Merge pull request #318 from drpatelh/sync

Fix #316

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#304](https://github.com/nf-core/viralrecon/pull/304)] - Re-factor code of `ivar_variants_to_vcf` script
 - [[#306](https://github.com/nf-core/viralrecon/issues/306)] - Add contig field information in vcf header in ivar_variants_to_vcf and use bcftools sort
 - [[#311](https://github.com/nf-core/viralrecon/issues/311)] - Invalid declaration val medaka_model_string
+- [[#316](https://github.com/nf-core/viralrecon/issues/316)] - Variant calling isn't run when using --skip_asciigenome with metagenomic data
 - [[nf-core/rnaseq#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
 - Updated pipeline template to [nf-core/tools 2.4.1](https://github.com/nf-core/tools/releases/tag/2.4.1)
 

workflows/illumina.nf

@@ -415,8 +415,8 @@ workflow ILLUMINA {
         VARIANTS_IVAR (
             ch_bam,
             PREPARE_GENOME.out.fasta,
-            PREPARE_GENOME.out.fai,
-            PREPARE_GENOME.out.chrom_sizes,
+            (params.protocol == 'amplicon' || !params.skip_asciigenome) ? PREPARE_GENOME.out.fai : [],
+            (params.protocol == 'amplicon' || !params.skip_asciigenome) ? PREPARE_GENOME.out.chrom_sizes : [],
             PREPARE_GENOME.out.gff,
             (params.protocol == 'amplicon' && params.primer_bed) ? PREPARE_GENOME.out.primer_bed : [],
             PREPARE_GENOME.out.snpeff_db,
@@ -439,7 +439,7 @@ workflow ILLUMINA {
         VARIANTS_BCFTOOLS (
             ch_bam,
             PREPARE_GENOME.out.fasta,
-            PREPARE_GENOME.out.chrom_sizes,
+            (params.protocol == 'amplicon' || !params.skip_asciigenome) ? PREPARE_GENOME.out.chrom_sizes : [],
             PREPARE_GENOME.out.gff,
             (params.protocol == 'amplicon' && params.primer_bed) ? PREPARE_GENOME.out.primer_bed : [],
             PREPARE_GENOME.out.snpeff_db,