Merge pull request #606 from nf-core/index_managed_variants

Add option to generate csi index for managed variants

CHANGELOG.md

@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- Default index for vcfanno extra annotation files from tbi to csi [#606](https://github.com/nf-core/raredisease/pull/606)
 - Updated the model for Sentieon DNAScope to v1.1 [#601](https://github.com/nf-core/raredisease/pull/601)
 - bwameme can no longer be used to align mitochondrial reads [#600](https://github.com/nf-core/raredisease/pull/600)
 - Males' X and Y chromosomes will be treated as haploids during variant calling by deepvariant [#598](https://github.com/nf-core/raredisease/pull/598)

conf/modules/prepare_references.config

@@ -100,6 +100,10 @@ process {
         ext.when = { !params.target_bed.equals(null) && !params.target_bed.endsWith(".gz") }
     }
 
+    withName: '.*PREPARE_REFERENCES:TABIX_BGZIPINDEX_VCFANNOEXTRA' {
+        ext.args2 = '-C'
+    }
+
     withName: '.*PREPARE_REFERENCES:GATK_BILT' {
         ext.when = { !params.target_bed.equals(null) }
         ext.prefix = { "${meta.id}_target" }

subworkflows/local/prepare_references.nf

@@ -103,8 +103,10 @@ workflow PREPARE_REFERENCES {
             .map { meta, tbi, vcf -> return [[vcf,tbi]]}
             .set {ch_vcfanno_index}
 
-        TABIX_BGZIPINDEX_VCFANNOEXTRA(ch_vcfanno_tabix_in.bgzipindex).gz_tbi
-            .map { meta, vcf, tbi -> return [[vcf,tbi]] }
+        TABIX_BGZIPINDEX_VCFANNOEXTRA(ch_vcfanno_tabix_in.bgzipindex)
+        Channel.empty()
+            .mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_tbi, TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_csi)
+            .map { meta, vcf, index -> return [[vcf,index]] }
             .set {ch_vcfanno_bgzip}
 
         Channel.empty()