull/653) - Coherent results subfolder structure between preprocessing, variantcalling and reporting
 
 ### Fixed

conf/modules.config

@@ -1091,21 +1091,21 @@ process{
 
     if (params.tools && params.tools.split(',').contains('tiddit')) {
     //TIDDIT
-        withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' {
+        withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_SOMATIC:RUN_TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' {
             ext.prefix       = {"${meta.id}.tiddit.normal"}
         }
 
-        withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' {
+        withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_SOMATIC:RUN_TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' {
             ext.prefix       = {"${meta.id}.tiddit.tumor"}
         }
 
         //SVDB
-        withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:SVDB_MERGE' {
+        withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_SOMATIC:SVDB_MERGE' {
             ext.prefix       = { "${meta.id}.tiddit" }
             publishDir       = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" },
-                pattern: "*vcf"
+                pattern: "*{vcf,vcf.gz}"
             ]
         }
     }

subworkflows/local/pair_variant_calling.nf

@@ -11,9 +11,7 @@ include { RUN_CNVKIT                                } from '../nf-core/variantca
 include { RUN_MPILEUP as RUN_MPILEUP_NORMAL         } from '../nf-core/variantcalling/mpileup/main'
 include { RUN_MPILEUP as RUN_MPILEUP_TUMOR          } from '../nf-core/variantcalling/mpileup/main'
 include { RUN_ASCAT_SOMATIC                         } from '../nf-core/variantcalling/ascat/main'
-include { RUN_TIDDIT as RUN_TIDDIT_NORMAL           } from '../nf-core/variantcalling/tiddit/main.nf'
-include { RUN_TIDDIT as RUN_TIDDIT_TUMOR            } from '../nf-core/variantcalling/tiddit/main.nf'
-include { SVDB_MERGE                                } from '../../modules/nf-core/modules/svdb/merge/main.nf'
+include { RUN_TIDDIT_SOMATIC                        } from '../nf-core/variantcalling/tiddit/tiddit_somatic/main'
 
 workflow PAIR_VARIANT_CALLING {
     take:
@@ -224,17 +222,9 @@ workflow PAIR_VARIANT_CALLING {
             [meta, tumor_cram, tumor_crai]
         }
 
-        RUN_TIDDIT_NORMAL(cram_normal, fasta, bwa)
-        RUN_TIDDIT_TUMOR(cram_tumor, fasta, bwa)
-        SVDB_MERGE(RUN_TIDDIT_NORMAL.out.tiddit_vcf.join(RUN_TIDDIT_TUMOR.out.tiddit_vcf)
-                                                    .map{meta, vcf_normal, vcf_tumor ->
-                                                        [meta, [vcf_normal, vcf_tumor]]
-                                                    }, false)
-        tiddit_vcf = SVDB_MERGE.out.vcf
-
-        ch_versions = ch_versions.mix(RUN_TIDDIT_NORMAL.out.versions)
-        ch_versions = ch_versions.mix(RUN_TIDDIT_TUMOR.out.versions)
-        ch_versions = ch_versions.mix(SVDB_MERGE.out.versions)
+        RUN_TIDDIT_SOMATIC(cram_normal, cram_tumor, fasta, bwa)
+        tiddit_vcf = RUN_TIDDIT_SOMATIC.out.tiddit_vcf
+        ch_versions = ch_versions.mix(RUN_TIDDIT_SOMATIC.out.versions)
     }
 
     emit: