update tiddit/sv

.github/workflows/ci.yml

@@ -33,27 +33,28 @@ jobs:
         test:
           - "aligner"
           - "annotation"
-          - "default"
           - "cnvkit"
           - "controlfreec"
           - "deepvariant"
+          - "default"
           - "freebayes"
           - "gatk4_spark"
           - "haplotypecaller"
           - "manta"
           - "markduplicates"
-          - "mutect2"
           - "msisensorpro"
-          # - 'save_bam_mapped'
+          - "mutect2"
           - "prepare_recalibration"
           - "recalibrate"
-          - "variantcalling_channel"
+          # - 'save_bam_mapped'
           - "skip_markduplicates"
+          - "split_fastq"
           - "strelka"
           - "strelkabp"
-          - "split_fastq"
           - "targeted"
+          - "tiddit"
           - "tumor_normal_pair"
+          - "variantcalling_channel"
 
     steps:
       - name: Check out pipeline code

CHANGELOG.md

@@ -60,6 +60,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#572](https://github.com/nf-core/sarek/pull/572) - Adjusted subway map svg for firefox compatibility
 - [#578](https://github.com/nf-core/sarek/pull/578) - Updated module deeptools/bamcoverage
 - [#585](https://github.com/nf-core/sarek/pull/585) - Remove explicit BAM to CRAM conversion after MarkduplicatesSpark; tool does it internally
+- [#581](https://github.com/nf-core/sarek/pull/581) - `TIDDIT` is updated to `3.1.0`
 
 ### Fixed
 
@@ -87,6 +88,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#567](https://github.com/nf-core/sarek/pull/567) - Fix interval name resolving during scatter/gather by moving logic to modules.config causing name to be correctly resolved on process execution; also fixed duplicate naming when variant callers produce multiple vcf files by adding field `type` to `meta` map
 - [#585](https://github.com/nf-core/sarek/pull/585) - Fix Spark usage for GATK4 modules
 - [#587](https://github.com/nf-core/sarek/pull/587) - Fix issue with VEP extra files
+- [#581](https://github.com/nf-core/sarek/pull/581) - `TIDDIT` is back
 - [#590](https://github.com/nf-core/sarek/pull/590) - Fix empty folders during scatter/gather
 
 ### Deprecated

conf/modules.config

@@ -652,12 +652,24 @@ process{
         ]
     }
 
-    // withName: 'TIDDIT_SV' {
-    //     publishDir       = [
-    //         mode: params.publish_dir_mode,
-    //         path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" }
-    //     ]
-    // }
+    //TIDDIT
+    withName: 'TIDDIT_SV' {
+        ext.when         = { params.tools && params.tools.contains('tiddit') }
+        ext.args         = { bwa_index ? "" : "--skip_assembly" }
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
+            pattern: "*tab",
+        ]
+    }
+    withName : 'TABIX_BGZIP_TIDDIT_SV' {
+        ext.prefix       = { "${meta.id}.vcf" }
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
+            pattern: "*{vcf.gz,vcf.gz.tbi}"
+        ]
+    }
 
 // TUMOR_VARIANT_CALLING
 

modules.json

@@ -232,7 +232,7 @@
                 "git_sha": "b3e9b88e80880f450ad79a95b2b7aa05e1de5484"
             },
             "tiddit/sv": {
-                "git_sha": "57cb730e78634673fb254a77606e014ce942734c"
+                "git_sha": "b689b8ed88a9f89eb2f7c75d3eb0bace77ade109"
             },
             "trimgalore": {
                 "git_sha": "85ec13ff1fc2196c5a507ea497de468101baabed"

subworkflows/local/germline_variant_calling.nf

@@ -2,20 +2,21 @@
 // GERMLINE VARIANT CALLING
 //
 
+include { RUN_CNVKIT_GERMLINE } from '../nf-core/variantcalling/cnvkit/germline/main.nf'
 include { RUN_DEEPVARIANT     } from '../nf-core/variantcalling/deepvariant/main.nf'
 include { RUN_FREEBAYES       } from '../nf-core/variantcalling/freebayes/main.nf'
 include { RUN_HAPLOTYPECALLER } from '../nf-core/variantcalling/haplotypecaller/main.nf'
 include { RUN_MANTA_GERMLINE  } from '../nf-core/variantcalling/manta/germline/main.nf'
 include { RUN_STRELKA_SINGLE  } from '../nf-core/variantcalling/strelka/single/main.nf'
-include { RUN_CNVKIT_GERMLINE } from '../nf-core/variantcalling/cnvkit/germline/main.nf'
-//include { TIDDIT          } from './variantcalling/tiddit.nf'
+include { RUN_TIDDIT          } from '../nf-core/variantcalling/tiddit/main.nf'
 
 workflow GERMLINE_VARIANT_CALLING {
     take:
         tools                         // Mandatory, list of tools to apply
         cram_recalibrated             // channel: [mandatory] cram
-        dbsnp
-        dbsnp_tbi                         // channel: []
+        bwa                           // channel: [mandatory] bwa
+        dbsnp                         // channel: [mandatory] dbsnp
+        dbsnp_tbi                     // channel: [mandatory] dbsnp_tbi
         known_sites
         known_sites_tbi
         dict                          // channel: [mandatory] dict
@@ -28,15 +29,16 @@ workflow GERMLINE_VARIANT_CALLING {
 
     main:
 
-    ch_versions          = Channel.empty()
+    ch_versions         = Channel.empty()
 
     //TODO: Temporary until the if's can be removed and printing to terminal is prevented with "when" in the modules.config
-    deepvariant_vcf      = Channel.empty()
-    freebayes_vcf        = Channel.empty()
-    haplotypecaller_vcf  = Channel.empty()
-    genotype_gvcf        = Channel.empty()
-    manta_vcf            = Channel.empty()
-    strelka_vcf          = Channel.empty()
+    deepvariant_vcf     = Channel.empty()
+    freebayes_vcf       = Channel.empty()
+    genotype_gvcf       = Channel.empty()
+    haplotypecaller_vcf = Channel.empty()
+    manta_vcf           = Channel.empty()
+    strelka_vcf         = Channel.empty()
+    tiddit_vcf          = Channel.empty()
 
     // Remap channel with intervals
     cram_recalibrated_intervals = cram_recalibrated.combine(intervals)
@@ -137,15 +139,23 @@ workflow GERMLINE_VARIANT_CALLING {
     }
 
     //TIDDIT
-    //TODO
+    if (tools.contains('tiddit')){
+        RUN_TIDDIT(cram_recalibrated,
+                fasta,
+                bwa)
+
+        tiddit_vcf = RUN_TIDDIT.out.tiddit_vcf
+        ch_versions = ch_versions.mix(RUN_TIDDIT.out.versions)
+    }
 
     emit:
     deepvariant_vcf
     freebayes_vcf
-    haplotypecaller_vcf
     genotype_gvcf
+    haplotypecaller_vcf
     manta_vcf
     strelka_vcf
+    tiddit_vcf
 
     versions = ch_versions
 }

tests/test_tools.yml

@@ -70,6 +70,17 @@
     - path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted.cns
     - path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted.call.cns
 
+- name: Run variant calling on germline sample with tiddit
+  command: nextflow run main.nf -profile test,tools_germline,docker --tools tiddit -c ./tests/nextflow.config
+  tags:
+    - tiddit
+    - germline
+    - variant_calling
+  files:
+    - path: results/variant_calling/sample1/tiddit/sample1.ploidies.tab
+    - path: results/variant_calling/sample1/tiddit/sample1.vcf.gz
+    - path: results/variant_calling/sample1/tiddit/sample1.vcf.gz.tbi
+
 - name: Run variant calling on somatic samples with controlfreec
   command: nextflow run main.nf -profile test,tools_somatic,docker --tools controlfreec -c ./tests/nextflow.config
   tags:

workflows/sarek.nf

@@ -759,6 +759,7 @@ workflow SAREK {
         GERMLINE_VARIANT_CALLING(
             params.tools,
             cram_variant_calling_status_normal,
+            [],
             dbsnp,
             dbsnp_tbi,
             known_sites,
@@ -817,6 +818,7 @@ workflow SAREK {
         vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.freebayes_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.haplotypecaller_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.manta_vcf)
+        vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.tiddit_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.strelka_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.freebayes_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.mutect2_vcf)