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LouisLeNezetLouisLeNezet
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Merge pull request #185 from LouisLeNezet/csv
Fix csv generation
2 parents 0537a1e + 72ecdda commit c8ac468

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‎CHANGELOG.md

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@@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [#166](https://github.com/nf-core/phaseimpute/pull/166) - Fix depth type to `number` to enable float.
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- [#179](https://github.com/nf-core/phaseimpute/pull/179) - Fix VCF usage in `GLIMPSE2`.
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- [#183](https://github.com/nf-core/phaseimpute/pull/183) - Remove wrongfully added files in `BAM_EXTRACT_REGION_SAMTOOLS`.
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- [#185](https://github.com/nf-core/phaseimpute/pull/185) - Fix CSV generation and check that all mentioned path files exist.
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## v1.0.0 - Black Labrador [2024-12-09]
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‎conf/steps/panel_prep.config

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@@ -190,12 +190,6 @@ process {
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// Subworkflow: Make chunks
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:.*' {
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publishDir = [
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path: { "${params.outdir}/prep_panel/chunks/" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
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enabled: true
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]
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tag = {"${meta.id} ${meta.chr}"}
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}
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‎conf/test_all.config

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@@ -48,13 +48,28 @@ params {
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process {
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE_CHUNK' {
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ext.args = ["--window-size 10000", "--window-count 400", "--buffer-size 5000", "--buffer-count 30"].join(' ')
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ext.prefix = { "${meta.id}_${meta.chr}_chunks_glimpse1" }
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publishDir = [
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path: { "${params.outdir}/prep_panel/chunks/glimpse1/" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
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enabled: true
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]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE2_CHUNK' {
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ext.args = ["--window-mb 0.01", "--window-cm 0.01", "--window-count 200", "--buffer-mb 0.005", "--buffer-cm 0.005", "--buffer-count 30"].join(' ')
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ext.prefix = { "${meta.id}_${meta.chr}_chunks_glimpse2" }
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publishDir = [
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path: { "${params.outdir}/prep_panel/chunks/glimpse2/" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
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enabled: true
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]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_PHASE_SHAPEIT5:GLIMPSE2_CHUNK' {
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ext.args = ["--window-mb 0.01", "--window-cm 0.01", "--window-count 200", "--buffer-mb 0.005", "--buffer-cm 0.005", "--buffer-count 30"].join(' ')
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ext.prefix = { "${meta.id}_chunks" }
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}
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}

‎conf/test_dog.config

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@@ -45,13 +45,28 @@ params {
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process {
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE_CHUNK' {
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ext.args = ["--window-size 10000", "--window-count 400", "--buffer-size 5000", "--buffer-count 30"].join(' ')
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ext.prefix = { "${meta.id}_${meta.chr}_chunks_glimpse1" }
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publishDir = [
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path: { "${params.outdir}/prep_panel/chunks/glimpse1/" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
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enabled: true
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]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE2_CHUNK' {
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ext.args = ["--window-mb 0.01", "--window-cm 0.01", "--window-count 200", "--buffer-mb 0.005", "--buffer-cm 0.005", "--buffer-count 30"].join(' ')
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ext.prefix = { "${meta.id}_${meta.chr}_chunks_glimpse2" }
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publishDir = [
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path: { "${params.outdir}/prep_panel/chunks/glimpse2/" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
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enabled: true
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]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_PHASE_SHAPEIT5:GLIMPSE2_CHUNK' {
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ext.args = ["--window-mb 0.01", "--window-cm 0.01", "--window-count 200", "--buffer-mb 0.005", "--buffer-cm 0.005", "--buffer-count 30"].join(' ')
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ext.prefix = { "${meta.id}_chunks" }
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}
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}

‎conf/test_panelprep.config

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@@ -41,13 +41,28 @@ params {
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process {
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE_CHUNK' {
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ext.args = ["--window-size 10000", "--window-count 400", "--buffer-size 5000", "--buffer-count 30"].join(' ')
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ext.prefix = { "${meta.id}_${meta.chr}_chunks_glimpse1" }
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publishDir = [
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path: { "${params.outdir}/prep_panel/chunks/glimpse1/" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
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enabled: true
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]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE2_CHUNK' {
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ext.args = ["--window-mb 0.01", "--window-cm 0.01", "--window-count 200", "--buffer-mb 0.005", "--buffer-cm 0.005", "--buffer-count 30"].join(' ')
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ext.prefix = { "${meta.id}_${meta.chr}_chunks_glimpse2" }
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publishDir = [
57+
path: { "${params.outdir}/prep_panel/chunks/glimpse2/" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
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enabled: true
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]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_PHASE_SHAPEIT5:GLIMPSE2_CHUNK' {
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ext.args = ["--window-mb 0.01", "--window-cm 0.01", "--window-count 200", "--buffer-mb 0.005", "--buffer-cm 0.005", "--buffer-count 30"].join(' ')
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ext.prefix = { "${meta.id}_chunks" }
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}
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}

‎docs/output.md

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@@ -98,7 +98,7 @@ The files will be phased if the flag `--phase` is used (with `_phased` suffix).
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<summary>Output files</summary>
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- `prep_panel/csv/`
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- `chunks.csv`: A CSV file containing the list of chunks obtained for each chromosome and panel.
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- `chunks_glimpse1.csv`: A CSV file containing the list of chunks obtained for each chromosome and panel.
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- `panel.csv`: A CSV file containing the final phased and prepared for each chromosome and input panel.
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- `posfile.csv`: A CSV file containing the final list of panel positions, in VCF and TSV files, for each chromosome and input panel.
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‎workflows/phaseimpute/main.nf

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@@ -125,7 +125,7 @@ workflow PHASEIMPUTE {
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// Program to filter chromosomes
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filter_chr_program = ch_region
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.collect{ meta, region -> meta.chr }
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.collect{ meta, _region -> meta.chr }
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.map { chr ->
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"BEGIN { FS=\"\t\";\nsplit(\"" + chr.join(" ") + '", chr, " ");\n' +
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'for (i in chr) {\nchr_map[chr[i]] = 1;\n}\n}\n' +
@@ -137,7 +137,6 @@ workflow PHASEIMPUTE {
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// Compute coverage of input files
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SAMTOOLS_COVERAGE_INP(ch_input_sim, ch_fasta)
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ch_versions = ch_versions.mix(SAMTOOLS_COVERAGE_INP.out.versions)
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ch_coverage = SAMTOOLS_COVERAGE_INP.out.coverage
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FILTER_CHR_INP(
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SAMTOOLS_COVERAGE_INP.out.coverage,
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// Posfile
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exportCsv(
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ch_posfile.map{ meta, vcf, index, hap, legend ->
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[meta, [2:"prep_panel/sites", 3:"prep_panel/haplegend", 4:"prep_panel/haplegend"], vcf, index, hap, legend]
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[meta, [2:"prep_panel/sites", 3:"prep_panel/sites", 4:"prep_panel/haplegend", 5:"prep_panel/haplegend"], vcf, index, hap, legend]
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},
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["id", "chr"], "panel,chr,vcf,index,hap,legend",
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"posfile.csv", "prep_panel/csv"
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)
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// Chunks
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exportCsv(
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VCF_CHUNK_GLIMPSE.out.chunks.map{ meta, file ->
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[meta, [2:"prep_panel/chunks"], file]
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[meta, [2:"prep_panel/chunks/glimpse1"], file]
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},
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["id", "chr"], "panel,chr,file",
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"chunks.csv", "prep_panel/csv"
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"chunks_glimpse1.csv", "prep_panel/csv"
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)
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}
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@@ -424,9 +423,9 @@ workflow PHASEIMPUTE {
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// Export all files to csv
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exportCsv(
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ch_input_validate.map{ meta, file, index ->
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[meta, [2:"imputation/${meta.tools}/samples/", 3:"imputation/${meta.tools}/samples/"], file, index]
426+
[meta, [2:"imputation/${meta.tools}/samples", 3:"imputation/${meta.tools}/samples"], file, index]
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},
429-
["id", "tools"], "sample,tools,vcf,index",
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["id", "tools"], "sample,tools,file,index",
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"impute.csv", "imputation/csv"
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)
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}

‎workflows/phaseimpute/tests/main.nf.test.snap

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@@ -95,7 +95,7 @@
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"prep_panel/chunks/glimpse1/1000GP_chr22_chunks_glimpse1.txt",
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"prep_panel/chunks/glimpse2/1000GP_chr21_chunks_glimpse2.txt",
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"prep_panel/chunks/glimpse2/1000GP_chr22_chunks_glimpse2.txt",
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"prep_panel/csv/chunks.csv",
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"prep_panel/csv/chunks_glimpse1.csv",
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"prep_panel/csv/panel.csv",
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"prep_panel/csv/posfile.csv",
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"prep_panel/haplegend/1000GP_chr21.hap.gz",
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166166
]
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],
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"meta": {
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"nf-test": "0.9.2",
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"nf-test": "0.9.1",
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"nextflow": "24.10.1"
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},
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"timestamp": "2024-11-27T18:23:38.85114929"
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"timestamp": "2025-02-20T11:45:13.538903855"
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},
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"Check test_validate": {
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"content": [
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"prep_panel/chunks/glimpse1/1000GP_chr22_chunks_glimpse1.txt",
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"prep_panel/chunks/glimpse2/1000GP_chr21_chunks_glimpse2.txt",
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"prep_panel/chunks/glimpse2/1000GP_chr22_chunks_glimpse2.txt",
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"prep_panel/csv/chunks.csv",
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"prep_panel/csv/chunks_glimpse1.csv",
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"prep_panel/csv/panel.csv",
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"prep_panel/csv/posfile.csv",
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"prep_panel/haplegend/1000GP_chr21.hap.gz",
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349349
]
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],
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"meta": {
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"nf-test": "0.8.4",
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"nextflow": "24.04.4"
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"nf-test": "0.9.1",
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"nextflow": "24.10.1"
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},
355-
"timestamp": "2024-10-14T19:19:50.07758554"
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"timestamp": "2025-02-20T11:48:45.440753818"
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},
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"Check test_glimpse2": {
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"content": [
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"prep_panel/chunks/glimpse1/658Dog_chr22_chunks_glimpse1.txt",
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"prep_panel/chunks/glimpse2/658Dog_chr21_chunks_glimpse2.txt",
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"prep_panel/chunks/glimpse2/658Dog_chr22_chunks_glimpse2.txt",
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"prep_panel/csv/chunks.csv",
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"prep_panel/csv/chunks_glimpse1.csv",
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"prep_panel/csv/panel.csv",
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"prep_panel/csv/posfile.csv",
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"prep_panel/haplegend/658Dog_chr21.hap.gz",
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473473
]
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],
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"meta": {
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"nf-test": "0.9.2",
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"nf-test": "0.9.1",
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"nextflow": "24.10.1"
478478
},
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"timestamp": "2024-11-27T18:25:56.980470563"
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"timestamp": "2025-02-20T11:47:19.564681513"
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}
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}

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