From 92e0e00a6f2fce34af73d247ec44fc7e80e9f8d4 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 2 Jun 2021 10:57:29 +0200
Subject: [PATCH] fix emit: for named workflow
---
src/nf_modules/bwa/main.nf | 4 ++--
src/nf_modules/gatk4/main.nf | 6 +++---
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index a70f4bb3..0490b082 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 bb072eb6..c17f4317 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 {
--
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