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Merged
atrigila merged 8 commits into from
Jan 25, 2026
Merged

Strict syntax #244

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e56f2e2
style: the use of Channel is deprecated
atrigila Jan 23, 2026
33417ba
style: the use of Channel is deprecated
atrigila Jan 23, 2026
d125bcb
style: fix variable was declared but not used
atrigila Jan 23, 2026
ad885f8
style: fix implicit closure parameter is deprecated
atrigila Jan 23, 2026
b029ee4
revert change
atrigila Jan 23, 2026
777a406
docs: update changelog
atrigila Jan 23, 2026
9526cea
chore: topics migration
atrigila Jan 23, 2026
0f6a87a
Revert "chore: topics migration"
atrigila Jan 23, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Changed`

- [#244](https://github.com/nf-core/phaseimpute/pull/244) - Start migration to strict syntax.
- [#237](https://github.com/nf-core/phaseimpute/pull/237) - Bump version to 1.2.0dev and update `CHANGELOG.md`.
- [#232](https://github.com/nf-core/phaseimpute/pull/232) - Make posfile generated in the panelprep step.
- [#231](https://github.com/nf-core/phaseimpute/pull/231) - Use "panel_id" instead of "id" in the meta map for the panel.
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6 changes: 3 additions & 3 deletions main.nf
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Expand Up @@ -52,9 +52,9 @@ workflow NFCORE_PHASEIMPUTE {
// Initialise input channels
//

ch_input_impute = Channel.empty()
ch_input_simulate = Channel.empty()
ch_input_validate = Channel.empty()
ch_input_impute = channel.empty()
ch_input_simulate = channel.empty()
ch_input_validate = channel.empty()

// Check input files for contigs names consistency
lst_chr = ch_regions.map { it[0].chr }
Expand Down
8 changes: 4 additions & 4 deletions modules/local/addcolumns/tests/main.nf.test
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Expand Up @@ -14,9 +14,9 @@ nextflow_process {
when {
process {
"""
file = Channel.of("# Other content\\ntest\\ntest1\\n#Genotype concordance by allele frequency bin (Variants: SNPs + indels)\\nCol1\\tCol2\\nA\\t1\\nB\\t2")
file = channel.of("# Other content\\ntest\\ntest1\\n#Genotype concordance by allele frequency bin (Variants: SNPs + indels)\\nCol1\\tCol2\\nA\\t1\\nB\\t2")
.collectFile(name: 'sample.txt', newLine: true)
input[0] = Channel.of([[id:"MyId", depth:2, gparray:"SNPArray", tools:"Glimpse", panel:"1000GP"]]).combine(file)
input[0] = channel.of([[id:"MyId", depth:2, gparray:"SNPArray", tools:"Glimpse", panel:"1000GP"]]).combine(file)
"""
}
}
Expand All @@ -36,11 +36,11 @@ nextflow_process {
when {
process {
"""
file = Channel.of("# Other content\\ntest\\ntest1\\n" +
file = channel.of("# Other content\\ntest\\ntest1\\n" +
"#Genotype concordance by allele frequency bin (Variants: SNPs + indels)\\n" +
"Col1\\tCol2\\nA\\t1\\nB\\t2")
.collectFile(name: 'sample.txt', newLine: true)
input[0] = Channel.of([[id:"MyId", tools:"Glimpse"]]).combine(file)
input[0] = channel.of([[id:"MyId", tools:"Glimpse"]]).combine(file)
"""
}
}
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2 changes: 1 addition & 1 deletion modules/local/bamchrextract/tests/main.nf.test
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Expand Up @@ -12,7 +12,7 @@ nextflow_process {
when {
process {
"""
input[0] = Channel.fromList([
input[0] = channel.fromList([
[
[ id:'test_single_end_bam' ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
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2 changes: 1 addition & 1 deletion modules/local/listtofile/tests/main.nf.test
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Expand Up @@ -14,7 +14,7 @@ nextflow_process {
when {
process {
"""
input[0] = Channel.of([
input[0] = channel.of([
[id: "all"],
[file("file1.txt"), file("file2.txt")],
["A", "B"]
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2 changes: 1 addition & 1 deletion modules/local/vcfchrextract/tests/main.nf.test
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Expand Up @@ -12,7 +12,7 @@ nextflow_process {
when {
process {
"""
input[0] = Channel.fromList([
input[0] = channel.fromList([
[
[id:'test_bcf'], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.bcf', checkIfExists: true)
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2 changes: 1 addition & 1 deletion subworkflows/local/bam_chr_rename_samtools/main.nf
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Expand Up @@ -7,7 +7,7 @@ workflow BAM_CHR_RENAME_SAMTOOLS {

main:

ch_versions = Channel.empty()
ch_versions = channel.empty()

// Rename the chromosome with or without prefix
SAMTOOLS_REHEADER(
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4 changes: 2 additions & 2 deletions subworkflows/local/bam_chr_rename_samtools/tests/main.nf.test
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Expand Up @@ -21,7 +21,7 @@ nextflow_workflow {
when {
workflow {
"""
input[0] = Channel.fromList([
input[0] = channel.fromList([
[
[id: "test_paired"],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExist:true),
Expand Down Expand Up @@ -64,7 +64,7 @@ nextflow_workflow {
script "../main.nf"
process {
"""
input[0] = Channel.fromList([
input[0] = channel.fromList([
[
[id: "test_paired"],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExist:true),
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/local/bam_downsample_samtools/main.nf
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Expand Up @@ -10,7 +10,7 @@ workflow BAM_DOWNSAMPLE_SAMTOOLS {
ch_fasta // channel: [ [genome], fasta, fai ]

main:
ch_versions = Channel.empty()
ch_versions = channel.empty()

// Compute mean depth
SAMTOOLS_DEPTH(ch_bam, [[], []])
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12 changes: 6 additions & 6 deletions subworkflows/local/bam_downsample_samtools/tests/main.nf.test
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Expand Up @@ -25,7 +25,7 @@ nextflow_workflow {
}
workflow {
"""
input[0] = Channel.fromList([
input[0] = channel.fromList([
[
[id: "NA12878"],
file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s.bam", checkIfExist:true),
Expand All @@ -37,8 +37,8 @@ nextflow_workflow {
file(params.pipelines_testdata_base_path + "hum_data/individuals/NA19401/NA19401.s.bam.bai", checkIfExist:true),
],
])
input[1] = Channel.of([[depth: 2], 2]).collect()
input[2] = Channel.of([
input[1] = channel.of([[depth: 2], 2]).collect()
input[2] = channel.of([
[id: "GRCh38"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz.fai", checkIfExist:true),
Expand Down Expand Up @@ -74,7 +74,7 @@ nextflow_workflow {
}
workflow {
"""
input[0] = Channel.fromList([
input[0] = channel.fromList([
[
[id: "NA12878"],
file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s.bam", checkIfExist:true),
Expand All @@ -86,8 +86,8 @@ nextflow_workflow {
file(params.pipelines_testdata_base_path + "hum_data/individuals/NA19401/NA19401.s.bam.bai", checkIfExist:true),
],
])
input[1] = Channel.of([[depth: 4], 4]).collect()
input[2] = Channel.of([
input[1] = channel.of([[depth: 4], 4]).collect()
input[2] = channel.of([
[id: "GRCh38"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz.fai", checkIfExist:true),
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2 changes: 1 addition & 1 deletion subworkflows/local/bam_extract_region_samtools/main.nf
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Expand Up @@ -10,7 +10,7 @@ workflow BAM_EXTRACT_REGION_SAMTOOLS {
ch_fasta // channel: [ [genome], fasta, fai ]
main:

ch_versions = Channel.empty()
ch_versions = channel.empty()

// Add fasta and region to bam channel
ch_input_region = ch_bam
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12 changes: 6 additions & 6 deletions subworkflows/local/bam_extract_region_samtools/tests/main.nf.test
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Expand Up @@ -24,7 +24,7 @@ nextflow_workflow {
}
workflow {
"""
input[0] = input[0] = Channel.fromList([
input[0] = input[0] = channel.fromList([
[
[id: "NA12878"],
file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s.bam", checkIfExist:true),
Expand All @@ -36,10 +36,10 @@ nextflow_workflow {
file(params.pipelines_testdata_base_path + "hum_data/individuals/NA19401/NA19401.s.bam.bai", checkIfExist:true),
],
])
input[1] = Channel.of([
input[1] = channel.of([
[chr: "chr22", region: "chr22:16600000-16610000"], "chr22:16600000-16610000"
]).collect()
input[2] = Channel.of([
input[2] = channel.of([
[id: "GRCh38"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz.fai", checkIfExist:true),
Expand Down Expand Up @@ -75,7 +75,7 @@ nextflow_workflow {
}
workflow {
"""
input[0] = input[0] = Channel.fromList([
input[0] = input[0] = channel.fromList([
[
[id: "NA12878"],
file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s.bam", checkIfExist:true),
Expand All @@ -87,10 +87,10 @@ nextflow_workflow {
file(params.pipelines_testdata_base_path + "hum_data/individuals/NA19401/NA19401.s.bam.bai", checkIfExist:true),
],
])
input[1] = Channel.of([
input[1] = channel.of([
[chr: "chr22", region: "chr22:16609000-16610000"], "chr22:16609000-16610000"
]).collect()
input[2] = Channel.of([
input[2] = channel.of([
[id: "GRCh38"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz.fai", checkIfExist:true),
Expand Down
12 changes: 6 additions & 6 deletions subworkflows/local/bam_gl_bcftools/tests/main.nf.test
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Expand Up @@ -22,7 +22,7 @@ nextflow_workflow {
when {
workflow {
"""
input[0] = Channel.fromList([
input[0] = channel.fromList([
[
[id: "NA12878"],
file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s.bam", checkIfExist:true),
Expand All @@ -34,11 +34,11 @@ nextflow_workflow {
file(params.pipelines_testdata_base_path + "hum_data/individuals/NA19401/NA19401.s.bam.bai", checkIfExist:true),
],
])
input[1] = Channel.of([
input[1] = channel.of([
[panel_id: "1000GP", chr: "22"],
file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.posfile", checkIfExist:true)
]).collect()
input[2] = Channel.of([
input[2] = channel.of([
[id: "GRCh38"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz.fai", checkIfExist:true),
Expand Down Expand Up @@ -70,18 +70,18 @@ nextflow_workflow {
when {
workflow {
"""
input[0] = Channel.fromList([
input[0] = channel.fromList([
[
[id: "NA12878"],
file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s.bam", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s.bam.bai", checkIfExist:true),
],
])
input[1] = Channel.of([
input[1] = channel.of([
[panel_id: "1000GP", chr: "22"],
file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.posfile", checkIfExist:true)
]).collect()
input[2] = Channel.of([
input[2] = channel.of([
[id: "GRCh38"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz.fai", checkIfExist:true),
Expand Down
4 changes: 2 additions & 2 deletions subworkflows/local/bam_impute_quilt/main.nf
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Expand Up @@ -11,7 +11,7 @@ workflow BAM_IMPUTE_QUILT {

main:

ch_versions = Channel.empty()
ch_versions = channel.empty()

genetic_map_file = []

Expand Down Expand Up @@ -46,7 +46,7 @@ workflow BAM_IMPUTE_QUILT {
// Annotate the variants
BCFTOOLS_ANNOTATE(QUILT_QUILT.out.vcf
.join(QUILT_QUILT.out.tbi)
.combine(Channel.of([[], [], [], []]))
.combine(channel.of([[], [], [], []]))
)
ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions.first())

Expand Down
32 changes: 16 additions & 16 deletions subworkflows/local/bam_impute_quilt/tests/main.nf.test
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Expand Up @@ -21,11 +21,11 @@ nextflow_workflow {
when {
workflow {
"""
bampath = Channel.of(
bampath = channel.of(
"NA12878.s.bam",
"NA19401.s.bam"
).collectFile(name: 'bampath.txt', newLine: true)
ch_samples = Channel.fromList([
ch_samples = channel.fromList([
[
[id: "allid"],
[
Expand All @@ -38,17 +38,17 @@ nextflow_workflow {
]
],
])
input[0] = ch_samples.combine(bampath).combine(Channel.of([[]]))
input[1] = Channel.of([
input[0] = ch_samples.combine(bampath).combine(channel.of([[]]))
input[1] = channel.of([
[panel_id: "1000GP", chr: "chr22"],
file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.hap.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.legend.gz", checkIfExist:true)
]).collect()
input[2] = Channel.of(
input[2] = channel.of(
[[chr: "chr22", panel_id: "1000GP"], "chr22", "16570065", "16597215"],
[[chr: "chr22", panel_id: "1000GP"], "chr22", "16587172", "16609999"]
)
input[3] = Channel.of([
input[3] = channel.of([
[id: "GRCh38"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz.fai", checkIfExist:true)
Expand Down Expand Up @@ -78,15 +78,15 @@ nextflow_workflow {
when {
workflow {
"""
bampath = Channel.of(
bampath = channel.of(
"NA12878.s.bam",
"NA19401.s.bam"
).collectFile(name: 'bampath.txt', newLine: true)
bamname = Channel.of(
bamname = channel.of(
"MySample1",
"MySample2"
).collectFile(name: 'bamname.txt', newLine: true)
ch_samples = Channel.fromList([
ch_samples = channel.fromList([
[
[id: "allid"],
[
Expand All @@ -100,16 +100,16 @@ nextflow_workflow {
],
])
input[0] = ch_samples.combine(bampath).combine(bamname)
input[1] = Channel.of([
input[1] = channel.of([
[panel_id: "1000GP", chr: "chr22"],
file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.hap.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.legend.gz", checkIfExist:true)
]).collect()
input[2] = Channel.of(
input[2] = channel.of(
[[chr: "chr22", panel_id: "1000GP"], "chr22", "16570065", "16597215"],
[[chr: "chr22", panel_id: "1000GP"], "chr22", "16587172", "16609999"]
)
input[3] = Channel.of([
input[3] = channel.of([
[id: "GRCh38"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz.fai", checkIfExist:true)
Expand Down Expand Up @@ -140,7 +140,7 @@ nextflow_workflow {
when {
workflow {
"""
input[0] = Channel.fromList([
input[0] = channel.fromList([
[
[id: "NA12878"],
file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s.bam", checkIfExist:true),
Expand All @@ -149,16 +149,16 @@ nextflow_workflow {
[]
]
])
input[1] = Channel.of([
input[1] = channel.of([
[panel_id: "1000GP", chr: "chr22"],
file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.hap.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.legend.gz", checkIfExist:true)
]).collect()
input[2] = Channel.of(
input[2] = channel.of(
[[chr: "chr22", panel_id: "1000GP"], "chr22", "16570065", "16597215"],
[[chr: "chr22", panel_id: "1000GP"], "chr22", "16587172", "16609999"]
)
input[3] = Channel.of([
input[3] = channel.of([
[id: "GRCh38"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz.fai", checkIfExist:true)
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
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Expand Up @@ -172,7 +172,7 @@ workflow PIPELINE_INITIALISATION {
error "Panel file provided is of another format than CSV (not yet supported). Please separate your panel by chromosome and use the samplesheet format."
}
} else {
ch_input_truth = Channel.of([[], [], []])
ch_input_truth = channel.of([[], [], []])
input_truth_ext = ""
}

Expand Down
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