Merge pull request #597 from WackerO/tiddit

Tiddit for tumor varcalling
nf-core · Jun 23, 2022 · cd503d1 · cd503d1
2 parents a1e271c + 656af02
commit cd503d1
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Showing 7 changed files with 137 additions and 73 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -32,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#582](https://github.com/nf-core/sarek/pull/582) - Added option `--vep_out_format` for setting the format of the output-file from VEP to `json`, `tab` or `vcf` (default)
 - [#594](https://github.com/nf-core/sarek/pull/594) - Add parameter `--save_output_as_bam` to allow output of result files in BAM format
 - [#600](https://github.com/nf-core/sarek/pull/600) - Added description for UMI related params in schema
+- [#597](https://github.com/nf-core/sarek/pull/597) - Added tiddit for tumor variant calling
 
 ### Changed
 

diff --git a/docs/images/sarek_subway.png b/docs/images/sarek_subway.png
diff --git a/docs/images/sarek_subway.svg b/docs/images/sarek_subway.svg
diff --git a/subworkflows/local/germline_variant_calling.nf b/subworkflows/local/germline_variant_calling.nf
@@ -18,14 +18,14 @@ workflow GERMLINE_VARIANT_CALLING {
         bwa                           // channel: [mandatory] bwa
         dbsnp                         // channel: [mandatory] dbsnp
         dbsnp_tbi                     // channel: [mandatory] dbsnp_tbi
-        known_sites
-        known_sites_tbi
         dict                          // channel: [mandatory] dict
         fasta                         // channel: [mandatory] fasta
         fasta_fai                     // channel: [mandatory] fasta_fai
         intervals                     // channel: [mandatory] intervals/target regions
         intervals_bed_gz_tbi          // channel: [mandatory] intervals/target regions index zipped and indexed
         intervals_bed_combined        // channel: [mandatory] intervals/target regions in one file unzipped
+        known_sites
+        known_sites_tbi
         // joint_germline                // val: true/false on whether to run joint_germline calling, only works in combination with haplotypecaller at the moment
 
     main:

diff --git a/subworkflows/local/tumor_variant_calling.nf b/subworkflows/local/tumor_variant_calling.nf
@@ -10,25 +10,27 @@ include { RUN_STRELKA_SINGLE                      } from '../nf-core/variantcall
 include { RUN_CONTROLFREEC_TUMORONLY              } from '../nf-core/variantcalling/controlfreec/tumoronly/main.nf'
 include { RUN_CNVKIT_TUMORONLY                    } from '../nf-core/variantcalling/cnvkit/tumoronly/main.nf'
 include { RUN_MPILEUP                             } from '../nf-core/variantcalling/mpileup/main'
+include { RUN_TIDDIT                              } from '../nf-core/variantcalling/tiddit/main.nf'
 
 workflow TUMOR_ONLY_VARIANT_CALLING {
     take:
         tools                         // Mandatory, list of tools to apply
         cram_recalibrated             // channel: [mandatory] cram
+        bwa                           // channel: [optional] bwa
+        chr_files
         dbsnp                         // channel: [mandatory] dbsnp
         dbsnp_tbi                     // channel: [mandatory] dbsnp_tbi
         dict                          // channel: [mandatory] dict
         fasta                         // channel: [mandatory] fasta
         fasta_fai                     // channel: [mandatory] fasta_fai
+        germline_resource             // channel: [optional]  germline_resource
+        germline_resource_tbi         // channel: [optional]  germline_resource_tbi
         intervals                     // channel: [mandatory] intervals/target regions
         intervals_bed_gz_tbi          // channel: [mandatory] intervals/target regions index zipped and indexed
         intervals_bed_combined        // channel: [mandatory] intervals/target regions in one file unzipped
-        germline_resource             // channel: [optional]  germline_resource
-        germline_resource_tbi         // channel: [optional]  germline_resource_tbi
+        mappability
         panel_of_normals              // channel: [optional]  panel_of_normals
         panel_of_normals_tbi          // channel: [optional]  panel_of_normals_tbi
-        chr_files
-        mappability
 
     main:
 
@@ -39,6 +41,7 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
     manta_vcf           = Channel.empty()
     mutect2_vcf         = Channel.empty()
     strelka_vcf         = Channel.empty()
+    tiddit_vcf          = Channel.empty()
 
     // Remap channel with intervals
     cram_recalibrated_intervals = cram_recalibrated.combine(intervals)
@@ -152,16 +155,23 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
         ch_versions = ch_versions.mix(RUN_STRELKA_SINGLE.out.versions)
     }
 
+        //TIDDIT
+    if (tools.contains('tiddit')){
+        RUN_TIDDIT(cram_recalibrated,
+                fasta,
+                bwa)
 
-    // if (tools.contains('tiddit')){
-    // }
+        tiddit_vcf = RUN_TIDDIT.out.tiddit_vcf
+        ch_versions = ch_versions.mix(RUN_TIDDIT.out.versions)
+    }
 
-    emit:
-    versions = ch_versions
 
+    emit:
     freebayes_vcf
     manta_vcf
     mutect2_vcf
     strelka_vcf
+    tiddit_vcf
 
+    versions = ch_versions
 }
diff --git a/tests/test_tools.yml b/tests/test_tools.yml
@@ -81,6 +81,17 @@
     - path: results/variant_calling/sample1/tiddit/sample1.vcf.gz
     - path: results/variant_calling/sample1/tiddit/sample1.vcf.gz.tbi
 
+- name: Run variant calling on tumor_only sample with tiddit
+  command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools tiddit -c ./tests/nextflow.config
+  tags:
+    - tiddit
+    - tumor_only
+    - variant_calling
+  files:
+    - path: results/variant_calling/sample2/tiddit/sample2.ploidies.tab
+    - path: results/variant_calling/sample2/tiddit/sample2.vcf.gz
+    - path: results/variant_calling/sample2/tiddit/sample2.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:

diff --git a/workflows/sarek.nf b/workflows/sarek.nf
@@ -802,34 +802,35 @@ workflow SAREK {
             [],
             dbsnp,
             dbsnp_tbi,
-            known_sites,
-            known_sites_tbi,
             dict,
             fasta,
             fasta_fai,
             intervals,
             intervals_bed_gz_tbi,
-            intervals_bed_combined)
+            intervals_bed_combined,
+            known_sites,
+            known_sites_tbi)
             // params.joint_germline)
 
         // TUMOR ONLY VARIANT CALLING
         TUMOR_ONLY_VARIANT_CALLING(
             params.tools,
             cram_variant_calling_tumor_only,
+            [],
+            chr_files,
             dbsnp,
             dbsnp_tbi,
             dict,
             fasta,
             fasta_fai,
+            germline_resource,
+            germline_resource_tbi,
             intervals,
             intervals_bed_gz_tbi,
             intervals_bed_combined,
-            germline_resource,
-            germline_resource_tbi,
+            mappability,
             pon,
-            pon_tbi,
-            chr_files,
-            mappability
+            pon_tbi
         )
 
         // PAIR VARIANT CALLING
@@ -865,6 +866,7 @@ workflow SAREK {
         vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.mutect2_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.manta_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.strelka_vcf)
+        vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.tiddit_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.mutect2_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.manta_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.strelka_vcf)