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drpatelhdrpatelh
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Merge pull request #1220 from adamrtalbot/nf-test-init
nf-test at the pipeline level
2 parents 48663bf + e05cc55 commit 8be7d70

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‎.gitignore

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*.pyc
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.DS_Store
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.nextflow*
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work/
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.nf-test.log
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data/
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nf-test
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.nf-test*
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results/
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.DS_Store
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testing/
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test.xml
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testing*
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*.pyc
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testing/
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work/

‎.nf-core.yml

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files_unchanged:
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- assets/email_template.html
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- assets/email_template.txt
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- .gitignore
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files_exist:
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- conf/modules.config
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nextflow_config:

‎CHANGELOG.md

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- [PR #1213](https://github.com/nf-core/rnaseq/pull/1213) - Pass transcriptome fasta through to samtools stats
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- [PR #1216](https://github.com/nf-core/rnaseq/pull/1216) - Delocalise catadditionalfasta ([#1162](https://github.com/nf-core/rnaseq/issues/1162))
2020
- [PR #1218](https://github.com/nf-core/rnaseq/pull/1218) - Template update for nf-core/tools v2.13
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- [PR #1220](https://github.com/nf-core/rnaseq/pull/1220) - Initialise nf-test and add pipeline level test
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### Parameters
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‎nf-test.config

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config {
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// Location of nf-tests
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testsDir "."
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// nf-test directory used to create temporary files for each test
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workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
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// Location of an optional nextflow.config file specific for executing pipeline tests
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configFile "tests/nextflow.config"
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profile "test"
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}

‎tests/lib/UTILS.groovy

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// Function to remove Nextflow version from software_versions.yml
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class UTILS {
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public static String removeNextflowVersion(outputDir) {
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def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
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if (softwareVersions.containsKey("Workflow")) {
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softwareVersions.Workflow.remove("Nextflow")
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}
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return softwareVersions
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}
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}

‎tests/main.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 "rnaseq"
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tag "PIPELINE"
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test("Run with profile test") {
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when {
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params {
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outdir = "$outputDir"
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv'
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}
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}
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then {
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assert workflow.success
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assertAll(
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{ assert workflow.success },
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{ assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") },
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{ assert snapshot(path("$outputDir/bbsplit/").list(),
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path("$outputDir/salmon/").list(),
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path("$outputDir/star_salmon/").list(),
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path("$outputDir/trimgalore/").list()) },
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{ assert new File("$outputDir/fastqc/RAP1_IAA_30M_REP1_1_fastqc.html").exists() },
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{ assert new File("$outputDir/fastqc/RAP1_IAA_30M_REP1_2_fastqc.html").exists() },
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{ assert new File("$outputDir/fastqc/RAP1_UNINDUCED_REP1_fastqc.html").exists() },
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{ assert new File("$outputDir/fastqc/RAP1_UNINDUCED_REP2_fastqc.html").exists() },
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{ assert new File("$outputDir/fastqc/WT_REP1_1_fastqc.html").exists() },
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{ assert new File("$outputDir/fastqc/WT_REP1_2_fastqc.html").exists() },
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{ assert new File("$outputDir/fastqc/WT_REP2_1_fastqc.html").exists() },
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{ assert new File("$outputDir/fastqc/WT_REP2_2_fastqc.html").exists() },
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{ assert new File("$outputDir/multiqc/star_salmon/multiqc_report.html").exists() }
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)
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}
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}
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}

‎tests/main.nf.test.snap

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{
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"single_end_software_versions": {
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"content": [
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"{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, CAT_ADDITIONAL_FASTA={python=3.9.5}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DESEQ2_QC_PSEUDO={bioconductor-deseq2=1.28.0, r-base=4.0.3}, DESEQ2_QC_STAR_SALMON={bioconductor-deseq2=1.28.0, r-base=4.0.3}, DUPRADAR={bioconductor-dupradar=1.28.0, r-base=4.2.1}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.10}, GUNZIP_GTF={gunzip=1.10}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.0.0}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SE_GENE={bioconductor-summarizedexperiment=1.24.0, r-base=4.1.1}, STAR_ALIGN={gawk=5.1.0, samtools=1.16.1, star=2.7.9a}, STAR_GENOMEGENERATE={gawk=5.1.0, samtools=1.16.1, star=2.7.9a}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, TX2GENE={python=3.9.5}, TXIMPORT={bioconductor-tximeta=1.12.0, r-base=4.1.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.30}, Workflow={nf-core/rnaseq=3.15.0dev}}"
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],
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"meta": {
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"nf-test": "0.8.4",
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"nextflow": "23.10.1"
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},
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"timestamp": "2024-02-09T16:13:24.846838"
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}
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}

‎tests/nextflow.config

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/*
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========================================================================================
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Nextflow config file for running tests
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========================================================================================
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*/
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params {
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// Base directory for nf-core/modules test data
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modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
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// Base directory for nf-core/rnaseq test data
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pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15'
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}
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// Impose sensible resource limits for testing
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process {
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withName: '.*' {
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cpus = 2
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memory = 3.GB
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time = 2.h
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}
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}
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// Impose same minimum Nextflow version as the pipeline for testing
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manifest {
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nextflowVersion = '!>=23.04.0'
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}
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// Disable all Nextflow reporting options
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timeline { enabled = false }
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report { enabled = false }
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trace { enabled = false }
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dag { enabled = false }

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