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nf-core lint
1 parent b17aca4 commit 8e115d6

12 files changed

Lines changed: 646 additions & 84 deletions

‎.nf-core.yml‎

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lint:
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files_exist:
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- tests/default.nf.test
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files_unchanged:
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- .github/CONTRIBUTING.md
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nextflow_config:
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- config_defaults:
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- params.fastq_screen_references

‎ro-crate-metadata.json‎

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‎tests/MiSeq.main.nf.test‎

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@@ -28,8 +28,6 @@ nextflow_pipeline {
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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

‎tests/MiSeq.main.nf.test.snap‎

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},
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"MiSeq data test (single end reads)": {
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"content": [
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6,
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{
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"BWAMEM2_INDEX": {
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"bwamem2": "2.2.1"
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"nf-test": "0.9.3",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-11-06T17:09:30.687814423"
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"timestamp": "2025-11-07T10:23:17.145777453"
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},
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"Miseq data test (skip fastqc)": {
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"content": [

‎tests/MiSeq_PairedEnd.main.nf.test‎

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@@ -28,8 +28,6 @@ nextflow_pipeline {
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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

‎tests/MiSeq_PairedEnd.main.nf.test.snap‎

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{
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"MiSeq data test (paired end reads)": {
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"content": [
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{
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"BWAMEM2_INDEX": {
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"bwamem2": "2.2.1"
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"nf-test": "0.9.3",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-11-06T17:11:17.153150613"
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"timestamp": "2025-11-07T10:24:43.782493978"
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}
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}

‎tests/NovaSeq6000.main.nf.test‎

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@@ -28,8 +28,6 @@ nextflow_pipeline {
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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

‎tests/NovaSeq6000.main.nf.test.snap‎

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{
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"NovaSeq6000 data test": {
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"content": [
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{
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"BWAMEM2_INDEX": {
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"bwamem2": "2.2.1"
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"nf-test": "0.9.3",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-11-06T17:12:19.300655258"
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"timestamp": "2025-11-07T10:25:42.576692828"
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}
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}

‎tests/NovaSeq6000.main_subsample.nf.test‎

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@@ -15,35 +15,26 @@ 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("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
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path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
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path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
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path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt"),
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path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt"),
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path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt"),
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path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt"),
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path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt"),
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path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt"),
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path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt"),
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path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt"),
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path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt"),
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path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt"),
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path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
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path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
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path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
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path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt"),
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).match()
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},
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$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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