Merge pull request #608 from WackerO/manta

Remove candidates from manta publishdir and tests

Author: FriederikeHanssen

CHANGELOG.md

@@ -69,6 +69,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#581](https://github.com/nf-core/sarek/pull/581) - `TIDDIT` is updated to `3.1.0`
 - [#593](https://github.com/nf-core/sarek/pull/593) - update `ensembl-vep` cache version and module
 - [#600](https://github.com/nf-core/sarek/pull/600) - Remove `TODO` in awsfulltest
+- [#608](https://github.com/nf-core/sarek/pull/608) - Prevent candidate VCFs from getting published in manta
 
 ### Fixed
 

conf/modules.config

@@ -632,7 +632,7 @@ process{
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/manta" },
-            pattern: "*{vcf.gz,vcf.gz.tbi}"
+            pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}"
         ]
     }
     withName: 'MERGE_MANTA_DIPLOID' {
@@ -651,7 +651,7 @@ process{
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/" },
-            pattern: "*{vcf.gz,vcf.gz.tbi}",
+            pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}",
             saveAs: { meta.num_intervals > 1 ? null : "manta/${it}" }
         ]
     }

tests/test_tools.yml

@@ -323,10 +323,6 @@
     - manta
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/manta/sample1.candidate_small_indels.vcf.gz
-    - path: results/variant_calling/sample1/manta/sample1.candidate_small_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample1/manta/sample1.candidate_sv.vcf.gz
-    - path: results/variant_calling/sample1/manta/sample1.candidate_sv.vcf.gz.tbi
     - path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz
     - path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz.tbi
 
@@ -338,10 +334,6 @@
     - no_intervals
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/manta/sample1.candidate_small_indels.vcf.gz
-    - path: results/variant_calling/sample1/manta/sample1.candidate_small_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample1/manta/sample1.candidate_sv.vcf.gz
-    - path: results/variant_calling/sample1/manta/sample1.candidate_sv.vcf.gz.tbi
     - path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz
     - path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz.tbi
 
@@ -352,10 +344,6 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/manta/sample2.candidate_small_indels.vcf.gz
-    - path: results/variant_calling/sample2/manta/sample2.candidate_small_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample2/manta/sample2.candidate_sv.vcf.gz
-    - path: results/variant_calling/sample2/manta/sample2.candidate_sv.vcf.gz.tbi
     - path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz
     - path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz.tbi
 
@@ -367,10 +355,6 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/manta/sample2.candidate_small_indels.vcf.gz
-    - path: results/variant_calling/sample2/manta/sample2.candidate_small_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample2/manta/sample2.candidate_sv.vcf.gz
-    - path: results/variant_calling/sample2/manta/sample2.candidate_sv.vcf.gz.tbi
     - path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz
     - path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz.tbi
 
@@ -381,18 +365,12 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/manta/sample3.candidate_small_indels.vcf.gz
-    - path: results/variant_calling/sample3/manta/sample3.candidate_small_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample3/manta/sample3.candidate_sv.vcf.gz
-    - path: results/variant_calling/sample3/manta/sample3.candidate_sv.vcf.gz.tbi
     - path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz
     - path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_small_indels.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_small_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_sv.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_sv.vcf.gz.tbi
     - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz
     - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz.tbi
 
 - name: Run variant calling on somatic sample with manta without intervals
   command: nextflow run main.nf -profile test,tools_somatic,docker --tools manta --no_intervals
@@ -402,18 +380,12 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/manta/sample3.candidate_small_indels.vcf.gz
-    - path: results/variant_calling/sample3/manta/sample3.candidate_small_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample3/manta/sample3.candidate_sv.vcf.gz
-    - path: results/variant_calling/sample3/manta/sample3.candidate_sv.vcf.gz.tbi
     - path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz
     - path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_small_indels.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_small_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_sv.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_sv.vcf.gz.tbi
     - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz
     - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz.tbi
 
 - name: Run variant calling on tumoronly sample with mutect2
   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools mutect2