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New tests for samplesheet (#1856)
<!-- # nf-core/sarek pull request Many thanks for contributing to nf-core/sarek! Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. - [ ] `README.md` is updated (including new tool citations and authors/contributors).
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‎CHANGELOG.md

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@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [1817](https://github.com/nf-core/sarek/pull/1817) - Added new contributor
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- [1841](https://github.com/nf-core/sarek/pull/1841) - Add pcr-indel-model parameter for GATK HaplotypeCaller
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- [1848](https://github.com/nf-core/sarek/pull/1848) - Add parameter for setting pixel distance for GATK MarkDuplicates
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- [1856](https://github.com/nf-core/sarek/pull/1856) - Added early failure when more than 1 normal sample per patient is provided for somatic variant calling
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### Changed
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‎subworkflows/local/samplesheet_to_channel/main.nf

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@@ -1,40 +1,60 @@
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workflow SAMPLESHEET_TO_CHANNEL{
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take:
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ch_from_samplesheet //
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aligner //
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ascat_alleles //
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ascat_loci //
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ascat_loci_gc //
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ascat_loci_rt //
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bcftools_annotations //
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bcftools_annotations_tbi //
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bcftools_header_lines //
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build_only_index //
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dbsnp //
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fasta //
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germline_resource //
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intervals //
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joint_germline //
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joint_mutect2 //
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known_indels //
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known_snps //
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no_intervals //
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pon //
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sentieon_dnascope_emit_mode //
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sentieon_haplotyper_emit_mode //
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seq_center //
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seq_platform //
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skip_tools //
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snpeff_cache //
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snpeff_db //
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step //
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tools //
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umi_read_structure //
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wes //
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ch_from_samplesheet // samplesheet
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aligner // String: aligner
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ascat_alleles // Path: ascat alleles
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ascat_loci // Path: ascat loci
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ascat_loci_gc // Path: ascat loci gc
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ascat_loci_rt // Path: ascat loci rt
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bcftools_annotations // Path: bcftools annotations
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bcftools_annotations_tbi // Path: bcftools annotations tbi
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bcftools_header_lines // Path: bcftools header lines
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build_only_index // Boolean: build only index
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dbsnp // Path: dbsnp
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fasta // Path: fasta
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germline_resource // Path: germline resource
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intervals // Path: intervals
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joint_germline // Boolean: joint_germline
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joint_mutect2 // Boolean: joint_mutect2
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known_indels // Path: known indels
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known_snps // Path: known snps
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no_intervals // Boolean: no intervals
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pon // Path: pon
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sentieon_dnascope_emit_mode // String: sentieon dnascope emit mode
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sentieon_haplotyper_emit_mode // String: sentieon haplotyper emit mode
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seq_center // String: seq center
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seq_platform // String: seq platform
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skip_tools // Array: skip tools
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snpeff_cache // Path: snpeff cache
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snpeff_db // String: snpeff db
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step // String: step
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tools // Array: tools
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umi_read_structure // String: umi read structure
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wes // wes
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main:
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ch_from_samplesheet.dump(tag:"ch_from_samplesheet")
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ch_from_samplesheet
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.map { meta, _fastq_1, _fastq_2, _spring_1, _spring_2, _table, _cram, _crai, _bam, _bai, _vcf, _variantcaller ->
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// Get only the patient, sample and status fields from the meta map
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[meta.patient, meta.subMap('sample', 'status')]
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}
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.unique()
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.groupTuple()
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.map { patient, samples ->
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// Count samples with status 0 and status 1
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def status0_count = samples.count { it.status == 0 }
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def status1_count = samples.count { it.status == 1 }
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// Check the condition and exit with an error if met
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if (status1_count == 1 && status0_count > 1) {
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System.err.println("Patient [${patient}] has more than one sample [${status0_count}] with normal status [0] and one sample with tumor status [1].")
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error("Execution halted due to sample status inconsistency.")
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}
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}
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input_sample = ch_from_samplesheet.map{ meta, fastq_1, fastq_2, spring_1, spring_2, table, cram, crai, bam, bai, vcf, variantcaller ->
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// generate patient_sample key to group lanes together
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[ meta.patient + meta.sample, [meta, fastq_1, fastq_2, spring_1, spring_2, table, cram, crai, bam, bai, vcf, variantcaller] ]

‎tests/csv/3.0/recalibrated_somatic_two_normal_one_sample.csv

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patient,sex,status,sample,cram,crai
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test,XX,0,sample1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai
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test,XX,0,sample1B,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai
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test,XX,1,sample2,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai

‎tests/default.nf.test

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@@ -49,21 +49,4 @@ nextflow_pipeline {
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)
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}
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}
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test("-profile test --input tests/csv/3.0/sample_with_space.csv") {
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when {
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params {
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input = "${projectDir}/tests/csv/3.0/sample_with_space.csv"
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outdir = "$outputDir"
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}
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}
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then {
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assertAll(
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{ assert workflow.failed},
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{ assert workflow.stderr.toString().contains("Sample ID must be provided, cannot contain spaces and must be a string value") }
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)
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}
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}
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}

‎tests/default.nf.test.snap

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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.4"
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"nextflow": "25.02.1"
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},
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"timestamp": "2025-03-10T11:13:17.000556982"
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"timestamp": "2025-04-02T15:44:44.567674265"
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}
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}

‎tests/samplesheets.nf.test

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nextflow_pipeline {
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name "Test pipeline"
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script "../main.nf"
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tag "pipeline"
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tag "pipeline_sarek"
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tag "cpu"
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test("-profile test --input tests/csv/3.0/sample_with_space.csv") {
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when {
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params {
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input = "${projectDir}/tests/csv/3.0/sample_with_space.csv"
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outdir = "$outputDir"
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}
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}
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then {
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assertAll(
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{ assert workflow.failed},
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{ assert snapshot(
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workflow.stderr.toString().split(",")[0..1,3..5]
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).match() }
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)
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}
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}
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test("-profile test --step variant_calling --input tests/csv/3.0/recalibrated_somatic_two_normal_one_sample.csv") {
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when {
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params {
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modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
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input = "${projectDir}/tests/csv/3.0/recalibrated_somatic_two_normal_one_sample.csv"
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outdir = "$outputDir"
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step = "variant_calling"
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}
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}
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then {
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assertAll(
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{ assert workflow.failed},
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{ assert snapshot(
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workflow.stderr.toString().split(",")[0]
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).match() }
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)
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}
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}
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}

‎tests/samplesheets.nf.test.snap

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{
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"-profile test --step variant_calling --input tests/csv/3.0/recalibrated_somatic_two_normal_one_sample.csv": {
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"content": [
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"[Patient [test] has more than one sample [2] with normal status [0] and one sample with tumor status [1].]"
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.5"
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},
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"timestamp": "2025-04-03T17:48:43.052129562"
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},
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"-profile test --input tests/csv/3.0/sample_with_space.csv": {
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"content": [
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[
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"[\u001b[0;31mThe following invalid input values have been detected:",
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" ",
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" \t-> Entry 2: Error for field 'sample' (test 2): \"test 2\" does not match regular expression [^\\S+$] (Sample ID must be provided",
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" cannot contain spaces and must be a string value)",
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" \u001b[0m"
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]
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.5"
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},
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"timestamp": "2025-04-03T12:12:16.909966356"
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}
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}

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