Merge pull request #586 from FriederikeHanssen/manta_vep

Fix Manta/VEP incompatibility

Author: maxulysse

conf/modules.config

@@ -1022,7 +1022,7 @@ process{
     withName: 'ENSEMBLVEP' {
         ext.prefix       = { "${vcf.baseName.minus(".vcf")}_VEP" }
         ext.args          = [
-            '--everything --filter_common --per_gene --total_length --offline',
+            '--everything --filter_common --per_gene --total_length --offline --format vcf',
             (params.vep_dbnsfp && params.dbnsfp)                                  ? '--plugin dbNSFP,dbNSFP.gz,rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF' : '',
             (params.vep_loftee)                                                   ? '--plugin LoF,loftee_path:/opt/conda/envs/nf-core-vep-104.3/share/ensembl-vep-104.3-0'                                      : '',
             (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? '--plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz,indel=spliceai_scores.raw.indel.hg38.vcf.gz'                     : '',

subworkflows/local/pair_variant_calling.nf

@@ -146,7 +146,7 @@ workflow PAIR_VARIANT_CALLING {
                             fasta,
                             fasta_fai)
 
-        strelka_vcf  = Channel.empty().mix(RUN_STRELKA_SOMATIC.out.strelka_vcf_snvs, RUN_STRELKA_SOMATIC.out.strelka_vcf_indels)
+        strelka_vcf  = Channel.empty().mix(RUN_STRELKA_SOMATIC.out.strelka_vcf)
         ch_versions = ch_versions.mix(RUN_STRELKA_SOMATIC.out.versions)
     }
 

subworkflows/nf-core/variantcalling/strelka/somatic/main.nf

@@ -818,17 +818,16 @@ workflow SAREK {
         vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.deepvariant_vcf)
         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.manta_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)
-        //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.manta_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.strelka_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.manta_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.strelka_vcf)
 
-
         // Gather used softwares versions
         ch_versions = ch_versions.mix(GERMLINE_VARIANT_CALLING.out.versions)
         ch_versions = ch_versions.mix(PAIR_VARIANT_CALLING.out.versions)