add snpeff sw and properly import it

nf-core · Dec 8, 2021 · 06d100b · 06d100b
1 parent fc89462
commit 06d100b
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Showing 5 changed files with 66 additions and 36 deletions.
diff --git a/subworkflows/local/annotate.nf b/subworkflows/local/annotate.nf
@@ -2,9 +2,9 @@
 // ANNOTATION
 //
 
-include { SNPEFF_ANNOTATE                       } from '../nf-core/snpeff_annotate'
-include { ANNOTATION_ENSEMBLVEP as MERGE_ANNOTATE } from '../nf-core/annotation_ensembl/main'
-include { ANNOTATION_ENSEMBLVEP                   } from '../nf-core/annotation_ensembl/main'
+include { ANNOTATION_SNPEFF                       } from '../nf-core/annotation_snpeff/main'
+include { ANNOTATION_ENSEMBLVEP as MERGE_ANNOTATE } from '../nf-core/annotation_ensemblvep/main'
+include { ANNOTATION_ENSEMBLVEP                   } from '../nf-core/annotation_ensemblvep/main'
 
 workflow ANNOTATE {
     take:
@@ -23,15 +23,15 @@ workflow ANNOTATE {
     ch_versions = Channel.empty()
 
     if (tools.contains('merge') || tools.contains('snpeff')) {
-        SNPEFF_ANNOTATE(vcf, snpeff_db, snpeff_cache)
+        ANNOTATION_SNPEFF(vcf, snpeff_db, snpeff_cache)
 
-        ch_reports  = ch_reports.mix(SNPEFF_ANNOTATE.out.reports)
-        ch_vcf_ann  = ch_vcf_ann.mix(SNPEFF_ANNOTATE.out.vcf_tbi)
-        ch_versions = ch_versions.mix(SNPEFF_ANNOTATE.out.versions.first())
+        ch_reports  = ch_reports.mix(ANNOTATION_SNPEFF.out.reports)
+        ch_vcf_ann  = ch_vcf_ann.mix(ANNOTATION_SNPEFF.out.vcf_tbi)
+        ch_versions = ch_versions.mix(ANNOTATION_SNPEFF.out.versions.first())
     }
 
     if (tools.contains('merge')) {
-        vcf_ann_for_merge = SNPEFF_ANNOTATE.out.vcf_tbi.map{ meta, vcf, tbi -> [meta, vcf] }
+        vcf_ann_for_merge = ANNOTATION_SNPEFF.out.vcf_tbi.map{ meta, vcf, tbi -> [meta, vcf] }
         MERGE_ANNOTATE(vcf_ann_for_merge, vep_genome, vep_species, vep_cache_version, vep_cache)
 
         ch_reports  = ch_reports.mix(MERGE_ANNOTATE.out.reports)
@@ -40,11 +40,11 @@ workflow ANNOTATE {
     }
 
     if (tools.contains('vep')) {
-        ENSEMBLVEP_ANNOTATE(vcf, vep_genome, vep_species, vep_cache_version, vep_cache)
+        ANNOTATION_ENSEMBLVEP(vcf, vep_genome, vep_species, vep_cache_version, vep_cache)
 
-        ch_reports  = ch_reports.mix(ENSEMBLVEP_ANNOTATE.out.reports)
-        ch_vcf_ann  = ch_vcf_ann.mix(ENSEMBLVEP_ANNOTATE.out.vcf_tbi)
-        ch_versions = ch_versions.mix(ENSEMBLVEP_ANNOTATE.out.versions.first())
+        ch_reports  = ch_reports.mix(ANNOTATION_ENSEMBLVEP.out.reports)
+        ch_vcf_ann  = ch_vcf_ann.mix(ANNOTATION_ENSEMBLVEP.out.vcf_tbi)
+        ch_versions = ch_versions.mix(ANNOTATION_ENSEMBLVEP.out.versions.first())
     }
 
     emit:

diff --git a/subworkflows/nf-core/annotation_ensemblvep/main.nf b/subworkflows/nf-core/annotation_ensemblvep/main.nf
diff --git a/subworkflows/nf-core/annotation_snpeff/main.nf b/subworkflows/nf-core/annotation_snpeff/main.nf
diff --git a/subworkflows/nf-core/annotation_snpeff/meta.yml b/subworkflows/nf-core/annotation_snpeff/meta.yml
diff --git a/subworkflows/nf-core/snpeff_annotate.nf b/subworkflows/nf-core/snpeff_annotate.nf