Merge pull request #1022 from asp8200/fix_variantrecalibrator

Fix input channels for variantrecalibrator

CHANGELOG.md

@@ -58,6 +58,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#988](https://github.com/nf-core/sarek/pull/988) - Updated ascat module to fix seed for reproducibility
 - [#998](https://github.com/nf-core/sarek/pull/998) - Remove parallelization within a sample for `Manta`
 - [#1014](https://github.com/nf-core/sarek/pull/1014) - Fix calls to `ensemblvep` and `snpeff` containers
+- [#1022](https://github.com/nf-core/sarek/pull/1022) - Fix call to variantrecalibrator. (Making sure that dbsnp_vqsr, known_indels_vqsr and known_snps_vqsr are channels, and not strings.)
 
 ### Deprecated
 

workflows/sarek.nf

@@ -153,9 +153,9 @@ pon                = params.pon                ? Channel.fromPath(params.pon).co
 
 // Initialize value channels based on params, defined in the params.genomes[params.genome] scope
 ascat_genome       = params.ascat_genome       ?: Channel.empty()
-dbsnp_vqsr         = params.dbsnp_vqsr         ?: Channel.empty()
-known_indels_vqsr  = params.known_indels_vqsr  ?: Channel.empty()
-known_snps_vqsr    = params.known_snps_vqsr    ?: Channel.empty()
+dbsnp_vqsr         = params.dbsnp_vqsr         ? Channel.value(params.dbsnp_vqsr) : Channel.empty()
+known_indels_vqsr  = params.known_indels_vqsr  ? Channel.value(params.known_indels_vqsr) : Channel.empty()
+known_snps_vqsr    = params.known_snps_vqsr    ? Channel.value(params.known_snps_vqsr) : Channel.empty()
 snpeff_db          = params.snpeff_db          ?: Channel.empty()
 vep_cache_version  = params.vep_cache_version  ?: Channel.empty()
 vep_genome         = params.vep_genome         ?: Channel.empty()