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AratzAratz
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Merge pull request #75 from Aratz/nft-utils
Set up nft-utils in tests
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‎CHANGELOG.md‎

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@@ -9,6 +9,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
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### `Added`
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- [#75](https://github.com/nf-core/seqinspector/pull/75) Set up nft-utils
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- [#68](https://github.com/nf-core/seqinspector/pull/68) Add tool selector
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- [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
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- [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.

‎nf-test.config‎

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@@ -5,4 +5,7 @@ config {
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configFile "tests/nextflow.config"
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profile "test,docker"
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plugins {
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load "[email protected]"
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}
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}

‎tests/.nftignore‎

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.DS_Store
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multiqc/{global_report,group_reports/*}/multiqc_data/multiqc.log
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multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_data.json
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multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_general_stats.txt
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multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_software_versions.txt
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multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_sources.txt
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multiqc/{global_report,group_reports/*}/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
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multiqc/{global_report,group_reports/*}/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
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multiqc/{global_report,group_reports/*}/multiqc_report.html
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pipeline_info/*.{html,json,txt,yml}
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fastqscreen/*_screen.html
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fastqc/*_fastqc.{html,zip}

‎tests/MiSeq.main.nf.test‎

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@@ -15,15 +15,28 @@ nextflow_pipeline {
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}
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then {
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// stable_name: All files + folders in ${params.outdir}/ with a stable name
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def stable_name = getAllFilesFromDir(
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params.outdir,
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relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
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)
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// stable_path: All files in ${params.outdir}/ with stable content
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def stable_path = getAllFilesFromDir(
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params.outdir,
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ignoreFile: 'tests/.nftignore'
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)
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assertAll(
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{ assert workflow.success },
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{ assert workflow.success},
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{ assert snapshot(
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path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
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path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
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path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
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path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
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).match()
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}
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
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// All stable path names, with a relative path
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stable_name,
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// All files with stable contents
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stable_path
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).match() }
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)
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}
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}
@@ -38,15 +51,64 @@ nextflow_pipeline {
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}
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then {
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// stable_name: All files + folders in ${params.outdir}/ with a stable name
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def stable_name = getAllFilesFromDir(
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params.outdir,
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relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
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)
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// stable_path: All files in ${params.outdir}/ with stable content
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def stable_path = getAllFilesFromDir(
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params.outdir,
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ignoreFile: 'tests/.nftignore'
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)
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assertAll(
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{ assert workflow.success},
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{ assert snapshot(
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
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// All stable path names, with a relative path
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stable_name,
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// All files with stable contents
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stable_path
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).match() }
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)
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}
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}
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test("Miseq data test (skip all tools)") {
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when {
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config "./MiSeq.main.nf.test.config"
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params {
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outdir = "$outputDir"
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skip_tools = "fastqc,fastqscreen,seqfu_stats,seqtk_sample"
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}
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}
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then {
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// stable_name: All files + folders in ${params.outdir}/ with a stable name
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def stable_name = getAllFilesFromDir(
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params.outdir,
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relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
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)
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// stable_path: All files in ${params.outdir}/ with stable content
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def stable_path = getAllFilesFromDir(
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params.outdir,
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ignoreFile: 'tests/.nftignore'
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)
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assertAll(
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{ assert workflow.success },
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{ assert workflow.success},
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{ assert snapshot(
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path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
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).match()
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},
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{
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assert !path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt").exists()
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}
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
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// All stable path names, with a relative path
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stable_name,
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// All files with stable contents
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stable_path
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).match() }
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)
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}
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}

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