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Remove .view() #9567

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Merged
LouisLeNezet merged 1 commit into from
Dec 15, 2025
Merged

Remove .view() #9567

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2 changes: 1 addition & 1 deletion modules/nf-core/genmap/map/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
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1 change: 0 additions & 1 deletion modules/nf-core/glimpse2/concordance/tests/main.nf.test
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Expand Up @@ -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", [], [], [], []])
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4 changes: 2 additions & 2 deletions subworkflows/nf-core/bam_vcf_impute_glimpse2/main.nf
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Expand Up @@ -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,
)
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