Turn off ME calling for mitochondria

CHANGELOG.md

@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Use distinct output filenames for bcfools (in call_mobile_elements subworkflow) and svdb (in call_sv_tiddit subworkflow) [#716](https://github.com/nf-core/raredisease/pull/716)
 - Use nf-core's most severe consequence & pli scripts instead of local ones [#732](https://github.com/nf-core/raredisease/pull/732)
 - Use nf-core's VCF_FILTER_BCFTOOLS_ENSEMBLVEP subworkflow to generate clinical set instead of a local subworkflow [#727](https://github.com/nf-core/raredisease/pull/727)
+- Don't call mobile elements in mitochondrial DNA. [#741](https://github.com/nf-core/raredisease/pull/741)
 
 ### `Fixed`
 

subworkflows/local/call_mobile_elements.nf

@@ -21,15 +21,14 @@ workflow CALL_MOBILE_ELEMENTS {
         ch_genome_fai       // channel: [mandatory] [ val(meta), path(fai) ]
         ch_me_references    // channel: [mandatory] [path(tsv)]
         ch_case_info        // channel: [mandatory] [ val(case_info) ]
-        val_genome_build    // string: [mandatory] GRCh37 or GRCh38
 
     main:
         ch_versions = Channel.empty()
 
         // Building chromosome channels based on fasta index
         ch_genome_fai
-            .splitCsv( sep: "\t", elem: 1, limit: 25 )
-            .map { meta, fai -> [ fai.first() ] }
+            .splitCsv( sep: "\t", elem: 1, limit: 24 )
+            .map { _meta, fai -> [ fai.first() ] }
             .collect()
             .map { chr -> [ chr, chr.size() ] }
             .transpose()

workflows/raredisease.nf

@@ -728,8 +728,7 @@ workflow RAREDISEASE {
             ch_genome_fasta,
             ch_genome_fai,
             ch_me_references,
-            ch_case_info,
-            params.genome
+            ch_case_info
         )
         ch_versions = ch_versions.mix(CALL_MOBILE_ELEMENTS.out.versions)