diff --git a/modules/nf-core/genmap/map/tests/main.nf.test b/modules/nf-core/genmap/map/tests/main.nf.test index d557cd6ce89e..1bbb9fb0fd99 100644 --- a/modules/nf-core/genmap/map/tests/main.nf.test +++ b/modules/nf-core/genmap/map/tests/main.nf.test @@ -33,7 +33,7 @@ nextflow_process { } process { """ - input[0] = GENMAP_INDEX.out.index.view() + input[0] = GENMAP_INDEX.out.index input[1] = [ [id:"bed"], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists:true) diff --git a/modules/nf-core/glimpse2/concordance/tests/main.nf.test b/modules/nf-core/glimpse2/concordance/tests/main.nf.test index f37c3da863f7..94ea7958ea0a 100644 --- a/modules/nf-core/glimpse2/concordance/tests/main.nf.test +++ b/modules/nf-core/glimpse2/concordance/tests/main.nf.test @@ -80,7 +80,6 @@ nextflow_process { .combine( allele_freq ) .combine( Channel.of([[]]) ) .combine( Channel.of([["chr22", "chr22"]]) ) - .view() input[0] = list_inputs input[1] = Channel.of([[id:"params"], [],"0 0.01 0.05 0.1 0.2 0.5", [], [], [], []]) diff --git a/subworkflows/nf-core/bam_vcf_impute_glimpse2/main.nf b/subworkflows/nf-core/bam_vcf_impute_glimpse2/main.nf index c6062a1033c3..42c2105f844b 100644 --- a/subworkflows/nf-core/bam_vcf_impute_glimpse2/main.nf +++ b/subworkflows/nf-core/bam_vcf_impute_glimpse2/main.nf @@ -103,13 +103,13 @@ workflow BAM_VCF_IMPUTE_GLIMPSE2 { ch_versions = ch_versions.mix(GLIMPSE2_PHASE.out.versions.first()) // Index phased file - BCFTOOLS_INDEX_PHASE(GLIMPSE2_PHASE.out.phased_variants.view()) + BCFTOOLS_INDEX_PHASE(GLIMPSE2_PHASE.out.phased_variants) ch_versions = ch_versions.mix(BCFTOOLS_INDEX_PHASE.out.versions.first()) // Ligate all phased files in one and index it ligate_input = GLIMPSE2_PHASE.out.phased_variants .join( - BCFTOOLS_INDEX_PHASE.out.tbi.mix(BCFTOOLS_INDEX_PHASE.out.csi).view(), + BCFTOOLS_INDEX_PHASE.out.tbi.mix(BCFTOOLS_INDEX_PHASE.out.csi), failOnMismatch: true, failOnDuplicate: true, )