diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf index a70f4bb3ec421ef9f52499b0456853c165c85e61..0490b082a4d71d8cef7aa68d44ccf96d2ea41d89 100644 --- a/src/nf_modules/bwa/main.nf +++ b/src/nf_modules/bwa/main.nf @@ -10,8 +10,8 @@ workflow mapping { index_fasta(fasta) mapping_fastq(index_fasta.out.index.collect(), fastq) emit: - bam: mapping_fastq.out.bam - report: mapping_fastq.out.report + bam = mapping_fastq.out.bam + report = mapping_fastq.out.report } diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf index bb072eb6d0b060b520756d06ab4b9d25275db47a..c17f43174aa4bb0d820b9c91199ba3a1d4a0048a 100644 --- a/src/nf_modules/gatk4/main.nf +++ b/src/nf_modules/gatk4/main.nf @@ -39,7 +39,7 @@ workflow germline_cohort_data_variant_calling { fasta_idx ) emit: - vcf: call_variants_all_sample.out.vcf + vcf = call_variants_all_sample.out.vcf } /*******************************************************************/ @@ -62,7 +62,7 @@ workflow base_quality_recalibrator{ compute_base_recalibration.out.table ) emit: - bam: apply_base_recalibration.out.bam + bam = apply_base_recalibration.out.bam } process index_vcf { @@ -195,7 +195,7 @@ workflow call_variants_all_sample { fasta_idx ) emit: - vcf: genomic_db_call.out.vcf + vcf = genomic_db_call.out.vcf } process consolidate_gvcf {