diff --git a/CHANGELOG.md b/CHANGELOG.md index 2588c30831..f23cf0aeb4 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 73f563e8f7..8fb685ac8f 100644 --- a/workflows/sarek.nf +++ b/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()