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prepare release 1.0.0 (#169)
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‎.nf-core.yml‎

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name: seqinspector
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org: nf-core
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outdir: .
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version: 1.0dev
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version: 1.0.0

‎CHANGELOG.md‎

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## v1.0dev - [date]
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## [1.0.0](https://github.com/nf-core/seqinspector/releases/tag/1.0.0) - Inspector Gadget
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Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-co.re/) template.
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- [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bugs in qc_bam and prepare_genome subworkflows and add tests
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- [#163](https://github.com/nf-core/seqinspector/pull/163) Run fastqscreen with subsampled data if available
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- [#167](https://github.com/nf-core/seqinspector/pull/167) RunDirParser is now skipped if no Run Directory information is available
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- [#169](https://github.com/nf-core/seqinspector/pull/169) Rescue missing versions from PREPARE_GENOME subworkflow
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### `Changed`
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- [#158](https://github.com/nf-core/seqinspector/pull/158) Moved picard_collectmultiplemetrics to the subworkflow QC_BAM
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- [#164](https://github.com/nf-core/seqinspector/pull/164) Refactor local subworkflow and pipeline tests
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- [#168](https://github.com/nf-core/seqinspector/pull/168) Adhere to strict syntax
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- [#169](https://github.com/nf-core/seqinspector/pull/169) Prepare release 1.0.0
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### `Dependencies`
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‎assets/multiqc_config.yml‎

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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/seqinspector/tree/dev" target="_blank">nf-core/seqinspector</a>
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analysis pipeline. For information about how to interpret these results, please see the
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<a href="https://nf-co.re/seqinspector/dev/docs/output" target="_blank">documentation</a>.
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This report has been generated by the <a href="https://github.com/nf-core/seqinspector/releases/tag/1.0.0" target="_blank">nf-core/seqinspector</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/seqinspector/1.0.0/docs/output" target="_blank">documentation</a>.
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report_section_order:
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"nf-core-seqinspector-index":
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order: -999
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# for SE: "SampleName_01" -> "SampleName #01"
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# for PE: "SampleName_01_1" -> "SampleName #01_1"
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# and: "SampleName_01_2" -> "SampleName #01_2"
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sample_names_replace_regex: True
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sample_names_replace_regex: true
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sample_names_replace:
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"(.+)_(\\d{2,}|\\d{2,}_[12])$": "\\1 #\\2"
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‎main.nf‎

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@@ -51,7 +51,7 @@ workflow NFCORE_SEQINSPECTOR {
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samplesheet,
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params.fasta,
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skip_tools,
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params.bwamem2
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params.bwamem2,
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)
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emit:
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params.input,
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params.help,
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params.help_full,
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params.show_hidden
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params.show_hidden,
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)
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//

‎nextflow.config‎

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mainScript = 'main.nf'
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defaultBranch = 'master'
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nextflowVersion = '!>=25.04.0'
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version = '1.0dev'
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version = '1.0.0'
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doi = ''
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}
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‎ro-crate-metadata.json‎

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‎tests/MiSeq.nf.test‎

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assertAll(
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{ assert snapshot(
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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("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
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removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
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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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assertAll(
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{ assert snapshot(
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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("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
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removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
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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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assertAll(
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{ assert snapshot(
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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("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
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removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
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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

‎tests/MiSeq.nf.test.snap‎

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"Miseq data test (skip all tools)": {
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"content": [
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{
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"Workflow": {
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"nf-core/seqinspector": "v1.0dev"
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"SAMTOOLS_FAIDX": {
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"samtools": "1.22.1"
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}
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},
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[
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.2"
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"nextflow": "25.10.3"
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},
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"timestamp": "2025-12-12T16:48:15.085074556"
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"timestamp": "2026-02-10T17:15:27.612715634"
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},
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"MiSeq data test (single 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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},
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"BWAMEM2_MEM": {
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"bwamem2": "2.2.1",
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"samtools": "1.22.1"
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"PICARD_COLLECTMULTIPLEMETRICS": {
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"picard": "3.4.0"
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},
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"SAMTOOLS_FAIDX": {
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"samtools": "1.22.1"
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},
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"SAMTOOLS_INDEX": {
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"samtools": "1.22.1"
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},
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"SEQFU_STATS": {
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"seqfu": "1.22.3"
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},
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"Workflow": {
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"nf-core/seqinspector": "v1.0dev"
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}
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},
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[
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.2"
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"nextflow": "25.10.3"
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},
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"timestamp": "2025-12-12T16:45:20.420081882"
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"timestamp": "2026-02-10T17:14:12.684188306"
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},
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"Miseq data test (skip fastqc)": {
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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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},
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"BWAMEM2_MEM": {
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"bwamem2": "2.2.1",
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"samtools": "1.22.1"
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"PICARD_COLLECTMULTIPLEMETRICS": {
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"picard": "3.4.0"
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},
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"SAMTOOLS_FAIDX": {
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"samtools": "1.22.1"
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},
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"SAMTOOLS_INDEX": {
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"samtools": "1.22.1"
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},
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"SEQFU_STATS": {
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"seqfu": "1.22.3"
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},
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"Workflow": {
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"nf-core/seqinspector": "v1.0dev"
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.2"
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"nextflow": "25.10.3"
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},
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"timestamp": "2025-12-12T16:47:54.570558579"
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"timestamp": "2026-02-10T17:14:58.212405529"
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}
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}

‎tests/MiSeq_PairedEnd.nf.test‎

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assertAll(
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{ assert snapshot(
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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("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
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removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
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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

‎tests/MiSeq_PairedEnd.nf.test.snap‎

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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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},
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"BWAMEM2_MEM": {
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"bwamem2": "2.2.1",
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"samtools": "1.22.1"
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"PICARD_COLLECTMULTIPLEMETRICS": {
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"picard": "3.4.0"
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},
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"SAMTOOLS_FAIDX": {
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"samtools": "1.22.1"
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},
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"SAMTOOLS_INDEX": {
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"samtools": "1.22.1"
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"SEQFU_STATS": {
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"seqfu": "1.22.3"
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},
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"Workflow": {
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"nf-core/seqinspector": "v1.0dev"
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.2"
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"nextflow": "25.10.3"
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},
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"timestamp": "2025-12-12T16:49:17.100345817"
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"timestamp": "2026-02-10T17:16:28.42493386"
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}
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}

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