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Merge pull request #1286 from RaqManzano/samplesheet_parsing
Created subworkflow for parsing samplesheet with nf-test
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| Original file line number | Diff line number | Diff line change |
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| config { | ||
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| testsDir "tests" | ||
| testsDir "." | ||
| workDir ".nf-test" | ||
| configFile "conf/test.config" | ||
| profile "test" | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
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| workflow SAMPLESHEET_TO_CHANNEL{ | ||
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| take: | ||
| ch_from_samplesheet | ||
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| main: | ||
| ch_from_samplesheet.dump(tag:"ch_from_samplesheet") | ||
| input_sample = ch_from_samplesheet | ||
| .map{ meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller -> | ||
| // generate patient_sample key to group lanes together | ||
| [ meta.patient + meta.sample, [meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller] ] | ||
| } | ||
| .tap{ ch_with_patient_sample } // save the channel | ||
| .groupTuple() //group by patient_sample to get all lanes | ||
| .map { patient_sample, ch_items -> | ||
| // get number of lanes per sample | ||
| [ patient_sample, ch_items.size() ] | ||
| } | ||
| .combine(ch_with_patient_sample, by: 0) // for each entry add numLanes | ||
| .map { patient_sample, num_lanes, ch_items -> | ||
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| (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller) = ch_items | ||
| if (meta.lane && fastq_2) { | ||
| meta = meta + [id: "${meta.sample}-${meta.lane}".toString()] | ||
| def CN = params.seq_center ? "CN:${params.seq_center}\\t" : '' | ||
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| def flowcell = flowcellLaneFromFastq(fastq_1) | ||
| // Don't use a random element for ID, it breaks resuming | ||
| def read_group = "\"@RG\\tID:${flowcell}.${meta.sample}.${meta.lane}\\t${CN}PU:${meta.lane}\\tSM:${meta.patient}_${meta.sample}\\tLB:${meta.sample}\\tDS:${params.fasta}\\tPL:${params.seq_platform}\"" | ||
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| meta = meta - meta.subMap('lane') + [num_lanes: num_lanes.toInteger(), read_group: read_group.toString(), data_type: 'fastq', size: 1] | ||
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| if (params.step == 'mapping') return [ meta, [ fastq_1, fastq_2 ] ] | ||
| else { | ||
| error("Samplesheet contains fastq files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations") | ||
| } | ||
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| // start from BAM | ||
| } else if (meta.lane && bam) { | ||
| if (params.step != 'mapping' && !bai) { | ||
| error("BAM index (bai) should be provided.") | ||
| } | ||
| meta = meta + [id: "${meta.sample}-${meta.lane}".toString()] | ||
| def CN = params.seq_center ? "CN:${params.seq_center}\\t" : '' | ||
| def read_group = "\"@RG\\tID:${meta.sample}_${meta.lane}\\t${CN}PU:${meta.lane}\\tSM:${meta.patient}_${meta.sample}\\tLB:${meta.sample}\\tDS:${params.fasta}\\tPL:${params.seq_platform}\"" | ||
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| meta = meta - meta.subMap('lane') + [num_lanes: num_lanes.toInteger(), read_group: read_group.toString(), data_type: 'bam', size: 1] | ||
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| if (params.step != 'annotate') return [ meta - meta.subMap('lane'), bam, bai ] | ||
| else { | ||
| error("Samplesheet contains bam files but step is `annotate`. The pipeline is expecting vcf files for the annotation. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations") | ||
| } | ||
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| // recalibration | ||
| } else if (table && cram) { | ||
| meta = meta + [id: meta.sample, data_type: 'cram'] | ||
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| if (!(params.step == 'mapping' || params.step == 'annotate')) return [ meta - meta.subMap('lane'), cram, crai, table ] | ||
| else { | ||
| error("Samplesheet contains cram files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations") | ||
| } | ||
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| // recalibration when skipping MarkDuplicates | ||
| } else if (table && bam) { | ||
| meta = meta + [id: meta.sample, data_type: 'bam'] | ||
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| if (!(params.step == 'mapping' || params.step == 'annotate')) return [ meta - meta.subMap('lane'), bam, bai, table ] | ||
| else { | ||
| error("Samplesheet contains bam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations") | ||
| } | ||
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| // prepare_recalibration or variant_calling | ||
| } else if (cram) { | ||
| meta = meta + [id: meta.sample, data_type: 'cram'] | ||
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| if (!(params.step == 'mapping' || params.step == 'annotate')) return [ meta - meta.subMap('lane'), cram, crai ] | ||
| else { | ||
| error("Samplesheet contains cram files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations") | ||
| } | ||
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| // prepare_recalibration when skipping MarkDuplicates or `--step markduplicates` | ||
| } else if (bam) { | ||
| meta = meta + [id: meta.sample, data_type: 'bam'] | ||
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| if (!(params.step == 'mapping' || params.step == 'annotate')) return [ meta - meta.subMap('lane'), bam, bai ] | ||
| else { | ||
| error("Samplesheet contains bam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations") | ||
| } | ||
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| // annotation | ||
| } else if (vcf) { | ||
| meta = meta + [id: meta.sample, data_type: 'vcf', variantcaller: variantcaller ?: ''] | ||
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| if (params.step == 'annotate') return [ meta - meta.subMap('lane'), vcf ] | ||
| else { | ||
| error("Samplesheet contains vcf files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations") | ||
| } | ||
| } else { | ||
| error("Missing or unknown field in csv file header. Please check your samplesheet") | ||
| } | ||
| } | ||
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| if (params.step != 'annotate' && params.tools && !params.build_only_index) { | ||
| // Two checks for ensuring that the pipeline stops with a meaningful error message if | ||
| // 1. the sample-sheet only contains normal-samples, but some of the requested tools require tumor-samples, and | ||
| // 2. the sample-sheet only contains tumor-samples, but some of the requested tools require normal-samples. | ||
| input_sample.filter{ it[0].status == 1 }.ifEmpty{ // In this case, the sample-sheet contains no tumor-samples | ||
| if (!params.build_only_index) { | ||
| def tools_tumor = ['ascat', 'controlfreec', 'mutect2', 'msisensorpro'] | ||
| def tools_tumor_asked = [] | ||
| tools_tumor.each{ tool -> | ||
| if (params.tools.split(',').contains(tool)) tools_tumor_asked.add(tool) | ||
| } | ||
| if (!tools_tumor_asked.isEmpty()) { | ||
| error('The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : ' + tools_tumor_asked.join(", ")) | ||
| } | ||
| } | ||
| } | ||
| input_sample.filter{ it[0].status == 0 }.ifEmpty{ // In this case, the sample-sheet contains no normal/germline-samples | ||
| def tools_requiring_normal_samples = ['ascat', 'deepvariant', 'haplotypecaller', 'msisensorpro'] | ||
| def requested_tools_requiring_normal_samples = [] | ||
| tools_requiring_normal_samples.each{ tool_requiring_normal_samples -> | ||
| if (params.tools.split(',').contains(tool_requiring_normal_samples)) requested_tools_requiring_normal_samples.add(tool_requiring_normal_samples) | ||
| } | ||
| if (!requested_tools_requiring_normal_samples.isEmpty()) { | ||
| error('The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : ' + requested_tools_requiring_normal_samples.join(", ")) | ||
| } | ||
| } | ||
| } | ||
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| // Fails when wrongfull extension for intervals file | ||
| if (params.wes && !params.step == 'annotate') { | ||
| if (params.intervals && !params.intervals.endsWith("bed")) error("Target file specified with `--intervals` must be in BED format for targeted data") | ||
| else log.warn("Intervals file was provided without parameter `--wes`: Pipeline will assume this is Whole-Genome-Sequencing data.") | ||
| } else if (params.intervals && !params.intervals.endsWith("bed") && !params.intervals.endsWith("list")) error("Intervals file must end with .bed, .list, or .interval_list") | ||
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| if (params.step == 'mapping' && params.aligner.contains("dragmap") && !(params.skip_tools && params.skip_tools.split(',').contains("baserecalibrator"))) { | ||
| log.warn("DragMap was specified as aligner. Base recalibration is not contained in --skip_tools. It is recommended to skip baserecalibration when using DragMap\nhttps://gatk.broadinstitute.org/hc/en-us/articles/4407897446939--How-to-Run-germline-single-sample-short-variant-discovery-in-DRAGEN-mode") | ||
| } | ||
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| if (params.step == 'mapping' && params.aligner.contains("sentieon-bwamem") && params.umi_read_structure) { | ||
| error("Sentieon BWA is currently not compatible with FGBio UMI handeling. Please choose a different aligner.") | ||
| } | ||
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| if (params.tools && params.tools.split(',').contains("sentieon_haplotyper") && params.joint_germline && (!params.sentieon_haplotyper_emit_mode || !(params.sentieon_haplotyper_emit_mode.contains('gvcf')))) { | ||
| error("When setting the option `--joint_germline` and including `sentieon_haplotyper` among the requested tools, please set `--sentieon_haplotyper_emit_mode` to include `gvcf`.") | ||
| } | ||
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| // Fails or warns when missing files or params for ascat | ||
| if (params.tools && params.tools.split(',').contains('ascat')) { | ||
| if (!params.ascat_alleles) { | ||
| error("No allele files were provided for running ASCAT. Please provide a zip folder with allele files.") | ||
| } | ||
| if (!params.ascat_loci) { | ||
| error("No loci files were provided for running ASCAT. Please provide a zip folder with loci files.") | ||
| } | ||
| if (!params.ascat_loci_gc && !params.ascat_loci_rt) { | ||
| log.warn("No LogRCorrection performed in ASCAT. For LogRCorrection to run, please provide either loci gc files or both loci gc files and loci rt files.") | ||
| } | ||
| if (params.wes) { | ||
| log.warn("Default reference files not suited for running ASCAT on WES data. It's recommended to use the reference files provided here: https://github.com/Wedge-lab/battenberg#required-reference-files") | ||
| } | ||
| } | ||
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| // Warns when missing files or params for mutect2 | ||
| if (params.tools && params.tools.split(',').contains('mutect2')) { | ||
| if (!params.pon) { | ||
| log.warn("No Panel-of-normal was specified for Mutect2.\nIt is highly recommended to use one: https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2\nFor more information on how to create one: https://gatk.broadinstitute.org/hc/en-us/articles/5358921041947-CreateSomaticPanelOfNormals-BETA-") | ||
| } | ||
| if (!params.germline_resource) { | ||
| log.warn("If Mutect2 is specified without a germline resource, no filtering will be done.\nIt is recommended to use one: https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2") | ||
| } | ||
| if (params.pon && params.pon.contains("/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz")) { | ||
| log.warn("The default Panel-of-Normals provided by GATK is used for Mutect2.\nIt is highly recommended to generate one from normal samples that are technical similar to the tumor ones.\nFor more information: https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON-") | ||
| } | ||
| } | ||
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| // Fails when missing resources for baserecalibrator | ||
| // Warns when missing resources for haplotypecaller | ||
| if (!params.dbsnp && !params.known_indels) { | ||
| if (params.step in ['mapping', 'markduplicates', 'prepare_recalibration', 'recalibrate'] && (!params.skip_tools || (params.skip_tools && !params.skip_tools.split(',').contains('baserecalibrator')))) { | ||
| error("Base quality score recalibration requires at least one resource file. Please provide at least one of `--dbsnp` or `--known_indels`\nYou can skip this step in the workflow by adding `--skip_tools baserecalibrator` to the command.") | ||
| } | ||
| if (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope'))) { | ||
| log.warn "If GATK's Haplotypecaller, Sentieon's Dnascpe or Sentieon's Haplotyper is specified, without `--dbsnp` or `--known_indels no filtering will be done. For filtering, please provide at least one of `--dbsnp` or `--known_indels`.\nFor more information see FilterVariantTranches (single-sample, default): https://gatk.broadinstitute.org/hc/en-us/articles/5358928898971-FilterVariantTranches\nFor more information see VariantRecalibration (--joint_germline): https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator\nFor more information on GATK Best practice germline variant calling: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-" | ||
| } | ||
| } | ||
| if (params.joint_germline && (!params.tools || !(params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope')))) { | ||
| error("The GATK's Haplotypecaller, Sentieon's Dnascope or Sentieon's Haplotyper should be specified as one of the tools when doing joint germline variant calling.) ") | ||
| } | ||
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| if ( | ||
| params.tools && | ||
| ( | ||
| params.tools.split(',').contains('haplotypecaller') || | ||
| params.tools.split(',').contains('sentieon_haplotyper') || | ||
| params.tools.split(',').contains('sentieon_dnascope') | ||
| ) && | ||
| params.joint_germline && | ||
| ( | ||
| !params.dbsnp || | ||
| !params.known_indels || | ||
| !params.known_snps || | ||
| params.no_intervals | ||
| ) | ||
| ) { | ||
| log.warn("""If GATK's Haplotypecaller, Sentieon's Dnascope and/or Sentieon's Haplotyper is specified, \ | ||
| but without `--dbsnp`, `--known_snps`, `--known_indels` or the associated resource labels (ie `known_snps_vqsr`), \ | ||
| no variant recalibration will be done. For recalibration you must provide all of these resources.\nFor more information \ | ||
| see VariantRecalibration: https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator \n\ | ||
| Joint germline variant calling also requires intervals in order to genotype the samples. \ | ||
| As a result, if `--no_intervals` is set to `true` the joint germline variant calling will not be performed.""") | ||
| } | ||
|
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| if (params.tools && | ||
| params.tools.split(',').contains('sentieon_dnascope') && | ||
| params.joint_germline && | ||
| ( | ||
| !params.sentieon_dnascope_emit_mode || | ||
| !params.sentieon_dnascope_emit_mode.split(',').contains('gvcf') | ||
| ) | ||
| ) { | ||
| error("When using Sentieon Dnascope for joint-germline variant-calling the option `--sentieon_dnascope_emit_mode` has to include `gvcf`.") | ||
| } | ||
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| if (params.tools && | ||
| params.tools.split(',').contains('sentieon_haplotyper') && | ||
| params.joint_germline && | ||
| ( | ||
| !params.sentieon_haplotyper_emit_mode || | ||
| !params.sentieon_haplotyper_emit_mode.split(',').contains('gvcf') | ||
| ) | ||
| ) { | ||
| error("When using Sentieon Haplotyper for joint-germline variant-calling the option `--sentieon_haplotyper_emit_mode` has to include `gvcf`.") | ||
| } | ||
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| // Fails when --joint_mutect2 is used without enabling mutect2 | ||
| if (params.joint_mutect2 && (!params.tools || !params.tools.split(',').contains('mutect2'))) { | ||
| error("The mutect2 should be specified as one of the tools when doing joint somatic variant calling with Mutect2. (The mutect2 could be specified by adding `--tools mutect2` to the nextflow command.)") | ||
| } | ||
|
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| // Fails when missing tools for variant_calling or annotate | ||
| if ((params.step == 'variant_calling' || params.step == 'annotate') && !params.tools) { | ||
| error("Please specify at least one tool when using `--step ${params.step}`.\nhttps://nf-co.re/sarek/parameters#tools") | ||
| } | ||
|
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| // Fails when missing sex information for CNV tools | ||
| if (params.tools && (params.tools.split(',').contains('ascat') || params.tools.split(',').contains('controlfreec'))) { | ||
| input_sample.map{ | ||
| if (it[0].sex == 'NA' ) { | ||
| error("Please specify sex information for each sample in your samplesheet when using '--tools' with 'ascat' or 'controlfreec'.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations") | ||
| } | ||
| } | ||
| } | ||
|
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| if ((params.download_cache) && (params.snpeff_cache || params.vep_cache)) { | ||
| error("Please specify either `--download_cache` or `--snpeff_cache`, `--vep_cache`.\nhttps://nf-co.re/sarek/usage#how-to-customise-snpeff-and-vep-annotation") | ||
| } | ||
|
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| emit: | ||
| input_sample | ||
| } | ||
|
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| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| FUNCTIONS | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| */ | ||
| // Parse first line of a FASTQ file, return the flowcell id and lane number. | ||
| def flowcellLaneFromFastq(path) { | ||
| // expected format: | ||
| // xx:yy:FLOWCELLID:LANE:... (seven fields) | ||
| // or | ||
| // FLOWCELLID:LANE:xx:... (five fields) | ||
| def line | ||
| path.withInputStream { | ||
| InputStream gzipStream = new java.util.zip.GZIPInputStream(it) | ||
| Reader decoder = new InputStreamReader(gzipStream, 'ASCII') | ||
| BufferedReader buffered = new BufferedReader(decoder) | ||
| line = buffered.readLine() | ||
| } | ||
| assert line.startsWith('@') | ||
| line = line.substring(1) | ||
| def fields = line.split(':') | ||
| String fcid | ||
|
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||
| if (fields.size() >= 7) { | ||
| // CASAVA 1.8+ format, from https://support.illumina.com/help/BaseSpace_OLH_009008/Content/Source/Informatics/BS/FileFormat_FASTQ-files_swBS.htm | ||
| // "@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos>:<UMI> <read>:<is filtered>:<control number>:<index>" | ||
| fcid = fields[2] | ||
| } else if (fields.size() == 5) { | ||
| fcid = fields[0] | ||
| } | ||
| return fcid | ||
| } | ||
|
|
||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| nextflow_workflow { | ||
|
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| name "Test Workflow SAMPLESHEET_TO_CHANNEL" | ||
| script "subworkflows/local/samplesheet_to_channel/main.nf" | ||
| workflow "SAMPLESHEET_TO_CHANNEL" | ||
|
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| test("Should run without failures") { | ||
|
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| when { | ||
| params { | ||
| // define parameters here. Example: | ||
| skip_tools = 'baserecalibrator' | ||
|
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| } | ||
| workflow { | ||
| """ | ||
| // define inputs of the workflow here. Example: | ||
| input[0] = Channel.of([['patient':'test', 'sample':'test', | ||
| 'sex':'XX', 'status':0, 'lane':'test_L1'], | ||
| file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), | ||
| file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), | ||
| [], [], [], [], [], [], []]) | ||
| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assert workflow.success | ||
| assert snapshot(workflow.out).match() | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
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