From 639a665753e4fa81fe535948d65d6dbeb8cdf208 Mon Sep 17 00:00:00 2001 From: matrulda Date: Wed, 11 Mar 2026 12:44:41 +0100 Subject: [PATCH 01/25] Install CheckQC module and import in seqinspector workflow --- modules.json | 5 ++ modules/nf-core/checkqc/environment.yml | 16 ++++++ modules/nf-core/checkqc/main.nf | 47 ++++++++++++++++ modules/nf-core/checkqc/meta.yml | 72 +++++++++++++++++++++++++ workflows/seqinspector.nf | 1 + 5 files changed, 141 insertions(+) create mode 100644 modules/nf-core/checkqc/environment.yml create mode 100644 modules/nf-core/checkqc/main.nf create mode 100644 modules/nf-core/checkqc/meta.yml diff --git a/modules.json b/modules.json index 0953506b..0160af91 100644 --- a/modules.json +++ b/modules.json @@ -15,6 +15,11 @@ "git_sha": "8325a8155a77a336a613a504b8e4d6cea7a2344a", "installed_by": ["modules"] }, + "checkqc": { + "branch": "master", + "git_sha": "b06df7c554e1eb06c35ad96c506b49444e0a1729", + "installed_by": ["modules"] + }, "fastqc": { "branch": "master", "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f", diff --git a/modules/nf-core/checkqc/environment.yml b/modules/nf-core/checkqc/environment.yml new file mode 100644 index 00000000..e9be6540 --- /dev/null +++ b/modules/nf-core/checkqc/environment.yml @@ -0,0 +1,16 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::sample-sheet=0.13.0 + - conda-forge::numpy=2.2.4 + - conda-forge::pandas=2.2.2 + - conda-forge::pip=25.2 + - conda-forge::python=3.10.19 + - conda-forge::tornado=6.3.2 + - conda-forge::xmltodict=0.13.0 + - pip: + - checkQC==4.1.0 + - interop==1.4.0 + - jsonschema==4.26.0 + - samshee==0.2.12 diff --git a/modules/nf-core/checkqc/main.nf b/modules/nf-core/checkqc/main.nf new file mode 100644 index 00000000..b9427aeb --- /dev/null +++ b/modules/nf-core/checkqc/main.nf @@ -0,0 +1,47 @@ +process CHECKQC { + tag "$meta.id" + label 'process_single' + + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6e/6ec3d6e7260c79ecd92ff53e66337a8f1db4ca8d0a3ba561c35f21fa9acdd6ba/data': + 'community.wave.seqera.io/library/sample-sheet_numpy_pandas_pip_pruned:0b9dc0869e46a949' }" + + input: + tuple val(meta), path(run_dir) + path(checkqc_config) + + output: + tuple val(meta), path("*checkqc_report.json"), emit: report + tuple val("${task.process}"), val('checkqc'), eval('checkqc --version | sed -e "s/checkqc, version //g"'), emit: versions_checkqc, topic: versions + + when: + task.ext.when == null || task.ext.when + + script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "CheckQC module does not support Conda yet. Please use Docker / Singularity / Podman instead." + } + + def args = task.ext.args ?: '' + def config = checkqc_config ? "--config $checkqc_config" : '' + + """ + checkqc \ + $args \ + $config \ + --json \ + $run_dir > checkqc_report.json || true + + # Check if the output JSON file is empty + if [[ ! -s checkqc_report.json ]] ; then + echo "Error: Empty JSON files. Most likely due to missing files in run directory. See .command.log file for errors." + exit 1 + fi + """ + + stub: + """ + touch checkqc_report.json + """ +} diff --git a/modules/nf-core/checkqc/meta.yml b/modules/nf-core/checkqc/meta.yml new file mode 100644 index 00000000..d979c0d1 --- /dev/null +++ b/modules/nf-core/checkqc/meta.yml @@ -0,0 +1,72 @@ +name: "checkqc" +description: A simple program to parse Illumina NGS data and check it for + quality criteria +keywords: + - QC + - Illumina + - genomics +tools: + - "checkqc": + description: "A simple program to parse Illumina NGS data and check it for quality + criteria." + homepage: "https://github.com/Molmed/checkQC" + documentation: "http://checkqc.readthedocs.io/en/latest/" + doi: "10.21105/joss.00556" + licence: + - "GPL v3" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - run_dir: + type: file + description: | + Illumina sequencing run directory + Can be directory or a compressed tar (tar.gz) of the directory + ontologies: [] + - checkqc_config: + type: file + description: CheckQC configuration file + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 +output: + report: + - - meta: + type: file + description: CheckQC report in json format + pattern: "*checkqc_report.json" + ontologies: + - edam: http://edamontology.org/format_3464 + - "*checkqc_report.json": + type: file + description: CheckQC report in json format + pattern: "*checkqc_report.json" + ontologies: + - edam: http://edamontology.org/format_3464 + versions_checkqc: + - - ${task.process}: + type: string + description: The name of the process + - checkqc: + type: string + description: The name of the tool + - 'checkqc --version | sed -e "s/checkqc, version //g"': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - checkqc: + type: string + description: The name of the tool + - 'checkqc --version | sed -e "s/checkqc, version //g"': + type: eval + description: The expression to obtain the version of the tool +authors: + - "@matrulda" diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf index fa5be702..dfabfe99 100644 --- a/workflows/seqinspector.nf +++ b/workflows/seqinspector.nf @@ -14,6 +14,7 @@ include { RUNDIRPARSER } from '../modules/local/rundirparser' include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index' include { SEQFU_STATS } from '../modules/nf-core/seqfu/stats' include { SEQTK_SAMPLE } from '../modules/nf-core/seqtk/sample' +include { CHECKQC } from '../modules/nf-core/checkqc/main' // subworkflow include { QC_BAM } from '../subworkflows/local/qc_bam' From 0229f18213ce32b48f72faf11677c8a1854362f7 Mon Sep 17 00:00:00 2001 From: matrulda Date: Wed, 11 Mar 2026 13:34:25 +0100 Subject: [PATCH 02/25] Add checkqc step to pipeline --- assets/checkqc_config.yaml | 792 ++++++++++++++++++ nextflow_schema.json | 4 +- .../main.nf | 2 + workflows/seqinspector.nf | 41 + 4 files changed, 837 insertions(+), 2 deletions(-) create mode 100644 assets/checkqc_config.yaml diff --git a/assets/checkqc_config.yaml b/assets/checkqc_config.yaml new file mode 100644 index 00000000..87dfb4f4 --- /dev/null +++ b/assets/checkqc_config.yaml @@ -0,0 +1,792 @@ +# For information about config usage, see http://checkqc.readthedocs.io/en/latest/#configuration-file + +# Use this section to provide configuration options to the parsers +parser_configurations: + StatsJsonParser: + # Path to where the bcl2fastq output (i.e. fastq files, etc) is located relative to + # the runfolder + bcl2fastq_output_path: Data/Intensities/BaseCalls + SamplesheetParser: + samplesheet_name: SampleSheet.csv + from_bclconvert: + reports_location: Reports + +default_view: illumina_data_view + +default_handlers: + - name: UndeterminedPercentageHandler + warning: unknown + error: 9 # <% Phix on lane> + < value as %> + - name: UnidentifiedIndexHandler + significance_threshold: 1 # % of reads in unidentified + # Indexes which are white-listed will only cause a warning even if they occur + # above the significance level. + # They will be matched like regular expressions, + # so e.g. NNN will match exactly three NNNs, while + # N{3,} will match three or more Ns. + white_listed_indexes: + - .*N.* + - G{6,} + +hiseq2500_rapidhighoutput_v4: + 51-71: + handlers: + - name: ClusterPFHandler + warning: 180 # Millons of clusters + error: unknown + - name: Q30Handler + warning: 85 # Give percentage for reads greater than Q30 + error: unknown # Give percentage for reads greater than Q30 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 135 # 75 % of threshold for clusters pass filter + view: illumina_data_view + 100-111: + handlers: + - name: ClusterPFHandler + warning: 180 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 135 + 121-131: + handlers: + - name: ClusterPFHandler + warning: 180 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 135 + +hiseq2500_rapidrun_v2: + 51: + handlers: + - name: ClusterPFHandler + warning: 110 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 82.5 + 101: + handlers: + - name: ClusterPFHandler + warning: 110 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 82.5 + 251: + handlers: + - name: ClusterPFHandler + warning: 110 + error: unknown + - name: Q30Handler + warning: unknown + error: 75 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: unknown + error: 5 + - name: ReadsPerSampleHandler + warning: unknown + error: 82.5 + +hiseqx_v2: + 151: + handlers: + - name: ClusterPFHandler + warning: 400 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 300 + +novaseq_SP: + 51: + handlers: + - name: ClusterPFHandler + warning: 325 + error: unknown + - name: Q30Handler + warning: 90 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 243.75 + 101: + handlers: + - name: ClusterPFHandler + warning: 325 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 243.75 + 151: + handlers: + - name: ClusterPFHandler + warning: 325 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 243.75 + 251: + handlers: + - name: ClusterPFHandler + warning: 325 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 243.75 + +novaseq_S1: + 51: + handlers: + - name: ClusterPFHandler + warning: 650 + error: unknown + - name: Q30Handler + warning: 90 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 487.5 + 101: + handlers: + - name: ClusterPFHandler + warning: 650 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 487.5 + 151: + handlers: + - name: ClusterPFHandler + warning: 650 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 487.5 + +novaseq_S2: + 51: + handlers: + - name: ClusterPFHandler + warning: 1650 + error: unknown + - name: Q30Handler + warning: 90 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 1237.5 + 101: + handlers: + - name: ClusterPFHandler + warning: 1650 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 1237.5 + 151: + handlers: + - name: ClusterPFHandler + warning: 1650 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 1237.5 + +novaseq_S4: + 101: + handlers: + - name: ClusterPFHandler + warning: 2000 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 1500 + 151: + handlers: + - name: ClusterPFHandler + warning: 2000 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 1500 + +novaseqxplus_1.5B: + 51: + handlers: + - name: ClusterPFHandler + warning: 800 + error: unknown + - name: Q30Handler + warning: 90 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 600 + 101: + handlers: + - name: ClusterPFHandler + warning: 800 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 600 + 151: + handlers: + - name: ClusterPFHandler + warning: 800 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 600 + +novaseqxplus_10B: + 51: + handlers: + - name: ClusterPFHandler + warning: 1250 + error: unknown + - name: Q30Handler + warning: 90 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 937.5 + 101: + handlers: + - name: ClusterPFHandler + warning: 1250 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 937.5 + 151: + handlers: + - name: ClusterPFHandler + warning: 1250 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 937.5 + +novaseqxplus_25B: + 151: + handlers: + - name: ClusterPFHandler + warning: 3250 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 2437.5 + +miseq_nano_v2: + 151: + handlers: + - name: ClusterPFHandler + warning: 1 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 7.5 + 251: + handlers: + - name: ClusterPFHandler + warning: 1 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 7.5 + +miseq_micro_v2: + 151: + handlers: + - name: ClusterPFHandler + warning: 4 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 7.5 + +miseq_v2: + 51: + handlers: + - name: ClusterPFHandler + warning: 10 + error: unknown + - name: Q30Handler + warning: 90 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 7.5 + 151: + handlers: + - name: ClusterPFHandler + warning: 10 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 7.5 + 251: + handlers: + - name: ClusterPFHandler + warning: 10 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 7.5 + +miseq_v3: + 76: + handlers: + - name: ClusterPFHandler + warning: 18 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 13.5 + 151: + handlers: + - name: ClusterPFHandler + warning: 18 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 13.5 + 301: + handlers: + - name: ClusterPFHandler + warning: 18 + error: unknown + - name: Q30Handler + warning: 70 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 13.5 + - name: UndeterminedPercentageHandler + warning: unknown + error: 14 # <% Phix on lane> + < value as %> + +iseq_v1: + 151: + handlers: + - name: ClusterPFHandler + warning: 4 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 3 + +nextseq500_high: + 76: + handlers: + - name: ClusterPFHandler + warning: 100 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 75 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 151: + handlers: + - name: ClusterPFHandler + warning: 100 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 75 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 301: + handlers: + - name: ClusterPFHandler + warning: 60 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 15 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + +nextseq500_mid: + 76: + handlers: + - name: ClusterPFHandler + warning: 32 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 24 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 151: + handlers: + - name: ClusterPFHandler + warning: 32 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 24 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 301: + handlers: + - name: ClusterPFHandler + warning: 32 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 24 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + +nextseq550_high: + 76: + handlers: + - name: ClusterPFHandler + warning: 100 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 75 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 151: + handlers: + - name: ClusterPFHandler + warning: 100 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 75 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 301: + handlers: + - name: ClusterPFHandler + warning: 100 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 75 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + +nextseq550_mid: + 76: + handlers: + - name: ClusterPFHandler + warning: 32 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 24 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 151: + handlers: + - name: ClusterPFHandler + warning: 32 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 24 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 301: + handlers: + - name: ClusterPFHandler + warning: 32 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 24 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + diff --git a/nextflow_schema.json b/nextflow_schema.json index b53e40fe..7210c451 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -51,7 +51,7 @@ "tools": { "type": "string", "description": "Comma-separated string of tools to run", - "pattern": "^((fastqc|fastqscreen|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats)?,?)*(? + with_rundir: meta.rundir.size() > 0 + without_rundir: true + } + + // Log warnings for samples without rundir + ch_rundir_branch.without_rundir.subscribe { meta, _reads -> + log.warn("Sample '${meta.id}' does not have a rundir specified") + } + + // From samplesheet channel serving (sampleMetaObj, sampleReadsPath) tuples: + // --> Create new rundir channel serving (rundirMetaObj, rundirPath) tuples + ch_rundir = ch_rundir_branch.with_rundir + .map { meta, _reads -> [meta.rundir, meta] } + .groupTuple() + .map { rundir, metas -> + // Collect all unique tags into a list + def all_tags = metas.collect { meta -> meta.tags }.flatten().unique() + // Create a new meta object whose attributes are... + // 1. tags: The list of merged tags, used for grouping MultiQC reports + // 2. dirname: The simple name of the rundir, used for setting unique output names in publishDir + def dir_meta = [tags: all_tags, dirname: rundir.simpleName] + // Return the new structure, to... + // 1. Feed into rundir specific processes + // 2. Mix with the ch_multiqc_files channel downstream + [dir_meta, rundir] + } + + ch_rundir.ifEmpty { log.warn("No samples with rundir found, skipping CHECKQC") } + + CHECKQC(ch_rundir, "assets/checkqc_config.yaml") + + ch_multiqc_files = ch_multiqc_files.mix(CHECKQC.out.report) + } + // // MODULE: Run Seqtk sample to perform subsampling From 09db116c86ed5b86fbdfe09225d06183c44ac349 Mon Sep 17 00:00:00 2001 From: Karthik Nair Date: Wed, 11 Mar 2026 14:23:08 +0100 Subject: [PATCH 03/25] Add CheckQC test --- tests/CheckQC.nf.test | 23 +++++++++++++++++++++++ workflows/seqinspector.nf | 2 +- 2 files changed, 24 insertions(+), 1 deletion(-) create mode 100644 tests/CheckQC.nf.test diff --git a/tests/CheckQC.nf.test b/tests/CheckQC.nf.test new file mode 100644 index 00000000..0e636999 --- /dev/null +++ b/tests/CheckQC.nf.test @@ -0,0 +1,23 @@ +def pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + + def test_scenario = [ + [ + name: "NovaSeq6000 data test", + params: [ + tools: 'checkqc', + ], + snapshot: 'stderr,stdout' + ], + ] + + // Generate tests for each scenario + test_scenario.each { scenario -> + test(scenario.name, UTILS.getTest(scenario)) + } +} diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf index 94cf6f04..a048dd97 100644 --- a/workflows/seqinspector.nf +++ b/workflows/seqinspector.nf @@ -132,7 +132,7 @@ workflow SEQINSPECTOR { ch_rundir.ifEmpty { log.warn("No samples with rundir found, skipping CHECKQC") } - CHECKQC(ch_rundir, "assets/checkqc_config.yaml") + CHECKQC(ch_rundir, "${projectDir}/assets/checkqc_config.yaml") ch_multiqc_files = ch_multiqc_files.mix(CHECKQC.out.report) } From 93f0a0771f93b09292d2b2669779330623a7794e Mon Sep 17 00:00:00 2001 From: matrulda Date: Thu, 12 Mar 2026 10:11:37 +0100 Subject: [PATCH 04/25] remove checkqc config and send empty array for config --- assets/checkqc_config.yaml | 792 ------------------------------------- workflows/seqinspector.nf | 2 +- 2 files changed, 1 insertion(+), 793 deletions(-) delete mode 100644 assets/checkqc_config.yaml diff --git a/assets/checkqc_config.yaml b/assets/checkqc_config.yaml deleted file mode 100644 index 87dfb4f4..00000000 --- a/assets/checkqc_config.yaml +++ /dev/null @@ -1,792 +0,0 @@ -# For information about config usage, see http://checkqc.readthedocs.io/en/latest/#configuration-file - -# Use this section to provide configuration options to the parsers -parser_configurations: - StatsJsonParser: - # Path to where the bcl2fastq output (i.e. fastq files, etc) is located relative to - # the runfolder - bcl2fastq_output_path: Data/Intensities/BaseCalls - SamplesheetParser: - samplesheet_name: SampleSheet.csv - from_bclconvert: - reports_location: Reports - -default_view: illumina_data_view - -default_handlers: - - name: UndeterminedPercentageHandler - warning: unknown - error: 9 # <% Phix on lane> + < value as %> - - name: UnidentifiedIndexHandler - significance_threshold: 1 # % of reads in unidentified - # Indexes which are white-listed will only cause a warning even if they occur - # above the significance level. - # They will be matched like regular expressions, - # so e.g. NNN will match exactly three NNNs, while - # N{3,} will match three or more Ns. - white_listed_indexes: - - .*N.* - - G{6,} - -hiseq2500_rapidhighoutput_v4: - 51-71: - handlers: - - name: ClusterPFHandler - warning: 180 # Millons of clusters - error: unknown - - name: Q30Handler - warning: 85 # Give percentage for reads greater than Q30 - error: unknown # Give percentage for reads greater than Q30 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 135 # 75 % of threshold for clusters pass filter - view: illumina_data_view - 100-111: - handlers: - - name: ClusterPFHandler - warning: 180 - error: unknown - - name: Q30Handler - warning: 80 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 2 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 135 - 121-131: - handlers: - - name: ClusterPFHandler - warning: 180 - error: unknown - - name: Q30Handler - warning: 80 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 2 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 135 - -hiseq2500_rapidrun_v2: - 51: - handlers: - - name: ClusterPFHandler - warning: 110 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 82.5 - 101: - handlers: - - name: ClusterPFHandler - warning: 110 - error: unknown - - name: Q30Handler - warning: 80 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 2 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 82.5 - 251: - handlers: - - name: ClusterPFHandler - warning: 110 - error: unknown - - name: Q30Handler - warning: unknown - error: 75 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: unknown - error: 5 - - name: ReadsPerSampleHandler - warning: unknown - error: 82.5 - -hiseqx_v2: - 151: - handlers: - - name: ClusterPFHandler - warning: 400 - error: unknown - - name: Q30Handler - warning: 75 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 300 - -novaseq_SP: - 51: - handlers: - - name: ClusterPFHandler - warning: 325 - error: unknown - - name: Q30Handler - warning: 90 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 243.75 - 101: - handlers: - - name: ClusterPFHandler - warning: 325 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 2 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 243.75 - 151: - handlers: - - name: ClusterPFHandler - warning: 325 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 243.75 - 251: - handlers: - - name: ClusterPFHandler - warning: 325 - error: unknown - - name: Q30Handler - warning: 75 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 243.75 - -novaseq_S1: - 51: - handlers: - - name: ClusterPFHandler - warning: 650 - error: unknown - - name: Q30Handler - warning: 90 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 487.5 - 101: - handlers: - - name: ClusterPFHandler - warning: 650 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 2 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 487.5 - 151: - handlers: - - name: ClusterPFHandler - warning: 650 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 487.5 - -novaseq_S2: - 51: - handlers: - - name: ClusterPFHandler - warning: 1650 - error: unknown - - name: Q30Handler - warning: 90 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 1237.5 - 101: - handlers: - - name: ClusterPFHandler - warning: 1650 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 2 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 1237.5 - 151: - handlers: - - name: ClusterPFHandler - warning: 1650 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 1237.5 - -novaseq_S4: - 101: - handlers: - - name: ClusterPFHandler - warning: 2000 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 2 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 1500 - 151: - handlers: - - name: ClusterPFHandler - warning: 2000 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 1500 - -novaseqxplus_1.5B: - 51: - handlers: - - name: ClusterPFHandler - warning: 800 - error: unknown - - name: Q30Handler - warning: 90 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 600 - 101: - handlers: - - name: ClusterPFHandler - warning: 800 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 2 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 600 - 151: - handlers: - - name: ClusterPFHandler - warning: 800 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 600 - -novaseqxplus_10B: - 51: - handlers: - - name: ClusterPFHandler - warning: 1250 - error: unknown - - name: Q30Handler - warning: 90 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 937.5 - 101: - handlers: - - name: ClusterPFHandler - warning: 1250 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 2 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 937.5 - 151: - handlers: - - name: ClusterPFHandler - warning: 1250 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 937.5 - -novaseqxplus_25B: - 151: - handlers: - - name: ClusterPFHandler - warning: 3250 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 2437.5 - -miseq_nano_v2: - 151: - handlers: - - name: ClusterPFHandler - warning: 1 - error: unknown - - name: Q30Handler - warning: 80 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 2 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 7.5 - 251: - handlers: - - name: ClusterPFHandler - warning: 1 - error: unknown - - name: Q30Handler - warning: 75 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 7.5 - -miseq_micro_v2: - 151: - handlers: - - name: ClusterPFHandler - warning: 4 - error: unknown - - name: Q30Handler - warning: 80 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 2 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 7.5 - -miseq_v2: - 51: - handlers: - - name: ClusterPFHandler - warning: 10 - error: unknown - - name: Q30Handler - warning: 90 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 7.5 - 151: - handlers: - - name: ClusterPFHandler - warning: 10 - error: unknown - - name: Q30Handler - warning: 80 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 2 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 7.5 - 251: - handlers: - - name: ClusterPFHandler - warning: 10 - error: unknown - - name: Q30Handler - warning: 75 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 7.5 - -miseq_v3: - 76: - handlers: - - name: ClusterPFHandler - warning: 18 - error: unknown - - name: Q30Handler - warning: 85 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 13.5 - 151: - handlers: - - name: ClusterPFHandler - warning: 18 - error: unknown - - name: Q30Handler - warning: 80 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 2 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 13.5 - 301: - handlers: - - name: ClusterPFHandler - warning: 18 - error: unknown - - name: Q30Handler - warning: 70 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 13.5 - - name: UndeterminedPercentageHandler - warning: unknown - error: 14 # <% Phix on lane> + < value as %> - -iseq_v1: - 151: - handlers: - - name: ClusterPFHandler - warning: 4 - error: unknown - - name: Q30Handler - warning: 80 - error: unknown - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 5 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 3 - -nextseq500_high: - 76: - handlers: - - name: ClusterPFHandler - warning: 100 - error: unknown - - name: Q30Handler - warning: 80 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 75 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - 151: - handlers: - - name: ClusterPFHandler - warning: 100 - error: unknown - - name: Q30Handler - warning: 75 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 75 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - 301: - handlers: - - name: ClusterPFHandler - warning: 60 - error: unknown - - name: Q30Handler - warning: 75 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 15 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - -nextseq500_mid: - 76: - handlers: - - name: ClusterPFHandler - warning: 32 - error: unknown - - name: Q30Handler - warning: 80 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 24 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - 151: - handlers: - - name: ClusterPFHandler - warning: 32 - error: unknown - - name: Q30Handler - warning: 75 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 24 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - 301: - handlers: - - name: ClusterPFHandler - warning: 32 - error: unknown - - name: Q30Handler - warning: 75 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 24 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - -nextseq550_high: - 76: - handlers: - - name: ClusterPFHandler - warning: 100 - error: unknown - - name: Q30Handler - warning: 80 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 75 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - 151: - handlers: - - name: ClusterPFHandler - warning: 100 - error: unknown - - name: Q30Handler - warning: 75 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 75 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - 301: - handlers: - - name: ClusterPFHandler - warning: 100 - error: unknown - - name: Q30Handler - warning: 75 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 75 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - -nextseq550_mid: - 76: - handlers: - - name: ClusterPFHandler - warning: 32 - error: unknown - - name: Q30Handler - warning: 80 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 24 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - 151: - handlers: - - name: ClusterPFHandler - warning: 32 - error: unknown - - name: Q30Handler - warning: 75 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 24 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - 301: - handlers: - - name: ClusterPFHandler - warning: 32 - error: unknown - - name: Q30Handler - warning: 75 - error: unknown - - name: ReadsPerSampleHandler - warning: unknown - error: 24 - - name: ErrorRateHandler - allow_missing_error_rate: False - warning: 1.5 - error: unknown - diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf index a048dd97..8b1b45e4 100644 --- a/workflows/seqinspector.nf +++ b/workflows/seqinspector.nf @@ -132,7 +132,7 @@ workflow SEQINSPECTOR { ch_rundir.ifEmpty { log.warn("No samples with rundir found, skipping CHECKQC") } - CHECKQC(ch_rundir, "${projectDir}/assets/checkqc_config.yaml") + CHECKQC(ch_rundir, []) ch_multiqc_files = ch_multiqc_files.mix(CHECKQC.out.report) } From 46cc60505579998c1c3c3d172738f29da2e8fdcd Mon Sep 17 00:00:00 2001 From: matrulda Date: Thu, 12 Mar 2026 10:13:53 +0100 Subject: [PATCH 05/25] Update checkqc module --- modules.json | 2 +- modules/nf-core/checkqc/main.nf | 31 ++++++++++++++++++++++++++++++- 2 files changed, 31 insertions(+), 2 deletions(-) diff --git a/modules.json b/modules.json index 0160af91..3737869e 100644 --- a/modules.json +++ b/modules.json @@ -17,7 +17,7 @@ }, "checkqc": { "branch": "master", - "git_sha": "b06df7c554e1eb06c35ad96c506b49444e0a1729", + "git_sha": "389ed64090aa4594276fb3d53923432c7728c5b4", "installed_by": ["modules"] }, "fastqc": { diff --git a/modules/nf-core/checkqc/main.nf b/modules/nf-core/checkqc/main.nf index b9427aeb..fc39ee0d 100644 --- a/modules/nf-core/checkqc/main.nf +++ b/modules/nf-core/checkqc/main.nf @@ -24,14 +24,43 @@ process CHECKQC { } def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' def config = checkqc_config ? "--config $checkqc_config" : '' + def input_tar = run_dir.toString().endsWith(".tar.gz") ? true : false + def input_dir = input_tar ? run_dir.toString() - '.tar.gz' : run_dir """ + if [ ! -d ${input_dir} ]; then + mkdir -p ${input_dir} + fi + + if ${input_tar}; then + ## Ensures --strip-components only applied when top level of tar contents is a directory + ## If just files or multiple directories, place all in ${input_dir} + + if [[ \$(tar -taf ${run_dir} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then + tar \\ + -C ${input_dir} --strip-components 1 \\ + -xavf \\ + ${args2} \\ + ${run_dir} \\ + ${args3} + else + tar \\ + -C ${input_dir} \\ + -xavf \\ + ${args2} \\ + ${run_dir} \\ + ${args3} + fi + fi + checkqc \ $args \ $config \ --json \ - $run_dir > checkqc_report.json || true + $input_dir > checkqc_report.json || true # Check if the output JSON file is empty if [[ ! -s checkqc_report.json ]] ; then From 1f2367d2c27438389e19124d8918170fdeaee30e Mon Sep 17 00:00:00 2001 From: Karthik Nair Date: Thu, 12 Mar 2026 11:13:07 +0100 Subject: [PATCH 06/25] Add checkqc args to config --- tests/nextflow.config | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/tests/nextflow.config b/tests/nextflow.config index 8d6d7704..059ae31f 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -6,3 +6,10 @@ // fixes S3 access issues on self-hosted runners aws.client.anonymous = true + + +process { + withName: CHECKQC { + ext.args = '--config checkqc_config.yml' + } +} From 6ad82d7834a522e4c0e3cbf371a01b1383427d7b Mon Sep 17 00:00:00 2001 From: matrulda Date: Thu, 12 Mar 2026 13:48:30 +0100 Subject: [PATCH 07/25] Update ext.args from checkqc --- tests/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/nextflow.config b/tests/nextflow.config index 059ae31f..36b153cd 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -10,6 +10,6 @@ aws.client.anonymous = true process { withName: CHECKQC { - ext.args = '--config checkqc_config.yml' + ext.args = '--config */checkqc_config.yml --use-closest-read-length' } } From d936ee668942331ee16fde59340fb5171bbc08bf Mon Sep 17 00:00:00 2001 From: matrulda Date: Thu, 12 Mar 2026 16:50:52 +0100 Subject: [PATCH 08/25] Do not specify checkqc config and add checkqc to NovaSeq 6000 test --- tests/NovaSeq6000.nf.test | 4 +++- tests/nextflow.config | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/tests/NovaSeq6000.nf.test b/tests/NovaSeq6000.nf.test index 1c868f26..9acae874 100644 --- a/tests/NovaSeq6000.nf.test +++ b/tests/NovaSeq6000.nf.test @@ -9,7 +9,9 @@ nextflow_pipeline { def test_scenario = [ [ name: "NovaSeq6000 data test", - params: [], + params: [ + tools: 'checkqc', + ], snapshot: 'stderr,stdout' ], [ diff --git a/tests/nextflow.config b/tests/nextflow.config index 36b153cd..1cbf2ff9 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -10,6 +10,6 @@ aws.client.anonymous = true process { withName: CHECKQC { - ext.args = '--config */checkqc_config.yml --use-closest-read-length' + ext.args = '--use-closest-read-length' } } From df711a4cb8cdc72a00fd1142cb5aa0b3ece75443 Mon Sep 17 00:00:00 2001 From: matrulda Date: Thu, 12 Mar 2026 17:00:18 +0100 Subject: [PATCH 09/25] Update NovaSeq6000 snapshot --- tests/NovaSeq6000.nf.test.snap | 76 ++++++++++++++++++++++++++++++---- 1 file changed, 67 insertions(+), 9 deletions(-) diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap index a373a30c..f2824bad 100644 --- a/tests/NovaSeq6000.nf.test.snap +++ b/tests/NovaSeq6000.nf.test.snap @@ -1,7 +1,7 @@ { "NovaSeq6000 data test": { "content": [ - 38, + 39, { "BWAMEM2_INDEX": { "bwamem2": "2.2.1" @@ -10,6 +10,9 @@ "bwamem2": "2.2.1", "samtools": "1.22.1" }, + "CHECKQC": { + "checkqc": "4.1.0" + }, "FASTQC": { "fastqc": "0.12.1" }, @@ -52,6 +55,8 @@ "bwamem2_mem/Undetermined_05.bam.bai", "bwamem2_mem/sampletest_04.bam", "bwamem2_mem/sampletest_04.bam.bai", + "checkqc", + "checkqc/checkqc_report.json", "fastqc", "fastqc/Sample1_01_fastqc.html", "fastqc/Sample1_01_fastqc.zip", @@ -82,6 +87,7 @@ "multiqc", "multiqc/global_report", "multiqc/global_report/multiqc_data", + "multiqc/global_report/multiqc_data/checkqc_reads-per-sample-plot.txt", "multiqc/global_report/multiqc_data/fastq_screen_plot.txt", "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt", "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt", @@ -97,6 +103,7 @@ "multiqc/global_report/multiqc_data/llms-full.txt", "multiqc/global_report/multiqc_data/multiqc.log", "multiqc/global_report/multiqc_data/multiqc.parquet", + "multiqc/global_report/multiqc_data/multiqc_checkqc.txt", "multiqc/global_report/multiqc_data/multiqc_citations.txt", "multiqc/global_report/multiqc_data/multiqc_data.json", "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt", @@ -125,6 +132,8 @@ "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_plots", "multiqc/global_report/multiqc_plots/pdf", + "multiqc/global_report/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", @@ -152,6 +161,8 @@ "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf", "multiqc/global_report/multiqc_plots/png", + "multiqc/global_report/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", + "multiqc/global_report/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png", "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png", @@ -179,6 +190,8 @@ "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png", "multiqc/global_report/multiqc_plots/svg", + "multiqc/global_report/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg", "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg", @@ -209,6 +222,7 @@ "multiqc/group_reports", "multiqc/group_reports/group1", "multiqc/group_reports/group1/multiqc_data", + "multiqc/group_reports/group1/multiqc_data/checkqc_reads-per-sample-plot.txt", "multiqc/group_reports/group1/multiqc_data/fastq_screen_plot.txt", "multiqc/group_reports/group1/multiqc_data/fastqc-status-check-heatmap.txt", "multiqc/group_reports/group1/multiqc_data/fastqc_overrepresented_sequences_plot.txt", @@ -224,6 +238,7 @@ "multiqc/group_reports/group1/multiqc_data/llms-full.txt", "multiqc/group_reports/group1/multiqc_data/multiqc.log", "multiqc/group_reports/group1/multiqc_data/multiqc.parquet", + "multiqc/group_reports/group1/multiqc_data/multiqc_checkqc.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_data.json", "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt", @@ -252,6 +267,8 @@ "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/group1/multiqc_plots", "multiqc/group_reports/group1/multiqc_plots/pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", @@ -279,6 +296,8 @@ "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu_mqc.pdf", "multiqc/group_reports/group1/multiqc_plots/png", + "multiqc/group_reports/group1/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", + "multiqc/group_reports/group1/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png", "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png", "multiqc/group_reports/group1/multiqc_plots/png/fastqc-status-check-heatmap.png", @@ -306,6 +325,8 @@ "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/group1/multiqc_plots/png/seqfu_mqc.png", "multiqc/group_reports/group1/multiqc_plots/svg", + "multiqc/group_reports/group1/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastqc-status-check-heatmap.svg", @@ -335,6 +356,7 @@ "multiqc/group_reports/group1/multiqc_report.html", "multiqc/group_reports/group2", "multiqc/group_reports/group2/multiqc_data", + "multiqc/group_reports/group2/multiqc_data/checkqc_reads-per-sample-plot.txt", "multiqc/group_reports/group2/multiqc_data/fastq_screen_plot.txt", "multiqc/group_reports/group2/multiqc_data/fastqc-status-check-heatmap.txt", "multiqc/group_reports/group2/multiqc_data/fastqc_overrepresented_sequences_plot.txt", @@ -350,6 +372,7 @@ "multiqc/group_reports/group2/multiqc_data/llms-full.txt", "multiqc/group_reports/group2/multiqc_data/multiqc.log", "multiqc/group_reports/group2/multiqc_data/multiqc.parquet", + "multiqc/group_reports/group2/multiqc_data/multiqc_checkqc.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_data.json", "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt", @@ -378,6 +401,8 @@ "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/group2/multiqc_plots", "multiqc/group_reports/group2/multiqc_plots/pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-pct.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", @@ -405,6 +430,8 @@ "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu_mqc.pdf", "multiqc/group_reports/group2/multiqc_plots/png", + "multiqc/group_reports/group2/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", + "multiqc/group_reports/group2/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png", "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png", "multiqc/group_reports/group2/multiqc_plots/png/fastqc-status-check-heatmap.png", @@ -432,6 +459,8 @@ "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/group2/multiqc_plots/png/seqfu_mqc.png", "multiqc/group_reports/group2/multiqc_plots/svg", + "multiqc/group_reports/group2/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastqc-status-check-heatmap.svg", @@ -461,6 +490,7 @@ "multiqc/group_reports/group2/multiqc_report.html", "multiqc/group_reports/lane1", "multiqc/group_reports/lane1/multiqc_data", + "multiqc/group_reports/lane1/multiqc_data/checkqc_reads-per-sample-plot.txt", "multiqc/group_reports/lane1/multiqc_data/fastq_screen_plot.txt", "multiqc/group_reports/lane1/multiqc_data/fastqc-status-check-heatmap.txt", "multiqc/group_reports/lane1/multiqc_data/fastqc_overrepresented_sequences_plot.txt", @@ -476,6 +506,7 @@ "multiqc/group_reports/lane1/multiqc_data/llms-full.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc.log", "multiqc/group_reports/lane1/multiqc_data/multiqc.parquet", + "multiqc/group_reports/lane1/multiqc_data/multiqc_checkqc.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_data.json", "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt", @@ -504,6 +535,8 @@ "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/lane1/multiqc_plots", "multiqc/group_reports/lane1/multiqc_plots/pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", @@ -531,6 +564,8 @@ "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu_mqc.pdf", "multiqc/group_reports/lane1/multiqc_plots/png", + "multiqc/group_reports/lane1/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", + "multiqc/group_reports/lane1/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastqc-status-check-heatmap.png", @@ -558,6 +593,8 @@ "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/lane1/multiqc_plots/png/seqfu_mqc.png", "multiqc/group_reports/lane1/multiqc_plots/svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc-status-check-heatmap.svg", @@ -587,6 +624,7 @@ "multiqc/group_reports/lane1/multiqc_report.html", "multiqc/group_reports/test", "multiqc/group_reports/test/multiqc_data", + "multiqc/group_reports/test/multiqc_data/checkqc_reads-per-sample-plot.txt", "multiqc/group_reports/test/multiqc_data/fastq_screen_plot.txt", "multiqc/group_reports/test/multiqc_data/fastqc-status-check-heatmap.txt", "multiqc/group_reports/test/multiqc_data/fastqc_overrepresented_sequences_plot.txt", @@ -602,6 +640,7 @@ "multiqc/group_reports/test/multiqc_data/llms-full.txt", "multiqc/group_reports/test/multiqc_data/multiqc.log", "multiqc/group_reports/test/multiqc_data/multiqc.parquet", + "multiqc/group_reports/test/multiqc_data/multiqc_checkqc.txt", "multiqc/group_reports/test/multiqc_data/multiqc_citations.txt", "multiqc/group_reports/test/multiqc_data/multiqc_data.json", "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt", @@ -630,6 +669,8 @@ "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/test/multiqc_plots", "multiqc/group_reports/test/multiqc_plots/pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", @@ -657,6 +698,8 @@ "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/seqfu_mqc.pdf", "multiqc/group_reports/test/multiqc_plots/png", + "multiqc/group_reports/test/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", + "multiqc/group_reports/test/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png", "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png", "multiqc/group_reports/test/multiqc_plots/png/fastqc-status-check-heatmap.png", @@ -684,6 +727,8 @@ "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/test/multiqc_plots/png/seqfu_mqc.png", "multiqc/group_reports/test/multiqc_plots/svg", + "multiqc/group_reports/test/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", + "multiqc/group_reports/test/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastqc-status-check-heatmap.svg", @@ -776,6 +821,7 @@ "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b", "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e", "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc", + "checkqc_report.json:md5,8245b6a8b8e0e2d247cb7a151d53612f", "Sample1_01_screen.png:md5,562256290643b51e4374c2225a15f463", "Sample1_01_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28", "Sample23_03_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab", @@ -786,6 +832,7 @@ "Undetermined_05_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28", "sampletest_04_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e", "sampletest_04_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28", + "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", "fastq_screen_plot.txt:md5,990122d48fa4c1a170107a1ba034e4cf", "fastqc-status-check-heatmap.txt:md5,7a64380ec42aac56949a2d9a4176d4d9", "fastqc_overrepresented_sequences_plot.txt:md5,c7908980f1dba22b45cf6de14a66a686", @@ -797,7 +844,8 @@ "fastqc_sequence_counts_plot.txt:md5,d8ab86dbfce0c740f4a66a080803a0b9", "fastqc_sequence_duplication_levels_plot.txt:md5,f86012b3074d697c9a2b3bd67a074288", "fastqc_sequence_length_distribution_plot.txt:md5,9d4fd245e8e1d5baa473a8bdffcd3e38", - "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", + "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", + "multiqc_citations.txt:md5,50a90ac0283d35a2e474089c1027baef", "multiqc_fastq_screen.txt:md5,62240561100f78af37e7e2438cb58f90", "multiqc_fastqc.txt:md5,23b698f1e957a26f49a9ad9bbdece908", "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7", @@ -819,6 +867,7 @@ "picard_base_distribution_by_cycle__Undetermined.txt:md5,8aafe701b59b4e70ccec86748c7d6eb3", "picard_quality_by_cycle.txt:md5,366ee22c93a11c1335f867020bb03da5", "picard_quality_score_distribution.txt:md5,17d6f490cb59e16a7ed4b04ffaa1a100", + "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", "fastq_screen_plot.txt:md5,db7c9231e756a6e5999399a7385e4687", "fastqc-status-check-heatmap.txt:md5,fc37eaf184877ac80b92001a7bf2fa81", "fastqc_overrepresented_sequences_plot.txt:md5,0693849fc324ddf580e2c5a4d910bb4f", @@ -830,7 +879,8 @@ "fastqc_sequence_counts_plot.txt:md5,42b26ad3758717659763c81852c4f197", "fastqc_sequence_duplication_levels_plot.txt:md5,818f13a5372bad79e54cd984758096c5", "fastqc_sequence_length_distribution_plot.txt:md5,98316a2607a889ae1e7e79a4f64cc740", - "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", + "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", + "multiqc_citations.txt:md5,50a90ac0283d35a2e474089c1027baef", "multiqc_fastq_screen.txt:md5,024e1e7f9db3b0906c7aa0904229e176", "multiqc_fastqc.txt:md5,3407d8f06117a65efce4c70f19e91dd1", "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7", @@ -852,6 +902,7 @@ "picard_base_distribution_by_cycle__Undetermined.txt:md5,0ed7f750b500e7c5387ea5309e1ef467", "picard_quality_by_cycle.txt:md5,fe4e6ab1c849a4f833eae9a8554ea432", "picard_quality_score_distribution.txt:md5,c0864f8a1269d8ffd7a51abb6bd3ca2e", + "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", "fastq_screen_plot.txt:md5,4def6c6a888afe487ab6ebef3ba8a133", "fastqc-status-check-heatmap.txt:md5,61857d2c45cf0c080348047aa34e7525", "fastqc_overrepresented_sequences_plot.txt:md5,7949c64cc6cef77f29349a188fc09656", @@ -863,7 +914,8 @@ "fastqc_sequence_counts_plot.txt:md5,f4341795bdeba588248a74a095a97f8d", "fastqc_sequence_duplication_levels_plot.txt:md5,8fc995cb2192a2926eee242681bc3af6", "fastqc_sequence_length_distribution_plot.txt:md5,4513e22583677a4d6167b9094242eb0b", - "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", + "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", + "multiqc_citations.txt:md5,50a90ac0283d35a2e474089c1027baef", "multiqc_fastq_screen.txt:md5,fd3074930c72b666f201ae71fa27744b", "multiqc_fastqc.txt:md5,98111f17d1899cad6379e4e56ed11c53", "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7", @@ -885,6 +937,7 @@ "picard_base_distribution_by_cycle__Undetermined.txt:md5,0f2fd628631d42ed5e6a1db22578daaa", "picard_quality_by_cycle.txt:md5,3c34ae2bd2442a816577b1a794add2d6", "picard_quality_score_distribution.txt:md5,0d58c59eac2952e6f71cefc35d4c4477", + "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", "fastq_screen_plot.txt:md5,5abb5b9ed2c976f0ad83216ca3186201", "fastqc-status-check-heatmap.txt:md5,323d6082b73ddb6ee33385f5ea4301c1", "fastqc_overrepresented_sequences_plot.txt:md5,4e71d8913d40eb06db0f18d74ce6898f", @@ -896,7 +949,8 @@ "fastqc_sequence_counts_plot.txt:md5,36c68522023b8d536c9362403bf03c48", "fastqc_sequence_duplication_levels_plot.txt:md5,9ff0df466790d971b3c7ef838efc0f4f", "fastqc_sequence_length_distribution_plot.txt:md5,9fda632b92e3453f11cd0226484fce8e", - "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", + "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", + "multiqc_citations.txt:md5,50a90ac0283d35a2e474089c1027baef", "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272", "multiqc_fastqc.txt:md5,396b4cc0466a6642ec8b954237c42263", "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7", @@ -918,6 +972,7 @@ "picard_base_distribution_by_cycle__Undetermined.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6", "picard_quality_by_cycle.txt:md5,7cb705007bc97da8c0da7d93201e6975", "picard_quality_score_distribution.txt:md5,47d684abae0a8f4f09df43e91d54fb9a", + "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", "fastq_screen_plot.txt:md5,82ceb9f2109f865d6d1b943441c09550", "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1", "fastqc_overrepresented_sequences_plot.txt:md5,8e83abdbe7362e64d63339ee31ab3361", @@ -929,7 +984,8 @@ "fastqc_sequence_counts_plot.txt:md5,6e5804f553f656cffb02f927015d1026", "fastqc_sequence_duplication_levels_plot.txt:md5,fbe41935ea2e2faf7104393b476e5ac5", "fastqc_sequence_length_distribution_plot.txt:md5,e77dc4ab73252c2e09c7452c3b8e8ab3", - "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", + "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", + "multiqc_citations.txt:md5,50a90ac0283d35a2e474089c1027baef", "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2", "multiqc_fastqc.txt:md5,95c8ffb23baafec625aeb600047515ae", "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7", @@ -985,6 +1041,7 @@ "Input/output options", " input : https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/NovaSeq6000/samplesheet.csv", " outdir : [PATH]/tests/[NFT_HASH]/output", + " tools : checkqc", " tools_setup : default", "Reference genome options", " genome : R64-1-1", @@ -1011,7 +1068,7 @@ "* Software dependencies", " https://github.com/nf-core/seqinspector/blob/master/CITATIONS.md", "Extra informations", - " Tools selected to be run : fastqc,fastqscreen,picard_collectmultiplemetrics,rundirparser,seqfu_stats", + " Tools selected to be run : checkqc,fastqc,fastqscreen,picard_collectmultiplemetrics,rundirparser,seqfu_stats", "------------------------------------------------------", "-[nf-core/seqinspector] Pipeline completed successfully-", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (Sample1_01)", @@ -1019,6 +1076,7 @@ "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (SampleA_02)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (Undetermined_05)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (sampletest_04)", + "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:CHECKQC (null)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQC (Sample1_01)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQC (Sample23_03)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQC (SampleA_02)", @@ -1050,10 +1108,10 @@ "[NXF_HASH] Submitted process > PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa)" ] ], - "timestamp": "2026-03-11T08:59:54.671845262", + "timestamp": "2026-03-12T16:53:51.022201822", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } }, "NovaSeq6000 data test sample size": { From 2cd42749f7fe3cf02289234f82110af8f7150c2d Mon Sep 17 00:00:00 2001 From: matrulda Date: Fri, 13 Mar 2026 10:26:51 +0100 Subject: [PATCH 10/25] Update snapshot to include CheckQC --- tests/NovaSeq6000.nf.test.snap | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap index 73810f0d..daa039e1 100644 --- a/tests/NovaSeq6000.nf.test.snap +++ b/tests/NovaSeq6000.nf.test.snap @@ -1,7 +1,7 @@ { "NovaSeq6000 data test": { "content": [ - 43, + 44, { "BWAMEM2_INDEX": { "bwamem2": "2.2.1" @@ -1050,6 +1050,7 @@ "Input/output options", " input : https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/NovaSeq6000/samplesheet.csv", " outdir : [PATH]/tests/[NFT_HASH]/output", + " tools : checkqc", " tools_bundle : default", "Reference genome options", " genome : R64-1-1", @@ -1076,7 +1077,7 @@ "* Software dependencies", " https://github.com/nf-core/seqinspector/blob/master/CITATIONS.md", "Extra informations", - " Tools selected to be run : fastqc,fastqscreen,fq_lint,picard_collectmultiplemetrics,rundirparser,seqfu_stats", + " Tools selected to be run : checkqc,fastqc,fastqscreen,fq_lint,picard_collectmultiplemetrics,rundirparser,seqfu_stats", "------------------------------------------------------", "-[nf-core/seqinspector] Pipeline completed successfully-", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (Sample1_01)", @@ -1121,7 +1122,7 @@ "[NXF_HASH] Submitted process > PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa)" ] ], - "timestamp": "2026-03-12T16:18:44.078233725", + "timestamp": "2026-03-13T10:18:02.426461184", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.2" From a3aedad72421ed2c511e17570ddfbee9f090dc00 Mon Sep 17 00:00:00 2001 From: matrulda Date: Fri, 13 Mar 2026 10:32:44 +0100 Subject: [PATCH 11/25] pipeline lint --- modules.json | 4 ++-- ro-crate-metadata.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules.json b/modules.json index ef271d51..6d42ae12 100644 --- a/modules.json +++ b/modules.json @@ -19,6 +19,7 @@ "branch": "master", "git_sha": "389ed64090aa4594276fb3d53923432c7728c5b4", "installed_by": ["modules"] + }, "fastp": { "branch": "master", "git_sha": "1fb5a73bce8e4ac7079b0a9461b23d11e877ad14", @@ -37,8 +38,7 @@ "fastqscreen/fastqscreen": { "branch": "master", "git_sha": "ab2e7b785ee4fa6d108472862edbf983cea7db49", - "installed_by": ["modules"], - "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff" + "installed_by": ["modules"] }, "fq/lint": { "branch": "master", diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 688ae4d9..a194c9ea 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "InProgress", "datePublished": "2026-03-12T11:24:47+00:00", - "description": "

\n \n \n \"nf-core/seqinspector\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.18757486-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.18757486)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that processes raw sequence data (FASTQ) to provide comprehensive quality control.\nIt can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants.\nThe pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.\nIf provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n### Compatibility between tools and data type\n\n\n\n| Tool Type | Tool Name | Tool Description | Compatibility with Data | Dependencies | Default tool |\n| ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | --------------------------------------------------------------------------------------- | ------------ |\n| `Subsampling` | [`Seqtk`](https://github.com/lh3/seqtk) | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic] | [N/A] | no |\n| `Lint FASTQs` | [`fq`](https://github.com/stjude-rust-labs/fq) | fq filters, generates, subsamples, and validates FASTQ files. | [RNA, DNA, synthetic] | [N/A] | yes |\n| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2) | Align reads to reference | [RNA, DNA] | [N/A] | yes |\n| `Indexing` | [`SAMtools`](http://github.com/samtools) | Index aligned BAM files, create FASTA index | [DNA] | [N/A] | yes |\n| `QC` | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | Read QC | [RNA, DNA] | [N/A] | yes |\n| `QC` | [`FASTQE`](https://fastqe.com/) | Read QC | [RNA, DNA] | [N/A] | yes |\n| `QC` | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) | Basic contamination detection | [RNA, DNA] | [N/A] | yes |\n| `QC` | [`SeqFu Stats`](https://github.com/telatin/seqfu2) | Sequence statistics | [RNA, DNA] | [N/A] | yes |\n| `QC` | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics | [RNA, DNA] | [Bwamem2, SAMtools, `--genome`] | yes |\n| `QC` | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data. | [RNA, DNA] | [Bwamem2, SAMtools, `--fasta`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no |\n| `Reporting` | [`MultiQC`](http://multiqc.info/) | Present QC for raw reads | [RNA, DNA, synthetic] | [N/A] | yes |\n\n### Workflow diagram\n\n\n \n \n \"Fallback\n\n\n### Summary of tools and version used in the pipeline\n\n| Tool | Version |\n| ----------- | ------- |\n| bwamem2 | 2.3 |\n| fastqc | 0.12.1 |\n| fastqe | 0.5.2 |\n| fastqscreen | 0.16.0 |\n| multiqc | 1.33 |\n| picard | 3.4.0 |\n| samtools | 1.22.1 |\n| seqfu | 1.22.3 |\n| seqtk | 1.4 |\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end with only `fastq_1`) or a pair of fastq files (paired end with `fastq_1` and `fastq_2`).\n`rundir` is the path to the runfolder.\n`tags` is a colon-separated list of tags that will be added to the MultiQC report for this `sample`.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by [@agrima2010](https://github.com/agrima2010), [@Aratz](https://github.com/Aratz), [@FranBonath](https://github.com/FranBonath), [@kedhammar](https://github.com/kedhammar), and [@MatthiasZepper](https://github.com/MatthiasZepper) from the Swedish [National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nMaintenance is now lead by Maxime U Garcia ([National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/))\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@adamrtalbot](https://github.com/adamrtalbot)\n- [@alneberg](https://github.com/alneberg)\n- [@beatrizsavinhas](https://github.com/beatrizsavinhas)\n- [@ctuni](https://github.com/ctuni)\n- [@edmundmiller](https://github.com/edmundmiller)\n- [@EliottBo](https://github.com/EliottBo)\n- [@KarNair](https://github.com/KarNair)\n- [@kjellinjonas](https://github.com/kjellinjonas)\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n- [@matrulda](https://github.com/matrulda)\n- [@mirpedrol](https://github.com/mirpedrol)\n- [@nggvs](https://github.com/nggvs)\n- [@nkongenelly](https://github.com/nkongenelly)\n- [@Patricie34](https://github.com/Patricie34)\n- [@pontushojer](https://github.com/pontushojer)\n- [@ramprasadn](https://github.com/ramprasadn)\n- [@rannick](https://github.com/rannick)\n- [@torigiffin](https://github.com/torigiffin)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nYou can cite the seqinspector zenodo record for a specific version using the following [doi: 10.5281/zenodo.18757486](https://doi.org/10.5281/zenodo.18757486)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "description": "

\n \n \n \"nf-core/seqinspector\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.18757486-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.18757486)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that processes raw sequence data (FASTQ) to provide comprehensive quality control.\nIt can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants.\nThe pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.\nIf provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n### Compatibility between tools and data type\n\n\n\n| Tool Type | Tool Name | Tool Description | Compatibility with Data | Dependencies | Default tool |\n| ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | --------------------------------------------------------------------------------------- | ------------ |\n| `Subsampling` | [`Seqtk`](https://github.com/lh3/seqtk) | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA] | [N/A] | no |\n| `Lint FASTQs` | [`fq`](https://github.com/stjude-rust-labs/fq) | fq filters, generates, subsamples, and validates FASTQ files. | [RNA, DNA, synthetic] | [N/A] | yes |\n| `Trimming` | [`Fastp`](https://github.com/OpenGene/fastp) | Trimming of reads. Only performs trimming if `--tools` parameter is given. | [RNA, DNA, synthetic] | [N/A] | no |\n| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2) | Align reads to reference | [RNA, DNA] | [N/A] | yes |\n| `Indexing` | [`SAMtools`](http://github.com/samtools) | Index aligned BAM files, create FASTA index | [DNA] | [N/A] | yes |\n| `QC` | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | Read QC | [RNA, DNA] | [N/A] | yes |\n| `QC` | [`FASTQE`](https://fastqe.com/) | Read QC | [RNA, DNA] | [N/A] | yes |\n| `QC` | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) | Basic contamination detection | [RNA, DNA] | [N/A] | yes |\n| `QC` | [`SeqFu Stats`](https://github.com/telatin/seqfu2) | Sequence statistics | [RNA, DNA] | [N/A] | yes |\n| `QC` | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics | [RNA, DNA] | [Bwamem2, SAMtools, `--genome`] | yes |\n| `QC` | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data. | [RNA, DNA] | [Bwamem2, SAMtools, `--fasta`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no |\n| `Reporting` | [`MultiQC`](http://multiqc.info/) | Present QC for raw reads | [RNA, DNA, synthetic] | [N/A] | yes |\n\n### Workflow diagram\n\n\n \n \n \"Fallback\n\n\n### Summary of tools and version used in the pipeline\n\n| Tool | Version |\n| ----------- | ------- |\n| bwamem2 | 2.3 |\n| fq/lint | 0.12.0 |\n| fastp | 1.1.0 |\n| fastqc | 0.12.1 |\n| fastqe | 0.5.2 |\n| fastqscreen | 0.16.0 |\n| multiqc | 1.33 |\n| picard | 3.4.0 |\n| samtools | 1.22.1 |\n| seqfu | 1.22.3 |\n| seqtk | 1.4 |\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end with only `fastq_1`) or a pair of fastq files (paired end with `fastq_1` and `fastq_2`).\n`rundir` is the path to the runfolder.\n`tags` is a colon-separated list of tags that will be added to the MultiQC report for this `sample`.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by [@agrima2010](https://github.com/agrima2010), [@Aratz](https://github.com/Aratz), [@FranBonath](https://github.com/FranBonath), [@kedhammar](https://github.com/kedhammar), and [@MatthiasZepper](https://github.com/MatthiasZepper) from the Swedish [National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nMaintenance is now lead by Maxime U Garcia ([National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/))\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@adamrtalbot](https://github.com/adamrtalbot)\n- [@alneberg](https://github.com/alneberg)\n- [@beatrizsavinhas](https://github.com/beatrizsavinhas)\n- [@ctuni](https://github.com/ctuni)\n- [@edmundmiller](https://github.com/edmundmiller)\n- [@EliottBo](https://github.com/EliottBo)\n- [@KarNair](https://github.com/KarNair)\n- [@kjellinjonas](https://github.com/kjellinjonas)\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n- [@matrulda](https://github.com/matrulda)\n- [@mirpedrol](https://github.com/mirpedrol)\n- [@nggvs](https://github.com/nggvs)\n- [@nkongenelly](https://github.com/nkongenelly)\n- [@Patricie34](https://github.com/Patricie34)\n- [@pontushojer](https://github.com/pontushojer)\n- [@ramprasadn](https://github.com/ramprasadn)\n- [@rannick](https://github.com/rannick)\n- [@torigiffin](https://github.com/torigiffin)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nYou can cite the seqinspector zenodo record for a specific version using the following [doi: 10.5281/zenodo.18757486](https://doi.org/10.5281/zenodo.18757486)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" From f31f4e6b8eacc4d5010c9675dede70bfbdf1591a Mon Sep 17 00:00:00 2001 From: matrulda Date: Fri, 13 Mar 2026 10:45:28 +0100 Subject: [PATCH 12/25] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ca43be64..8197d6ea 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#202](https://github.com/nf-core/seqinspector/pull/202) Added support for fasta fai file as input (via params or igenomes) for the pipeline - [#206](https://github.com/nf-core/seqinspector/pull/206) Added FASTQE for more comprehensive QC of FASTQ files - [#208](https://github.com/nf-core/seqinspector/pull/208) Add FASTQ linting for early validation with FQ/LINT +- [#212](https://github.com/nf-core/seqinspector/pull/212) Add CheckQC module ### `Fixed` From 50b9b32728bd1598652b2ddc13d01642ab99eb12 Mon Sep 17 00:00:00 2001 From: matrulda Date: Fri, 13 Mar 2026 11:09:29 +0100 Subject: [PATCH 13/25] Add checkqc to output docs --- docs/output.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/docs/output.md b/docs/output.md index a3263ab4..bac20a20 100644 --- a/docs/output.md +++ b/docs/output.md @@ -13,6 +13,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and can generat - [Seqtk](#seqtk) - Subsample a specific number of reads per sample - [FastQC](#fastqc) - Raw read QC - [FASTQE](#fastqe) - Raw read QC +- [CheckQC](#checkqc) - QC of an Illumina run - [SeqFu Stats](#seqfu-stats) - Statistics for FASTA or FASTQ files - [FastQ Screen](#fastq-screen) - Mapping against a set of references for basic contamination QC - [BWA-MEM2_INDEX](#bwamem2_index) - Create BWA-MEM2 index of a chosen reference genome OR use pre-built index @@ -48,6 +49,16 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and can generat [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). +### CheckQC + +
+Output files + +- `checkqc/` + - `checkqc_report.json`: Reports sequencing metrics that is not fulfilled. Note that the CheckQC module in MultiQC currently does not support BCL Convert data, so if the report if based on data from that demultiplexer it will not be visualized in the MutliQC report. + +
+ ### FastP [FastP](https://github.com/OpenGene/fastp) is a tool designed to provide all-in-one preprocessing for FastQ files and as such is used for trimming and splitting. From dc70fc147c9f61c4cbf51ee33d69aa8a8bd0503d Mon Sep 17 00:00:00 2001 From: Karthik Nair Date: Fri, 13 Mar 2026 11:57:48 +0100 Subject: [PATCH 14/25] Update README and usage.md --- README.md | 2 ++ docs/usage.md | 52 ++++++++++++++++++++++++++++++++++----------------- 2 files changed, 37 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 0320c235..d7713730 100644 --- a/README.md +++ b/README.md @@ -37,6 +37,7 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run | `Trimming` | [`Fastp`](https://github.com/OpenGene/fastp) | Trimming of reads. Only performs trimming if `--tools` parameter is given. | [RNA, DNA, synthetic] | [N/A] | no | | `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2) | Align reads to reference | [RNA, DNA] | [N/A] | yes | | `Indexing` | [`SAMtools`](http://github.com/samtools) | Index aligned BAM files, create FASTA index | [DNA] | [N/A] | yes | +| `QC` | [`checkQC`](https://github.com/Molmed/checkQC) | Read QC | [RNA, DNA] | [N/A] | no | | `QC` | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | Read QC | [RNA, DNA] | [N/A] | yes | | `QC` | [`FASTQE`](https://fastqe.com/) | Read QC | [RNA, DNA] | [N/A] | yes | | `QC` | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) | Basic contamination detection | [RNA, DNA] | [N/A] | yes | @@ -58,6 +59,7 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run | Tool | Version | | ----------- | ------- | | bwamem2 | 2.3 | +| checkQC | 4.1.0 | | fq/lint | 0.12.0 | | fastp | 1.1.0 | | fastqc | 0.12.1 | diff --git a/docs/usage.md b/docs/usage.md index 7ae1bb1d..7a564e38 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -168,7 +168,8 @@ It is possible to also chose bundles of pre-specified tools using the `tools_bun Currently, the following bundles are available: -:::info{title="default"}{collapse} +
+default Requirements: @@ -183,9 +184,10 @@ Tools: - rundirparser - seqfu_stats -::: +
-:::info{title="all"}{collapse} +
+all Requirements: @@ -194,16 +196,18 @@ Requirements: Tools: +- checkQC - fastqc - fastqscreen - picard_collecthsmetrics - picard_collectmultiplemetrics - rundirparser - seqfu_stats +
-::: -:::info{title="minimal"}{collapse} +
+minimal Requirements: @@ -215,10 +219,10 @@ Tools: - fastqscreen - picard_collectmultiplemetrics - seqfu_stats +
-::: - -:::info{title="bam"}{collapse} +
+bam Requirements: @@ -229,18 +233,21 @@ Tools: - picard_collecthsmetrics - picard_collectmultiplemetrics -::: +
-:::info{title="fastq"}{collapse} +
+fastq Tools: - fastqc - fastqscreen -::: +
+ -:::info{title="illumina"}{collapse} +
+illumina Requirements: @@ -248,20 +255,20 @@ Requirements: Tools: +- checkQC - rundirparser - seqfu_stats +
-::: - -:::info{title="ont"}{collapse} +
+ont Tools: - fastqc - fastqscreen - seqfu_stats - -::: +
### Available functionality and tools @@ -367,6 +374,17 @@ A pipeline might not always support every possible argument or option of a parti To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. +#### Custom config for checkQC + +To run checkQC with custom configuration, add a yml file with the custom configuration to the rundir and add the following code block to any of your [nextflow config files](https://www.nextflow.io/docs/latest/config.html#configuration-files). + +```bash +process { + withName: CHECKQC { + ext.args = '--config */custom_checkqc.yml' + } +``` + ### nf-core/configs In most cases, you will only need to create a custom config as a one-off but if you and others within your organisation are likely to be running nf-core pipelines regularly and need to use the same settings regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter. You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile. From 81ba847e1261b24bf5ce1c75d0f47f6e9ddf7d44 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 13 Mar 2026 12:13:36 +0000 Subject: [PATCH 15/25] [automated] Fix code linting --- README.md | 2 +- docs/usage.md | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/README.md b/README.md index d7713730..5143ca86 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run | `Trimming` | [`Fastp`](https://github.com/OpenGene/fastp) | Trimming of reads. Only performs trimming if `--tools` parameter is given. | [RNA, DNA, synthetic] | [N/A] | no | | `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2) | Align reads to reference | [RNA, DNA] | [N/A] | yes | | `Indexing` | [`SAMtools`](http://github.com/samtools) | Index aligned BAM files, create FASTA index | [DNA] | [N/A] | yes | -| `QC` | [`checkQC`](https://github.com/Molmed/checkQC) | Read QC | [RNA, DNA] | [N/A] | no | +| `QC` | [`checkQC`](https://github.com/Molmed/checkQC) | Read QC | [RNA, DNA] | [N/A] | no | | `QC` | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | Read QC | [RNA, DNA] | [N/A] | yes | | `QC` | [`FASTQE`](https://fastqe.com/) | Read QC | [RNA, DNA] | [N/A] | yes | | `QC` | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) | Basic contamination detection | [RNA, DNA] | [N/A] | yes | diff --git a/docs/usage.md b/docs/usage.md index 7a564e38..820851af 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -205,7 +205,6 @@ Tools: - seqfu_stats -
minimal @@ -245,7 +244,6 @@ Tools:
-
illumina From 3a499e626ba419e13b5e52ddd849afeb677cede8 Mon Sep 17 00:00:00 2001 From: matrulda Date: Fri, 13 Mar 2026 13:38:00 +0100 Subject: [PATCH 16/25] Update snapshot --- tests/NovaSeq6000.nf.test.snap | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap index daa039e1..4482b278 100644 --- a/tests/NovaSeq6000.nf.test.snap +++ b/tests/NovaSeq6000.nf.test.snap @@ -1122,7 +1122,7 @@ "[NXF_HASH] Submitted process > PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa)" ] ], - "timestamp": "2026-03-13T10:18:02.426461184", + "timestamp": "2026-03-13T13:23:48.846109058", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.2" @@ -2125,10 +2125,10 @@ ], "No warnings" ], - "timestamp": "2026-03-12T16:20:40.276575593", + "timestamp": "2026-03-13T13:32:49.347143681", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } }, "NovaSeq6000 data test relative sample size": { @@ -3128,10 +3128,10 @@ ], "No warnings" ], - "timestamp": "2026-03-12T16:22:35.271019752", + "timestamp": "2026-03-13T13:26:41.591026679", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } }, "NovaSeq6000 data test - No rundirs": { @@ -4092,10 +4092,10 @@ "WARN: Sample 'sampletest_04' does not have a rundir specified" ] ], - "timestamp": "2026-03-12T16:26:16.838135479", + "timestamp": "2026-03-13T13:28:45.181835916", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } }, "NovaSeq6000 data test sample size exceeds available reads": { @@ -5101,10 +5101,10 @@ "WARN: sampletest_04: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads." ] ], - "timestamp": "2026-03-12T16:24:28.456349297", + "timestamp": "2026-03-13T13:27:49.421009962", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } }, "NovaSeq6000 data test - tag collision": { @@ -5892,10 +5892,10 @@ "WARN: Tag name collision: [test, Test, TEST]" ] ], - "timestamp": "2026-03-12T15:44:33.503707412", + "timestamp": "2026-03-13T13:29:34.78905167", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nextflow": "25.10.2" } } } \ No newline at end of file From d5204cb6049858881a6b7d79ca1cb6facc0b7bfc Mon Sep 17 00:00:00 2001 From: Karthik Nair Date: Fri, 13 Mar 2026 13:47:38 +0100 Subject: [PATCH 17/25] Prettify commit --- CITATIONS.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CITATIONS.md b/CITATIONS.md index 28030361..2a04232e 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -14,6 +14,10 @@ > Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE; 2019:314-324. doi:10.1109/IPDPS.2019.00041 +- [checkQC](https://github.com/Molmed/checkQC) + + > Åslin et al., (2018). CheckQC: Quick quality control of Illumina sequencing runs. Journal of Open Source Software, 3(22), 556, https://doi.org/10.21105/joss.00556 + - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. From ab6b2e1935de30d15f7910fe0be9fa6fc90115e1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matilda=20=C3=85slin?= Date: Fri, 13 Mar 2026 14:14:47 +0100 Subject: [PATCH 18/25] Update docs/output.md Co-authored-by: Franziska Bonath <41994400+FranBonath@users.noreply.github.com> --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index bac20a20..1a2e3354 100644 --- a/docs/output.md +++ b/docs/output.md @@ -55,7 +55,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and can generat Output files - `checkqc/` - - `checkqc_report.json`: Reports sequencing metrics that is not fulfilled. Note that the CheckQC module in MultiQC currently does not support BCL Convert data, so if the report if based on data from that demultiplexer it will not be visualized in the MutliQC report. + - `checkqc_report.json`: Reports sequencing metrics that are not fulfilled. Note that the CheckQC module in MultiQC currently does not support BCL Convert data, so if the report if based on data from that demultiplexer it will not be visualized in the MutliQC report. Results can be found in the output directory.
From f357330ddfdb7bfaa528a09930712f3b23651e7e Mon Sep 17 00:00:00 2001 From: Karthik Nair Date: Fri, 13 Mar 2026 14:31:27 +0100 Subject: [PATCH 19/25] Fix Requirements column --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 5143ca86..43fe6b77 100644 --- a/README.md +++ b/README.md @@ -30,14 +30,14 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run -| Tool Type | Tool Name | Tool Description | Compatibility with Data | Dependencies | Default tool | +| Tool Type | Tool Name | Tool Description | Compatibility with Data | Requirements | Default tool | | ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | --------------------------------------------------------------------------------------- | ------------ | | `Subsampling` | [`Seqtk`](https://github.com/lh3/seqtk) | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA] | [N/A] | no | | `Lint FASTQs` | [`fq`](https://github.com/stjude-rust-labs/fq) | fq filters, generates, subsamples, and validates FASTQ files. | [RNA, DNA, synthetic] | [N/A] | yes | | `Trimming` | [`Fastp`](https://github.com/OpenGene/fastp) | Trimming of reads. Only performs trimming if `--tools` parameter is given. | [RNA, DNA, synthetic] | [N/A] | no | | `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2) | Align reads to reference | [RNA, DNA] | [N/A] | yes | | `Indexing` | [`SAMtools`](http://github.com/samtools) | Index aligned BAM files, create FASTA index | [DNA] | [N/A] | yes | -| `QC` | [`checkQC`](https://github.com/Molmed/checkQC) | Read QC | [RNA, DNA] | [N/A] | no | +| `QC` | [`checkQC`](https://github.com/Molmed/checkQC) | Read QC | [RNA, DNA] | Illumina rundir | no | | `QC` | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | Read QC | [RNA, DNA] | [N/A] | yes | | `QC` | [`FASTQE`](https://fastqe.com/) | Read QC | [RNA, DNA] | [N/A] | yes | | `QC` | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) | Basic contamination detection | [RNA, DNA] | [N/A] | yes | From 3e30c346f46575f95cae17d63ed7b602fb8ba781 Mon Sep 17 00:00:00 2001 From: matrulda Date: Fri, 13 Mar 2026 16:34:15 +0100 Subject: [PATCH 20/25] Add checkqc_config parameter --- assets/checkqc_config.yml | 792 ++++++++++++++++++++++++ main.nf | 1 + nextflow.config | 3 + nextflow_schema.json | 11 +- tests/NovaSeq6000.nf.test | 9 +- tests/NovaSeq6000.nf.test.snap | 1048 +++++++++++++++++++++++++++++++- workflows/seqinspector.nf | 7 +- 7 files changed, 1865 insertions(+), 6 deletions(-) create mode 100644 assets/checkqc_config.yml diff --git a/assets/checkqc_config.yml b/assets/checkqc_config.yml new file mode 100644 index 00000000..87dfb4f4 --- /dev/null +++ b/assets/checkqc_config.yml @@ -0,0 +1,792 @@ +# For information about config usage, see http://checkqc.readthedocs.io/en/latest/#configuration-file + +# Use this section to provide configuration options to the parsers +parser_configurations: + StatsJsonParser: + # Path to where the bcl2fastq output (i.e. fastq files, etc) is located relative to + # the runfolder + bcl2fastq_output_path: Data/Intensities/BaseCalls + SamplesheetParser: + samplesheet_name: SampleSheet.csv + from_bclconvert: + reports_location: Reports + +default_view: illumina_data_view + +default_handlers: + - name: UndeterminedPercentageHandler + warning: unknown + error: 9 # <% Phix on lane> + < value as %> + - name: UnidentifiedIndexHandler + significance_threshold: 1 # % of reads in unidentified + # Indexes which are white-listed will only cause a warning even if they occur + # above the significance level. + # They will be matched like regular expressions, + # so e.g. NNN will match exactly three NNNs, while + # N{3,} will match three or more Ns. + white_listed_indexes: + - .*N.* + - G{6,} + +hiseq2500_rapidhighoutput_v4: + 51-71: + handlers: + - name: ClusterPFHandler + warning: 180 # Millons of clusters + error: unknown + - name: Q30Handler + warning: 85 # Give percentage for reads greater than Q30 + error: unknown # Give percentage for reads greater than Q30 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 135 # 75 % of threshold for clusters pass filter + view: illumina_data_view + 100-111: + handlers: + - name: ClusterPFHandler + warning: 180 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 135 + 121-131: + handlers: + - name: ClusterPFHandler + warning: 180 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 135 + +hiseq2500_rapidrun_v2: + 51: + handlers: + - name: ClusterPFHandler + warning: 110 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 82.5 + 101: + handlers: + - name: ClusterPFHandler + warning: 110 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 82.5 + 251: + handlers: + - name: ClusterPFHandler + warning: 110 + error: unknown + - name: Q30Handler + warning: unknown + error: 75 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: unknown + error: 5 + - name: ReadsPerSampleHandler + warning: unknown + error: 82.5 + +hiseqx_v2: + 151: + handlers: + - name: ClusterPFHandler + warning: 400 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 300 + +novaseq_SP: + 51: + handlers: + - name: ClusterPFHandler + warning: 325 + error: unknown + - name: Q30Handler + warning: 90 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 243.75 + 101: + handlers: + - name: ClusterPFHandler + warning: 325 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 243.75 + 151: + handlers: + - name: ClusterPFHandler + warning: 325 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 243.75 + 251: + handlers: + - name: ClusterPFHandler + warning: 325 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 243.75 + +novaseq_S1: + 51: + handlers: + - name: ClusterPFHandler + warning: 650 + error: unknown + - name: Q30Handler + warning: 90 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 487.5 + 101: + handlers: + - name: ClusterPFHandler + warning: 650 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 487.5 + 151: + handlers: + - name: ClusterPFHandler + warning: 650 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 487.5 + +novaseq_S2: + 51: + handlers: + - name: ClusterPFHandler + warning: 1650 + error: unknown + - name: Q30Handler + warning: 90 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 1237.5 + 101: + handlers: + - name: ClusterPFHandler + warning: 1650 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 1237.5 + 151: + handlers: + - name: ClusterPFHandler + warning: 1650 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 1237.5 + +novaseq_S4: + 101: + handlers: + - name: ClusterPFHandler + warning: 2000 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 1500 + 151: + handlers: + - name: ClusterPFHandler + warning: 2000 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 1500 + +novaseqxplus_1.5B: + 51: + handlers: + - name: ClusterPFHandler + warning: 800 + error: unknown + - name: Q30Handler + warning: 90 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 600 + 101: + handlers: + - name: ClusterPFHandler + warning: 800 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 600 + 151: + handlers: + - name: ClusterPFHandler + warning: 800 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 600 + +novaseqxplus_10B: + 51: + handlers: + - name: ClusterPFHandler + warning: 1250 + error: unknown + - name: Q30Handler + warning: 90 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 937.5 + 101: + handlers: + - name: ClusterPFHandler + warning: 1250 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 937.5 + 151: + handlers: + - name: ClusterPFHandler + warning: 1250 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 937.5 + +novaseqxplus_25B: + 151: + handlers: + - name: ClusterPFHandler + warning: 3250 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 2437.5 + +miseq_nano_v2: + 151: + handlers: + - name: ClusterPFHandler + warning: 1 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 7.5 + 251: + handlers: + - name: ClusterPFHandler + warning: 1 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 7.5 + +miseq_micro_v2: + 151: + handlers: + - name: ClusterPFHandler + warning: 4 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 7.5 + +miseq_v2: + 51: + handlers: + - name: ClusterPFHandler + warning: 10 + error: unknown + - name: Q30Handler + warning: 90 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 7.5 + 151: + handlers: + - name: ClusterPFHandler + warning: 10 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 7.5 + 251: + handlers: + - name: ClusterPFHandler + warning: 10 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 7.5 + +miseq_v3: + 76: + handlers: + - name: ClusterPFHandler + warning: 18 + error: unknown + - name: Q30Handler + warning: 85 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 13.5 + 151: + handlers: + - name: ClusterPFHandler + warning: 18 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 2 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 13.5 + 301: + handlers: + - name: ClusterPFHandler + warning: 18 + error: unknown + - name: Q30Handler + warning: 70 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 13.5 + - name: UndeterminedPercentageHandler + warning: unknown + error: 14 # <% Phix on lane> + < value as %> + +iseq_v1: + 151: + handlers: + - name: ClusterPFHandler + warning: 4 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 5 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 3 + +nextseq500_high: + 76: + handlers: + - name: ClusterPFHandler + warning: 100 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 75 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 151: + handlers: + - name: ClusterPFHandler + warning: 100 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 75 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 301: + handlers: + - name: ClusterPFHandler + warning: 60 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 15 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + +nextseq500_mid: + 76: + handlers: + - name: ClusterPFHandler + warning: 32 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 24 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 151: + handlers: + - name: ClusterPFHandler + warning: 32 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 24 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 301: + handlers: + - name: ClusterPFHandler + warning: 32 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 24 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + +nextseq550_high: + 76: + handlers: + - name: ClusterPFHandler + warning: 100 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 75 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 151: + handlers: + - name: ClusterPFHandler + warning: 100 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 75 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 301: + handlers: + - name: ClusterPFHandler + warning: 100 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 75 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + +nextseq550_mid: + 76: + handlers: + - name: ClusterPFHandler + warning: 32 + error: unknown + - name: Q30Handler + warning: 80 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 24 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 151: + handlers: + - name: ClusterPFHandler + warning: 32 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 24 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + 301: + handlers: + - name: ClusterPFHandler + warning: 32 + error: unknown + - name: Q30Handler + warning: 75 + error: unknown + - name: ReadsPerSampleHandler + warning: unknown + error: 24 + - name: ErrorRateHandler + allow_missing_error_rate: False + warning: 1.5 + error: unknown + diff --git a/main.nf b/main.nf index 18396f72..787c624e 100644 --- a/main.nf +++ b/main.nf @@ -119,6 +119,7 @@ workflow NFCORE_SEQINSPECTOR { samplesheet, params.bait_intervals, bwamem2, + params.checkqc_config, fasta, params.fastq_screen_references, params.multiqc_config, diff --git a/nextflow.config b/nextflow.config index 7e06b452..43fea387 100644 --- a/nextflow.config +++ b/nextflow.config @@ -23,6 +23,9 @@ params { igenomes_ignore = false sort_bam = true + // CheckQC options + checkqc_config = null + // fq/lint options fq_lint_args = "" continue_with_lint_fail = true diff --git a/nextflow_schema.json b/nextflow_schema.json index a4470eeb..c4b4fcf8 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -58,7 +58,8 @@ "type": "string", "description": "Select some default setup for the tools to be run, tools can still be used to add tools", "pattern": "^((all|bam|fastq|default|illumina|minimal|ont)?,?)*(? PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa)" ] ], - "timestamp": "2026-03-13T13:23:48.846109058", + "timestamp": "2026-03-13T16:25:23.075926527", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.2" diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf index a59ff926..4fbd3ff4 100644 --- a/workflows/seqinspector.nf +++ b/workflows/seqinspector.nf @@ -42,6 +42,7 @@ workflow SEQINSPECTOR { ch_samplesheet // channel: samplesheet read in from --input bait_intervals bwamem2_index + checkqc_config fasta_reference fastq_screen_references multiqc_config @@ -148,7 +149,11 @@ workflow SEQINSPECTOR { ch_rundir.ifEmpty { log.warn("No samples with rundir found, skipping CHECKQC") } - CHECKQC(ch_rundir, []) + CHECKQC(ch_rundir, + checkqc_config + ? file(checkqc_config, checkIfExists: true) + : [] + ) ch_multiqc_files = ch_multiqc_files.mix(CHECKQC.out.report) } From 099170c5c38d0091b9cb9639c6f1e58beefc03e5 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 13 Mar 2026 15:42:21 +0000 Subject: [PATCH 21/25] [automated] Fix code linting --- assets/checkqc_config.yml | 17 ++++++++--------- docs/usage.md | 2 +- 2 files changed, 9 insertions(+), 10 deletions(-) diff --git a/assets/checkqc_config.yml b/assets/checkqc_config.yml index 87dfb4f4..7831ec71 100644 --- a/assets/checkqc_config.yml +++ b/assets/checkqc_config.yml @@ -619,7 +619,7 @@ nextseq500_high: warning: 1.5 error: unknown 151: - handlers: + handlers: - name: ClusterPFHandler warning: 100 error: unknown @@ -634,7 +634,7 @@ nextseq500_high: warning: 1.5 error: unknown 301: - handlers: + handlers: - name: ClusterPFHandler warning: 60 error: unknown @@ -666,7 +666,7 @@ nextseq500_mid: warning: 1.5 error: unknown 151: - handlers: + handlers: - name: ClusterPFHandler warning: 32 error: unknown @@ -681,7 +681,7 @@ nextseq500_mid: warning: 1.5 error: unknown 301: - handlers: + handlers: - name: ClusterPFHandler warning: 32 error: unknown @@ -713,7 +713,7 @@ nextseq550_high: warning: 1.5 error: unknown 151: - handlers: + handlers: - name: ClusterPFHandler warning: 100 error: unknown @@ -728,7 +728,7 @@ nextseq550_high: warning: 1.5 error: unknown 301: - handlers: + handlers: - name: ClusterPFHandler warning: 100 error: unknown @@ -760,7 +760,7 @@ nextseq550_mid: warning: 1.5 error: unknown 151: - handlers: + handlers: - name: ClusterPFHandler warning: 32 error: unknown @@ -775,7 +775,7 @@ nextseq550_mid: warning: 1.5 error: unknown 301: - handlers: + handlers: - name: ClusterPFHandler warning: 32 error: unknown @@ -789,4 +789,3 @@ nextseq550_mid: allow_missing_error_rate: False warning: 1.5 error: unknown - diff --git a/docs/usage.md b/docs/usage.md index a2c37647..0f1bbbbe 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -204,7 +204,7 @@ Tools: - rundirparser - seqfu_stats - toulligqc - +
From 64784863111173937c741abdd6ef672868b03913 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Mon, 16 Mar 2026 09:45:38 +0100 Subject: [PATCH 22/25] simplify tests --- ...{CheckQC.nf.test => tools_checkqc.nf.test} | 8 +- tests/tools_checkqc.nf.test.snap | 155 +++ tests/tools_fq_lint.nf.test | 6 + tests/tools_fq_lint.nf.test.snap | 1012 +---------------- workflows/seqinspector.nf | 11 +- 5 files changed, 184 insertions(+), 1008 deletions(-) rename tests/{CheckQC.nf.test => tools_checkqc.nf.test} (80%) create mode 100644 tests/tools_checkqc.nf.test.snap diff --git a/tests/CheckQC.nf.test b/tests/tools_checkqc.nf.test similarity index 80% rename from tests/CheckQC.nf.test rename to tests/tools_checkqc.nf.test index 0e636999..f7505885 100644 --- a/tests/CheckQC.nf.test +++ b/tests/tools_checkqc.nf.test @@ -8,13 +8,13 @@ nextflow_pipeline { def test_scenario = [ [ - name: "NovaSeq6000 data test", + name: "NovaSeq6000 data test - checkqc", params: [ tools: 'checkqc', - ], - snapshot: 'stderr,stdout' - ], + tools_bundle: null + ] ] + ] // Generate tests for each scenario test_scenario.each { scenario -> diff --git a/tests/tools_checkqc.nf.test.snap b/tests/tools_checkqc.nf.test.snap new file mode 100644 index 00000000..882a4dfa --- /dev/null +++ b/tests/tools_checkqc.nf.test.snap @@ -0,0 +1,155 @@ +{ + "NovaSeq6000 data test - checkqc": { + "content": [ + 6, + { + "CHECKQC": { + "checkqc": "4.1.0" + } + }, + [ + "checkqc", + "checkqc/checkqc_report.json", + "multiqc", + "multiqc/global_report", + "multiqc/global_report/multiqc_data", + "multiqc/global_report/multiqc_data/checkqc_reads-per-sample-plot.txt", + "multiqc/global_report/multiqc_data/llms-full.txt", + "multiqc/global_report/multiqc_data/multiqc.log", + "multiqc/global_report/multiqc_data/multiqc.parquet", + "multiqc/global_report/multiqc_data/multiqc_checkqc.txt", + "multiqc/global_report/multiqc_data/multiqc_citations.txt", + "multiqc/global_report/multiqc_data/multiqc_data.json", + "multiqc/global_report/multiqc_data/multiqc_software_versions.txt", + "multiqc/global_report/multiqc_data/multiqc_sources.txt", + "multiqc/global_report/multiqc_plots", + "multiqc/global_report/multiqc_plots/pdf", + "multiqc/global_report/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", + "multiqc/global_report/multiqc_plots/png", + "multiqc/global_report/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", + "multiqc/global_report/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", + "multiqc/global_report/multiqc_plots/svg", + "multiqc/global_report/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", + "multiqc/global_report/multiqc_report.html", + "multiqc/group_reports", + "multiqc/group_reports/group1", + "multiqc/group_reports/group1/multiqc_data", + "multiqc/group_reports/group1/multiqc_data/checkqc_reads-per-sample-plot.txt", + "multiqc/group_reports/group1/multiqc_data/llms-full.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc.log", + "multiqc/group_reports/group1/multiqc_data/multiqc.parquet", + "multiqc/group_reports/group1/multiqc_data/multiqc_checkqc.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_data.json", + "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/group1/multiqc_plots", + "multiqc/group_reports/group1/multiqc_plots/pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", + "multiqc/group_reports/group1/multiqc_plots/png", + "multiqc/group_reports/group1/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", + "multiqc/group_reports/group1/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", + "multiqc/group_reports/group1/multiqc_plots/svg", + "multiqc/group_reports/group1/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", + "multiqc/group_reports/group1/multiqc_report.html", + "multiqc/group_reports/group2", + "multiqc/group_reports/group2/multiqc_data", + "multiqc/group_reports/group2/multiqc_data/checkqc_reads-per-sample-plot.txt", + "multiqc/group_reports/group2/multiqc_data/llms-full.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc.log", + "multiqc/group_reports/group2/multiqc_data/multiqc.parquet", + "multiqc/group_reports/group2/multiqc_data/multiqc_checkqc.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_data.json", + "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/group2/multiqc_plots", + "multiqc/group_reports/group2/multiqc_plots/pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", + "multiqc/group_reports/group2/multiqc_plots/png", + "multiqc/group_reports/group2/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", + "multiqc/group_reports/group2/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", + "multiqc/group_reports/group2/multiqc_plots/svg", + "multiqc/group_reports/group2/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", + "multiqc/group_reports/group2/multiqc_report.html", + "multiqc/group_reports/lane1", + "multiqc/group_reports/lane1/multiqc_data", + "multiqc/group_reports/lane1/multiqc_data/checkqc_reads-per-sample-plot.txt", + "multiqc/group_reports/lane1/multiqc_data/llms-full.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc.log", + "multiqc/group_reports/lane1/multiqc_data/multiqc.parquet", + "multiqc/group_reports/lane1/multiqc_data/multiqc_checkqc.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_data.json", + "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/lane1/multiqc_plots", + "multiqc/group_reports/lane1/multiqc_plots/pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", + "multiqc/group_reports/lane1/multiqc_plots/png", + "multiqc/group_reports/lane1/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", + "multiqc/group_reports/lane1/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", + "multiqc/group_reports/lane1/multiqc_plots/svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", + "multiqc/group_reports/lane1/multiqc_report.html", + "multiqc/group_reports/test", + "multiqc/group_reports/test/multiqc_data", + "multiqc/group_reports/test/multiqc_data/checkqc_reads-per-sample-plot.txt", + "multiqc/group_reports/test/multiqc_data/llms-full.txt", + "multiqc/group_reports/test/multiqc_data/multiqc.log", + "multiqc/group_reports/test/multiqc_data/multiqc.parquet", + "multiqc/group_reports/test/multiqc_data/multiqc_checkqc.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_citations.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_data.json", + "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/test/multiqc_plots", + "multiqc/group_reports/test/multiqc_plots/pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", + "multiqc/group_reports/test/multiqc_plots/png", + "multiqc/group_reports/test/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", + "multiqc/group_reports/test/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", + "multiqc/group_reports/test/multiqc_plots/svg", + "multiqc/group_reports/test/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", + "multiqc/group_reports/test/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", + "multiqc/group_reports/test/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml" + ], + [ + "checkqc_report.json:md5,8245b6a8b8e0e2d247cb7a151d53612f", + "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", + "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", + "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18", + "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", + "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", + "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18", + "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", + "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", + "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18", + "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", + "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", + "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18", + "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", + "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", + "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18" + ], + "No BAM files", + "No warnings" + ], + "timestamp": "2026-03-16T09:42:19.096152642", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/tests/tools_fq_lint.nf.test b/tests/tools_fq_lint.nf.test index b13a5432..80cd4a40 100644 --- a/tests/tools_fq_lint.nf.test +++ b/tests/tools_fq_lint.nf.test @@ -11,6 +11,8 @@ nextflow_pipeline { params: [ input: pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet_wrongpair.csv', continue_with_lint_fail: true, + tools: 'fq_lint', + tools_bundle: null ] ], [ @@ -18,6 +20,8 @@ nextflow_pipeline { params: [ input: pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet_wrongpair.csv', continue_with_lint_fail: false, + tools: 'fq_lint', + tools_bundle: null ], snapshot_ignore:['Failed','exception'], failure:true @@ -26,6 +30,8 @@ nextflow_pipeline { name: "NovaSeq6000 data test - args for fq/lint", params: [ fq_lint_args: '--disable-validator P001', + tools: 'fq_lint', + tools_bundle: null ] ] ] diff --git a/tests/tools_fq_lint.nf.test.snap b/tests/tools_fq_lint.nf.test.snap index 984486f1..50dfbd55 100644 --- a/tests/tools_fq_lint.nf.test.snap +++ b/tests/tools_fq_lint.nf.test.snap @@ -1,988 +1,27 @@ { "NovaSeq6000 data test - args for fq/lint": { "content": [ - 43, + 5, { - "BWAMEM2_INDEX": { - "bwamem2": "2.2.1" - }, - "BWAMEM2_MEM": { - "bwamem2": "2.2.1", - "samtools": "1.22.1" - }, - "FASTQC": { - "fastqc": "0.12.1" - }, - "FASTQSCREEN_FASTQSCREEN": { - "fastqscreen": "0.16.0" - }, "FQ_LINT": { "fq": "0.12.0" - }, - "PICARD_COLLECTMULTIPLEMETRICS": { - "picard": "3.4.0" - }, - "RUNDIRPARSER": { - "PyYAML": "6.0.2", - "Python": "3.13.2" - }, - "SAMTOOLS_FAIDX": { - "samtools": "1.22.1" - }, - "SAMTOOLS_INDEX": { - "samtools": "1.22.1" - }, - "SEQFU_STATS": { - "seqfu": "1.22.3" } }, [ - "bwamem2_index", - "bwamem2_index/bwamem2", - "bwamem2_index/bwamem2/genome.fa.0123", - "bwamem2_index/bwamem2/genome.fa.amb", - "bwamem2_index/bwamem2/genome.fa.ann", - "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64", - "bwamem2_index/bwamem2/genome.fa.pac", - "bwamem2_mem", - "bwamem2_mem/Sample1_01.bam", - "bwamem2_mem/Sample1_01.bam.bai", - "bwamem2_mem/Sample23_03.bam", - "bwamem2_mem/Sample23_03.bam.bai", - "bwamem2_mem/SampleA_02.bam", - "bwamem2_mem/SampleA_02.bam.bai", - "bwamem2_mem/Undetermined_05.bam", - "bwamem2_mem/Undetermined_05.bam.bai", - "bwamem2_mem/sampletest_04.bam", - "bwamem2_mem/sampletest_04.bam.bai", - "fastqc", - "fastqc/Sample1_01_fastqc.html", - "fastqc/Sample1_01_fastqc.zip", - "fastqc/Sample23_03_fastqc.html", - "fastqc/Sample23_03_fastqc.zip", - "fastqc/SampleA_02_fastqc.html", - "fastqc/SampleA_02_fastqc.zip", - "fastqc/Undetermined_05_fastqc.html", - "fastqc/Undetermined_05_fastqc.zip", - "fastqc/sampletest_04_fastqc.html", - "fastqc/sampletest_04_fastqc.zip", - "fastqscreen", - "fastqscreen/Sample1_01_screen.html", - "fastqscreen/Sample1_01_screen.png", - "fastqscreen/Sample1_01_screen.txt", - "fastqscreen/Sample23_03_screen.html", - "fastqscreen/Sample23_03_screen.png", - "fastqscreen/Sample23_03_screen.txt", - "fastqscreen/SampleA_02_screen.html", - "fastqscreen/SampleA_02_screen.png", - "fastqscreen/SampleA_02_screen.txt", - "fastqscreen/Undetermined_05_screen.html", - "fastqscreen/Undetermined_05_screen.png", - "fastqscreen/Undetermined_05_screen.txt", - "fastqscreen/sampletest_04_screen.html", - "fastqscreen/sampletest_04_screen.png", - "fastqscreen/sampletest_04_screen.txt", "fq", "fq/Sample1_01.fq_lint.txt", "fq/Sample23_03.fq_lint.txt", "fq/SampleA_02.fq_lint.txt", "fq/Undetermined_05.fq_lint.txt", "fq/sampletest_04.fq_lint.txt", - "multiqc", - "multiqc/global_report", - "multiqc/global_report/multiqc_data", - "multiqc/global_report/multiqc_data/fastq_screen_plot.txt", - "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt", - "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt", - "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt", - "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", - "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", - "multiqc/global_report/multiqc_data/llms-full.txt", - 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"picard_base_distribution_by_cycle__Adenine.txt:md5,3c3671ac2aa18d883691d59adbfe3b2b", - "picard_base_distribution_by_cycle__Cytosine.txt:md5,6cc2ae1411899de5542321ff1592b192", - "picard_base_distribution_by_cycle__Guanine.txt:md5,326471bc846a9fb6b54ff38cbdfb8d90", - "picard_base_distribution_by_cycle__Thymine.txt:md5,3132dac406a9b9e1f18af658ab856a5c", - "picard_base_distribution_by_cycle__Undetermined.txt:md5,0ed7f750b500e7c5387ea5309e1ef467", - "picard_quality_by_cycle.txt:md5,fe4e6ab1c849a4f833eae9a8554ea432", - "picard_quality_score_distribution.txt:md5,c0864f8a1269d8ffd7a51abb6bd3ca2e", - "fastq_screen_plot.txt:md5,4def6c6a888afe487ab6ebef3ba8a133", - "fastqc-status-check-heatmap.txt:md5,61857d2c45cf0c080348047aa34e7525", - "fastqc_overrepresented_sequences_plot.txt:md5,7949c64cc6cef77f29349a188fc09656", - "fastqc_per_base_n_content_plot.txt:md5,0f2fd628631d42ed5e6a1db22578daaa", - "fastqc_per_base_sequence_quality_plot.txt:md5,0a8bfa32ab04eaaa509dec3c37acb2d2", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,8c85be0c70129ba739feceddd58f6c75", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,94b975906d8a07e1604e00d4004f7463", - "fastqc_per_sequence_quality_scores_plot.txt:md5,ec22c8e4836aa726680f0ca767c778a0", - "fastqc_sequence_counts_plot.txt:md5,f4341795bdeba588248a74a095a97f8d", - "fastqc_sequence_duplication_levels_plot.txt:md5,8fc995cb2192a2926eee242681bc3af6", - "fastqc_sequence_length_distribution_plot.txt:md5,4513e22583677a4d6167b9094242eb0b", - "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", - "multiqc_fastq_screen.txt:md5,fd3074930c72b666f201ae71fa27744b", - "multiqc_fastqc.txt:md5,98111f17d1899cad6379e4e56ed11c53", - "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7", - "multiqc_picard_AlignmentSummaryMetrics.txt:md5,3b1929de09267fc1c1a15804cb5bf536", - "multiqc_picard_baseContent.txt:md5,ff36be9e2642089aa711c637d3cdba29", - "multiqc_picard_quality_by_cycle.txt:md5,9521c83313eaf5f681ac9a75de83a4b7", - "multiqc_picard_quality_score_distribution.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0", - "multiqc_seqfu_mqc.txt:md5,f821357507fda2d4cfd9299f52fa7dc1", - "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_MeanQualityByCycle_histogram_1.txt:md5,9521c83313eaf5f681ac9a75de83a4b7", - "picard_QualityScoreDistribution_histogram.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0", - "picard_alignment_readlength_plot.txt:md5,9c80659c5c9b2fe9926b789fb67ba6ac", - "picard_alignment_summary.txt:md5,27bbb1fcdeecd26641938e5622087c23", - "picard_base_distribution_by_cycle__Adenine.txt:md5,99c5e961a4d26754e68047c8eb983798", - "picard_base_distribution_by_cycle__Cytosine.txt:md5,44981dd399013d8c06481958be338040", - "picard_base_distribution_by_cycle__Guanine.txt:md5,b6369a23d3926edb90ae9bfdc6d90526", - "picard_base_distribution_by_cycle__Thymine.txt:md5,b253d3fca7c07b6a6dfea91725c58102", - "picard_base_distribution_by_cycle__Undetermined.txt:md5,0f2fd628631d42ed5e6a1db22578daaa", - "picard_quality_by_cycle.txt:md5,3c34ae2bd2442a816577b1a794add2d6", - "picard_quality_score_distribution.txt:md5,0d58c59eac2952e6f71cefc35d4c4477", - "fastq_screen_plot.txt:md5,5abb5b9ed2c976f0ad83216ca3186201", - "fastqc-status-check-heatmap.txt:md5,323d6082b73ddb6ee33385f5ea4301c1", - "fastqc_overrepresented_sequences_plot.txt:md5,4e71d8913d40eb06db0f18d74ce6898f", - "fastqc_per_base_n_content_plot.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6", - "fastqc_per_base_sequence_quality_plot.txt:md5,e6f44d08f4185f680d4748a3b37201e2", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1dc8a968f32bcf8a9b4c5f43d299dfa", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,e41b6dc1344f1aee379993daff310187", - "fastqc_per_sequence_quality_scores_plot.txt:md5,76f792b939233b070562cc46617f6371", - "fastqc_sequence_counts_plot.txt:md5,36c68522023b8d536c9362403bf03c48", - "fastqc_sequence_duplication_levels_plot.txt:md5,9ff0df466790d971b3c7ef838efc0f4f", - "fastqc_sequence_length_distribution_plot.txt:md5,9fda632b92e3453f11cd0226484fce8e", - "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", - "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272", - "multiqc_fastqc.txt:md5,396b4cc0466a6642ec8b954237c42263", - "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7", - "multiqc_picard_AlignmentSummaryMetrics.txt:md5,153c6e6a407ec128b1a02798ca2f1115", - "multiqc_picard_baseContent.txt:md5,6349e514552a0b5a0530fa6f311878a5", - "multiqc_picard_quality_by_cycle.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2", - "multiqc_picard_quality_score_distribution.txt:md5,40e0b6faa75e1b51af42407f7ededb0c", - "multiqc_seqfu_mqc.txt:md5,8cced36d66ca9d25d60c006e734aa7e9", - "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_MeanQualityByCycle_histogram_1.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2", - "picard_QualityScoreDistribution_histogram.txt:md5,40e0b6faa75e1b51af42407f7ededb0c", - "picard_alignment_readlength_plot.txt:md5,5a19b1f8e2ac49d97f36a7792429419c", - "picard_alignment_summary.txt:md5,f9f791b7c569cfae07aef70aa630d40e", - "picard_base_distribution_by_cycle__Adenine.txt:md5,0165f522c84da6b17a286d37dc30abec", - "picard_base_distribution_by_cycle__Cytosine.txt:md5,6fa0d29d40fe7fa24c166b664b6d4f4b", - "picard_base_distribution_by_cycle__Guanine.txt:md5,bf2426e09ac1ca4773edfc284c220122", - "picard_base_distribution_by_cycle__Thymine.txt:md5,3cbace572471ccf6c58673181dd0c0ec", - "picard_base_distribution_by_cycle__Undetermined.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6", - "picard_quality_by_cycle.txt:md5,7cb705007bc97da8c0da7d93201e6975", - "picard_quality_score_distribution.txt:md5,47d684abae0a8f4f09df43e91d54fb9a", - "fastq_screen_plot.txt:md5,82ceb9f2109f865d6d1b943441c09550", - "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1", - "fastqc_overrepresented_sequences_plot.txt:md5,8e83abdbe7362e64d63339ee31ab3361", - "fastqc_per_base_n_content_plot.txt:md5,33b70326d8f888ac5a3d99b85f365e43", - "fastqc_per_base_sequence_quality_plot.txt:md5,40bc954cc0d58a3197fdf124a40f1ca4", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e240e30996c81a34b5d1a6b5a98ae254", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b44d3376d503af12857d494c58b514bb", - "fastqc_per_sequence_quality_scores_plot.txt:md5,66b5b6d44f398fc9429460c0b9ba3ea9", - "fastqc_sequence_counts_plot.txt:md5,6e5804f553f656cffb02f927015d1026", - "fastqc_sequence_duplication_levels_plot.txt:md5,fbe41935ea2e2faf7104393b476e5ac5", - "fastqc_sequence_length_distribution_plot.txt:md5,e77dc4ab73252c2e09c7452c3b8e8ab3", - "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", - "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2", - "multiqc_fastqc.txt:md5,95c8ffb23baafec625aeb600047515ae", - "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7", - "multiqc_picard_AlignmentSummaryMetrics.txt:md5,2d05e826f5152fd0143edf7270de1235", - "multiqc_picard_baseContent.txt:md5,f3f23899a30a96260d8b5b3020708703", - "multiqc_picard_quality_by_cycle.txt:md5,c7edfc271ab59ecedad0ab046afd3563", - "multiqc_picard_quality_score_distribution.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54", - "multiqc_seqfu_mqc.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8", - "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_MeanQualityByCycle_histogram_1.txt:md5,c7edfc271ab59ecedad0ab046afd3563", - "picard_QualityScoreDistribution_histogram.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54", - "picard_alignment_readlength_plot.txt:md5,c1519319c4942162b05e6225fea10569", - "picard_alignment_summary.txt:md5,49f5c0d2cf21a13d5f363cb42cf3790e", - "picard_base_distribution_by_cycle__Adenine.txt:md5,466a14fc9c09f9f4de02a00e8763cd2a", - "picard_base_distribution_by_cycle__Cytosine.txt:md5,d5854c22df4ac60b8c47c4002d975fe9", - "picard_base_distribution_by_cycle__Guanine.txt:md5,c27b5aa2b90397b1302b880dff3ec958", - "picard_base_distribution_by_cycle__Thymine.txt:md5,6f2a3e9d03f17a93c69476607a1a580d", - "picard_base_distribution_by_cycle__Undetermined.txt:md5,33b70326d8f888ac5a3d99b85f365e43", - "picard_quality_by_cycle.txt:md5,0aa028d69d8bb02f0a2bcd0ed08f4235", - "picard_quality_score_distribution.txt:md5,a2882ff59902dc95830ed4bdb955561a", - "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40", - "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", - "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6", - "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a", - "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc", - "Sample23_03_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027", - "SampleA_02_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775", - "SampleA_02_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27", - "Undetermined_05_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e", - "Undetermined_05_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d", - "sampletest_04_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377", - "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2" - ], - [ - "Sample1_01.bam:md5,d06ccfde49cc474faebcab2ebf71b324", - "Sample23_03.bam:md5,5ff9f554c6255fd07d3841c6616c5031", - "SampleA_02.bam:md5,250d0031520e59ee59a7112ab1ea32e1", - "Undetermined_05.bam:md5,8fcc158f1e0736b366152d5e187644ca", - "sampletest_04.bam:md5,f80371e37421d97499b3bfd55221ed00" + "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml" ], + "No stable content", + "No BAM files", "No warnings" ], - "timestamp": "2026-03-12T16:33:49.096054029", + "timestamp": "2026-03-16T09:40:34.164513363", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -995,11 +34,9 @@ ], "No stable content", "No BAM files", - [ - "WARN: No samples with rundir found, skipping RUNDIRPARSER" - ] + "No warnings" ], - "timestamp": "2026-03-13T16:00:47.718722732", + "timestamp": "2026-03-16T09:40:03.529857594", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -1007,42 +44,19 @@ }, "NovaSeq6000 data test - fq_lint force success": { "content": [ - 2, + 0, { - "BWAMEM2_INDEX": { - "bwamem2": "2.2.1" - }, - "SAMTOOLS_FAIDX": { - "samtools": "1.22.1" - } + }, [ - "bwamem2_index", - "bwamem2_index/bwamem2", - "bwamem2_index/bwamem2/genome.fa.0123", - "bwamem2_index/bwamem2/genome.fa.amb", - "bwamem2_index/bwamem2/genome.fa.ann", - "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64", - "bwamem2_index/bwamem2/genome.fa.pac", "pipeline_info", - "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", - "samtools_faidx", - "samtools_faidx/genome.fa.fai" - ], - [ - "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3", - "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f", - "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b", - "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e", - "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc", - "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b" + "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml" ], + "No stable content", "No BAM files", - [ - "WARN: No samples with rundir found, skipping RUNDIRPARSER" - ] + "No warnings" ], - "timestamp": "2026-03-12T14:52:51.835298832", + "timestamp": "2026-03-16T09:39:43.387936168", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf index 22069afb..dad4d00a 100644 --- a/workflows/seqinspector.nf +++ b/workflows/seqinspector.nf @@ -7,6 +7,7 @@ // modules include { BWAMEM2_MEM } from '../modules/nf-core/bwamem2/mem' +include { CHECKQC } from '../modules/nf-core/checkqc' include { FASTP } from '../modules/nf-core/fastp' include { FASTQC } from '../modules/nf-core/fastqc' include { FASTQE } from '../modules/nf-core/fastqe' @@ -18,7 +19,6 @@ include { RUNDIRPARSER } from '../modules/local/rundirparser' include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index' include { SEQFU_STATS } from '../modules/nf-core/seqfu/stats' include { SEQTK_SAMPLE } from '../modules/nf-core/seqtk/sample' -include { CHECKQC } from '../modules/nf-core/checkqc/main' include { TOULLIGQC } from '../modules/nf-core/toulligqc' // subworkflow @@ -153,10 +153,11 @@ workflow SEQINSPECTOR { ch_rundir.ifEmpty { log.warn("No samples with rundir found, skipping CHECKQC") } - CHECKQC(ch_rundir, - checkqc_config - ? file(checkqc_config, checkIfExists: true) - : [] + CHECKQC( + ch_rundir, + checkqc_config + ? file(checkqc_config, checkIfExists: true) + : [], ) ch_multiqc_files = ch_multiqc_files.mix(CHECKQC.out.report) From d1f109d1993539e92e6578329dbc2a9edb9621ed Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Mon, 16 Mar 2026 10:05:25 +0100 Subject: [PATCH 23/25] snapshots --- conf/test.config | 4 + docs/output.md | 4 +- nextflow_schema.json | 14 +-- tests/NovaSeq6000.nf.test | 11 +-- tests/NovaSeq6000.nf.test.snap | 80 +++------------- tests/nextflow.config | 7 -- tests/tools_checkqc.nf.test | 8 ++ tests/tools_checkqc.nf.test.snap | 153 +++++++++++++++++++++++++++++++ 8 files changed, 185 insertions(+), 96 deletions(-) diff --git a/conf/test.config b/conf/test.config index a924ce3d..3b0013cd 100644 --- a/conf/test.config +++ b/conf/test.config @@ -28,4 +28,8 @@ process { memory: '8.GB', time: '1.h' ] + + withName: CHECKQC { + ext.args = '--use-closest-read-length' + } } diff --git a/docs/output.md b/docs/output.md index e447b99f..3160aa00 100644 --- a/docs/output.md +++ b/docs/output.md @@ -13,11 +13,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and can generat - [Seqtk](#seqtk) - Subsample a specific number of reads per sample - [FastQC](#fastqc) - Raw read QC - [FASTQE](#fastqe) - Raw read QC - <<<<<<< HEAD -- # [CheckQC](#checkqc) - QC of an Illumina run +- [CheckQC](#checkqc) - QC of an Illumina run - [Kraken2](#kraken2) - Phylogenetic assignment of reads using k-mers - [Krona](#krona) - Interactive visualization of Kraken2 results - > > > > > > > dev - [SeqFu Stats](#seqfu-stats) - Statistics for FASTA or FASTQ files - [FastQ Screen](#fastq-screen) - Mapping against a set of references for basic contamination QC - [BWA-MEM2_INDEX](#bwamem2_index) - Create BWA-MEM2 index of a chosen reference genome OR use pre-built index diff --git a/nextflow_schema.json b/nextflow_schema.json index b5ab8219..dc82098c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -86,6 +86,12 @@ "description": "Whether to continue with the pipeline if linting fails for a single sample.", "help_text": "If set to true, the pipeline will continue with the remaining samples if linting fails for a single sample. If set to false, the pipeline will terminate if linting fails for a single sample.", "fa_icon": "fas fa-window-close " + }, + "checkqc_config": { + "type": "string", + "format": "file-path", + "description": "Path to custom CheckQC config", + "fa_icon": "fas fa-cog" } } }, @@ -388,11 +394,5 @@ { "$ref": "#/$defs/generic_options" } - ], - "properties": { - "checkqc_config": { - "type": "string", - "description": "Path to custom CheckQC config" - } - } + ] } diff --git a/tests/NovaSeq6000.nf.test b/tests/NovaSeq6000.nf.test index 4f07fdda..0531aea5 100644 --- a/tests/NovaSeq6000.nf.test +++ b/tests/NovaSeq6000.nf.test @@ -9,9 +9,7 @@ nextflow_pipeline { def test_scenario = [ [ name: "NovaSeq6000 data test", - params: [ - tools: 'checkqc', - ], + params: [], snapshot: 'stderr,stdout' ], [ @@ -46,13 +44,6 @@ nextflow_pipeline { tools: 'fastqc', ] ], - [ - name: "NovaSeq6000 data test - Checkqc with config", - params: [ - checkqc_config: "$projectDir/assets/checkqc_config.yml", - tools: 'checkqc', - ] - ], ] // Generate tests for each scenario diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap index 32cc7952..c8cd55cc 100644 --- a/tests/NovaSeq6000.nf.test.snap +++ b/tests/NovaSeq6000.nf.test.snap @@ -1046,7 +1046,7 @@ }, "NovaSeq6000 data test": { "content": [ - 44, + 43, { "BWAMEM2_INDEX": { "bwamem2": "2.2.1" @@ -1055,9 +1055,6 @@ "bwamem2": "2.2.1", "samtools": "1.22.1" }, - "CHECKQC": { - "checkqc": "4.1.0" - }, "FASTQC": { "fastqc": "0.12.1" }, @@ -1075,10 +1072,10 @@ "Python": "3.13.2" }, "SAMTOOLS_FAIDX": { - "samtools": "1.22.1" + "samtools": "1.23" }, "SAMTOOLS_INDEX": { - "samtools": "1.22.1" + "samtools": "1.23" }, "SEQFU_STATS": { "seqfu": "1.22.3" @@ -1103,8 +1100,6 @@ "bwamem2_mem/Undetermined_05.bam.bai", "bwamem2_mem/sampletest_04.bam", "bwamem2_mem/sampletest_04.bam.bai", - "checkqc", - "checkqc/checkqc_report.json", "fastqc", "fastqc/Sample1_01_fastqc.html", "fastqc/Sample1_01_fastqc.zip", @@ -1141,7 +1136,6 @@ "multiqc", "multiqc/global_report", "multiqc/global_report/multiqc_data", - "multiqc/global_report/multiqc_data/checkqc_reads-per-sample-plot.txt", "multiqc/global_report/multiqc_data/fastq_screen_plot.txt", "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt", "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt", @@ -1157,7 +1151,6 @@ "multiqc/global_report/multiqc_data/llms-full.txt", "multiqc/global_report/multiqc_data/multiqc.log", "multiqc/global_report/multiqc_data/multiqc.parquet", - "multiqc/global_report/multiqc_data/multiqc_checkqc.txt", "multiqc/global_report/multiqc_data/multiqc_citations.txt", "multiqc/global_report/multiqc_data/multiqc_data.json", "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt", @@ -1186,8 +1179,6 @@ "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_plots", "multiqc/global_report/multiqc_plots/pdf", - "multiqc/global_report/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", - "multiqc/global_report/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", @@ -1215,8 +1206,6 @@ "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf", "multiqc/global_report/multiqc_plots/png", - "multiqc/global_report/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", - "multiqc/global_report/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png", "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png", @@ -1244,8 +1233,6 @@ "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png", "multiqc/global_report/multiqc_plots/svg", - "multiqc/global_report/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", - "multiqc/global_report/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg", "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg", @@ -1276,7 +1263,6 @@ "multiqc/group_reports", "multiqc/group_reports/group1", "multiqc/group_reports/group1/multiqc_data", - "multiqc/group_reports/group1/multiqc_data/checkqc_reads-per-sample-plot.txt", "multiqc/group_reports/group1/multiqc_data/fastq_screen_plot.txt", "multiqc/group_reports/group1/multiqc_data/fastqc-status-check-heatmap.txt", "multiqc/group_reports/group1/multiqc_data/fastqc_overrepresented_sequences_plot.txt", @@ -1292,7 +1278,6 @@ "multiqc/group_reports/group1/multiqc_data/llms-full.txt", "multiqc/group_reports/group1/multiqc_data/multiqc.log", "multiqc/group_reports/group1/multiqc_data/multiqc.parquet", - "multiqc/group_reports/group1/multiqc_data/multiqc_checkqc.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_data.json", "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt", @@ -1321,8 +1306,6 @@ "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/group1/multiqc_plots", "multiqc/group_reports/group1/multiqc_plots/pdf", - "multiqc/group_reports/group1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", - "multiqc/group_reports/group1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", @@ -1350,8 +1333,6 @@ "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu_mqc.pdf", "multiqc/group_reports/group1/multiqc_plots/png", - "multiqc/group_reports/group1/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", - "multiqc/group_reports/group1/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png", "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png", "multiqc/group_reports/group1/multiqc_plots/png/fastqc-status-check-heatmap.png", @@ -1379,8 +1360,6 @@ "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/group1/multiqc_plots/png/seqfu_mqc.png", "multiqc/group_reports/group1/multiqc_plots/svg", - "multiqc/group_reports/group1/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", - "multiqc/group_reports/group1/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastqc-status-check-heatmap.svg", @@ -1410,7 +1389,6 @@ "multiqc/group_reports/group1/multiqc_report.html", "multiqc/group_reports/group2", "multiqc/group_reports/group2/multiqc_data", - "multiqc/group_reports/group2/multiqc_data/checkqc_reads-per-sample-plot.txt", "multiqc/group_reports/group2/multiqc_data/fastq_screen_plot.txt", "multiqc/group_reports/group2/multiqc_data/fastqc-status-check-heatmap.txt", "multiqc/group_reports/group2/multiqc_data/fastqc_overrepresented_sequences_plot.txt", @@ -1426,7 +1404,6 @@ "multiqc/group_reports/group2/multiqc_data/llms-full.txt", "multiqc/group_reports/group2/multiqc_data/multiqc.log", "multiqc/group_reports/group2/multiqc_data/multiqc.parquet", - "multiqc/group_reports/group2/multiqc_data/multiqc_checkqc.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_data.json", "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt", @@ -1455,8 +1432,6 @@ "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/group2/multiqc_plots", "multiqc/group_reports/group2/multiqc_plots/pdf", - "multiqc/group_reports/group2/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", - "multiqc/group_reports/group2/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-pct.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", @@ -1484,8 +1459,6 @@ "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu_mqc.pdf", "multiqc/group_reports/group2/multiqc_plots/png", - "multiqc/group_reports/group2/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", - "multiqc/group_reports/group2/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png", "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png", "multiqc/group_reports/group2/multiqc_plots/png/fastqc-status-check-heatmap.png", @@ -1513,8 +1486,6 @@ "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/group2/multiqc_plots/png/seqfu_mqc.png", "multiqc/group_reports/group2/multiqc_plots/svg", - "multiqc/group_reports/group2/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", - "multiqc/group_reports/group2/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastqc-status-check-heatmap.svg", @@ -1544,7 +1515,6 @@ "multiqc/group_reports/group2/multiqc_report.html", "multiqc/group_reports/lane1", "multiqc/group_reports/lane1/multiqc_data", - "multiqc/group_reports/lane1/multiqc_data/checkqc_reads-per-sample-plot.txt", "multiqc/group_reports/lane1/multiqc_data/fastq_screen_plot.txt", "multiqc/group_reports/lane1/multiqc_data/fastqc-status-check-heatmap.txt", "multiqc/group_reports/lane1/multiqc_data/fastqc_overrepresented_sequences_plot.txt", @@ -1560,7 +1530,6 @@ "multiqc/group_reports/lane1/multiqc_data/llms-full.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc.log", "multiqc/group_reports/lane1/multiqc_data/multiqc.parquet", - "multiqc/group_reports/lane1/multiqc_data/multiqc_checkqc.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_data.json", "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt", @@ -1589,8 +1558,6 @@ "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/lane1/multiqc_plots", "multiqc/group_reports/lane1/multiqc_plots/pdf", - "multiqc/group_reports/lane1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", - "multiqc/group_reports/lane1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", @@ -1618,8 +1585,6 @@ "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu_mqc.pdf", "multiqc/group_reports/lane1/multiqc_plots/png", - "multiqc/group_reports/lane1/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", - "multiqc/group_reports/lane1/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastqc-status-check-heatmap.png", @@ -1647,8 +1612,6 @@ "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/lane1/multiqc_plots/png/seqfu_mqc.png", "multiqc/group_reports/lane1/multiqc_plots/svg", - "multiqc/group_reports/lane1/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", - "multiqc/group_reports/lane1/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc-status-check-heatmap.svg", @@ -1678,7 +1641,6 @@ "multiqc/group_reports/lane1/multiqc_report.html", "multiqc/group_reports/test", "multiqc/group_reports/test/multiqc_data", - "multiqc/group_reports/test/multiqc_data/checkqc_reads-per-sample-plot.txt", "multiqc/group_reports/test/multiqc_data/fastq_screen_plot.txt", "multiqc/group_reports/test/multiqc_data/fastqc-status-check-heatmap.txt", "multiqc/group_reports/test/multiqc_data/fastqc_overrepresented_sequences_plot.txt", @@ -1694,7 +1656,6 @@ "multiqc/group_reports/test/multiqc_data/llms-full.txt", "multiqc/group_reports/test/multiqc_data/multiqc.log", "multiqc/group_reports/test/multiqc_data/multiqc.parquet", - "multiqc/group_reports/test/multiqc_data/multiqc_checkqc.txt", "multiqc/group_reports/test/multiqc_data/multiqc_citations.txt", "multiqc/group_reports/test/multiqc_data/multiqc_data.json", "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt", @@ -1723,8 +1684,6 @@ "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/test/multiqc_plots", "multiqc/group_reports/test/multiqc_plots/pdf", - "multiqc/group_reports/test/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", - "multiqc/group_reports/test/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", @@ -1752,8 +1711,6 @@ "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/seqfu_mqc.pdf", "multiqc/group_reports/test/multiqc_plots/png", - "multiqc/group_reports/test/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", - "multiqc/group_reports/test/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png", "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png", "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png", "multiqc/group_reports/test/multiqc_plots/png/fastqc-status-check-heatmap.png", @@ -1781,8 +1738,6 @@ "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/test/multiqc_plots/png/seqfu_mqc.png", "multiqc/group_reports/test/multiqc_plots/svg", - "multiqc/group_reports/test/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg", - "multiqc/group_reports/test/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastqc-status-check-heatmap.svg", @@ -1875,7 +1830,6 @@ "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b", "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e", "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc", - "checkqc_report.json:md5,8245b6a8b8e0e2d247cb7a151d53612f", "Sample1_01_screen.png:md5,562256290643b51e4374c2225a15f463", "Sample1_01_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28", "Sample23_03_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab", @@ -1886,7 +1840,6 @@ "Undetermined_05_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28", "sampletest_04_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e", "sampletest_04_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28", - "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", "fastq_screen_plot.txt:md5,990122d48fa4c1a170107a1ba034e4cf", "fastqc-status-check-heatmap.txt:md5,7a64380ec42aac56949a2d9a4176d4d9", "fastqc_overrepresented_sequences_plot.txt:md5,c7908980f1dba22b45cf6de14a66a686", @@ -1898,8 +1851,7 @@ "fastqc_sequence_counts_plot.txt:md5,d8ab86dbfce0c740f4a66a080803a0b9", "fastqc_sequence_duplication_levels_plot.txt:md5,f86012b3074d697c9a2b3bd67a074288", "fastqc_sequence_length_distribution_plot.txt:md5,9d4fd245e8e1d5baa473a8bdffcd3e38", - "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", - "multiqc_citations.txt:md5,50a90ac0283d35a2e474089c1027baef", + "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,62240561100f78af37e7e2438cb58f90", "multiqc_fastqc.txt:md5,23b698f1e957a26f49a9ad9bbdece908", "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7", @@ -1921,7 +1873,6 @@ "picard_base_distribution_by_cycle__Undetermined.txt:md5,8aafe701b59b4e70ccec86748c7d6eb3", "picard_quality_by_cycle.txt:md5,366ee22c93a11c1335f867020bb03da5", "picard_quality_score_distribution.txt:md5,17d6f490cb59e16a7ed4b04ffaa1a100", - "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", "fastq_screen_plot.txt:md5,db7c9231e756a6e5999399a7385e4687", "fastqc-status-check-heatmap.txt:md5,fc37eaf184877ac80b92001a7bf2fa81", "fastqc_overrepresented_sequences_plot.txt:md5,0693849fc324ddf580e2c5a4d910bb4f", @@ -1933,8 +1884,7 @@ "fastqc_sequence_counts_plot.txt:md5,42b26ad3758717659763c81852c4f197", "fastqc_sequence_duplication_levels_plot.txt:md5,818f13a5372bad79e54cd984758096c5", "fastqc_sequence_length_distribution_plot.txt:md5,98316a2607a889ae1e7e79a4f64cc740", - "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", - "multiqc_citations.txt:md5,50a90ac0283d35a2e474089c1027baef", + "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,024e1e7f9db3b0906c7aa0904229e176", "multiqc_fastqc.txt:md5,3407d8f06117a65efce4c70f19e91dd1", "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7", @@ -1956,7 +1906,6 @@ "picard_base_distribution_by_cycle__Undetermined.txt:md5,0ed7f750b500e7c5387ea5309e1ef467", "picard_quality_by_cycle.txt:md5,fe4e6ab1c849a4f833eae9a8554ea432", "picard_quality_score_distribution.txt:md5,c0864f8a1269d8ffd7a51abb6bd3ca2e", - "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", "fastq_screen_plot.txt:md5,4def6c6a888afe487ab6ebef3ba8a133", "fastqc-status-check-heatmap.txt:md5,61857d2c45cf0c080348047aa34e7525", "fastqc_overrepresented_sequences_plot.txt:md5,7949c64cc6cef77f29349a188fc09656", @@ -1968,8 +1917,7 @@ "fastqc_sequence_counts_plot.txt:md5,f4341795bdeba588248a74a095a97f8d", "fastqc_sequence_duplication_levels_plot.txt:md5,8fc995cb2192a2926eee242681bc3af6", "fastqc_sequence_length_distribution_plot.txt:md5,4513e22583677a4d6167b9094242eb0b", - "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", - "multiqc_citations.txt:md5,50a90ac0283d35a2e474089c1027baef", + "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,fd3074930c72b666f201ae71fa27744b", "multiqc_fastqc.txt:md5,98111f17d1899cad6379e4e56ed11c53", "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7", @@ -1991,7 +1939,6 @@ "picard_base_distribution_by_cycle__Undetermined.txt:md5,0f2fd628631d42ed5e6a1db22578daaa", "picard_quality_by_cycle.txt:md5,3c34ae2bd2442a816577b1a794add2d6", "picard_quality_score_distribution.txt:md5,0d58c59eac2952e6f71cefc35d4c4477", - "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", "fastq_screen_plot.txt:md5,5abb5b9ed2c976f0ad83216ca3186201", "fastqc-status-check-heatmap.txt:md5,323d6082b73ddb6ee33385f5ea4301c1", "fastqc_overrepresented_sequences_plot.txt:md5,4e71d8913d40eb06db0f18d74ce6898f", @@ -2003,8 +1950,7 @@ "fastqc_sequence_counts_plot.txt:md5,36c68522023b8d536c9362403bf03c48", "fastqc_sequence_duplication_levels_plot.txt:md5,9ff0df466790d971b3c7ef838efc0f4f", "fastqc_sequence_length_distribution_plot.txt:md5,9fda632b92e3453f11cd0226484fce8e", - "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", - "multiqc_citations.txt:md5,50a90ac0283d35a2e474089c1027baef", + "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272", "multiqc_fastqc.txt:md5,396b4cc0466a6642ec8b954237c42263", "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7", @@ -2026,7 +1972,6 @@ "picard_base_distribution_by_cycle__Undetermined.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6", "picard_quality_by_cycle.txt:md5,7cb705007bc97da8c0da7d93201e6975", "picard_quality_score_distribution.txt:md5,47d684abae0a8f4f09df43e91d54fb9a", - "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167", "fastq_screen_plot.txt:md5,82ceb9f2109f865d6d1b943441c09550", "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1", "fastqc_overrepresented_sequences_plot.txt:md5,8e83abdbe7362e64d63339ee31ab3361", @@ -2038,8 +1983,7 @@ "fastqc_sequence_counts_plot.txt:md5,6e5804f553f656cffb02f927015d1026", "fastqc_sequence_duplication_levels_plot.txt:md5,fbe41935ea2e2faf7104393b476e5ac5", "fastqc_sequence_length_distribution_plot.txt:md5,e77dc4ab73252c2e09c7452c3b8e8ab3", - "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902", - "multiqc_citations.txt:md5,50a90ac0283d35a2e474089c1027baef", + "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2", "multiqc_fastqc.txt:md5,95c8ffb23baafec625aeb600047515ae", "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7", @@ -2095,7 +2039,6 @@ "Input/output options", " input : https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/NovaSeq6000/samplesheet.csv", " outdir : [PATH]/tests/[NFT_HASH]/output", - " tools : checkqc", "Reference genome options", " genome : R64-1-1", " fasta : s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa", @@ -2121,7 +2064,7 @@ "* Software dependencies", " https://github.com/nf-core/seqinspector/blob/master/CITATIONS.md", "Extra informations", - " Tools selected to be run : checkqc,fastqc,fastqscreen,fq_lint,picard_collectmultiplemetrics,rundirparser,seqfu_stats", + " Tools selected to be run : fastqc,fastqscreen,fq_lint,picard_collectmultiplemetrics,rundirparser,seqfu_stats", "------------------------------------------------------", "-[nf-core/seqinspector] Pipeline completed successfully-", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (Sample1_01)", @@ -2129,7 +2072,6 @@ "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (SampleA_02)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (Undetermined_05)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (sampletest_04)", - "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:CHECKQC (null)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQC (Sample1_01)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQC (Sample23_03)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQC (SampleA_02)", @@ -2166,10 +2108,10 @@ "[NXF_HASH] Submitted process > PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa)" ] ], - "timestamp": "2026-03-13T15:53:03.277536715", + "timestamp": "2026-03-16T09:53:50.996018165", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.2" + "nextflow": "25.10.4" } }, "NovaSeq6000 data test sample size": { diff --git a/tests/nextflow.config b/tests/nextflow.config index 1cbf2ff9..8d6d7704 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -6,10 +6,3 @@ // fixes S3 access issues on self-hosted runners aws.client.anonymous = true - - -process { - withName: CHECKQC { - ext.args = '--use-closest-read-length' - } -} diff --git a/tests/tools_checkqc.nf.test b/tests/tools_checkqc.nf.test index f7505885..07a1b024 100644 --- a/tests/tools_checkqc.nf.test +++ b/tests/tools_checkqc.nf.test @@ -13,6 +13,14 @@ nextflow_pipeline { tools: 'checkqc', tools_bundle: null ] + ], + [ + name: "NovaSeq6000 data test - checkqc with config", + params: [ + checkqc_config: "$projectDir/assets/checkqc_config.yml", + tools: 'checkqc', + tools_bundle: null + ] ] ] diff --git a/tests/tools_checkqc.nf.test.snap b/tests/tools_checkqc.nf.test.snap index 882a4dfa..85547f6e 100644 --- a/tests/tools_checkqc.nf.test.snap +++ b/tests/tools_checkqc.nf.test.snap @@ -151,5 +151,158 @@ "nf-test": "0.9.4", "nextflow": "25.10.4" } + }, + "NovaSeq6000 data test - checkqc with config": { + "content": [ + 6, + { + "CHECKQC": { + "checkqc": "4.1.0" + } + }, + [ + "checkqc", + "checkqc/checkqc_report.json", + "multiqc", + "multiqc/global_report", + "multiqc/global_report/multiqc_data", + "multiqc/global_report/multiqc_data/checkqc_reads-per-sample-plot.txt", + "multiqc/global_report/multiqc_data/llms-full.txt", + "multiqc/global_report/multiqc_data/multiqc.log", + "multiqc/global_report/multiqc_data/multiqc.parquet", + "multiqc/global_report/multiqc_data/multiqc_checkqc.txt", + "multiqc/global_report/multiqc_data/multiqc_citations.txt", + "multiqc/global_report/multiqc_data/multiqc_data.json", + "multiqc/global_report/multiqc_data/multiqc_software_versions.txt", + "multiqc/global_report/multiqc_data/multiqc_sources.txt", + "multiqc/global_report/multiqc_plots", + "multiqc/global_report/multiqc_plots/pdf", + "multiqc/global_report/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf", + "multiqc/global_report/multiqc_plots/png", + "multiqc/global_report/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png", + 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Garcia" Date: Mon, 16 Mar 2026 10:43:09 +0100 Subject: [PATCH 24/25] cleanup code --- conf/modules.config | 6 +- tests/NovaSeq6000.nf.test.snap | 1045 -------------------------------- 2 files changed, 5 insertions(+), 1046 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index da9ea722..6bf4a705 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -50,7 +50,11 @@ process { ] } - withName: 'TOULLIGQC' { + withName: CHECKQC { + tag = { "${run_dir.simpleName}" } + } + + withName: TOULLIGQC { ext.args = '' publishDir = [[ path: { "${params.outdir}/toulligqc" }, diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap index c8cd55cc..957fef17 100644 --- a/tests/NovaSeq6000.nf.test.snap +++ b/tests/NovaSeq6000.nf.test.snap @@ -1,1049 +1,4 @@ { - "NovaSeq6000 data test - Checkqc with config": { - "content": [ - 44, - { - "BWAMEM2_INDEX": { - "bwamem2": "2.2.1" - }, - "BWAMEM2_MEM": { - "bwamem2": "2.2.1", - "samtools": "1.22.1" - }, - "CHECKQC": { - 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"nextflow": "25.10.2" - } - }, "NovaSeq6000 data test": { "content": [ 43, From 0346754e86c0e6a38baba49e36ce79445897de9a Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Mon, 16 Mar 2026 10:48:26 +0100 Subject: [PATCH 25/25] restore patch --- modules.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules.json b/modules.json index 2bae9f07..8ef26bfa 100644 --- a/modules.json +++ b/modules.json @@ -38,7 +38,8 @@ "fastqscreen/fastqscreen": { "branch": "master", "git_sha": "ab2e7b785ee4fa6d108472862edbf983cea7db49", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff" }, "fq/lint": { "branch": "master",