From 7bc4502d58ab7251d14d894ab7ac1ff5cc198d5f Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Wed, 29 Oct 2025 19:56:41 +0000 Subject: [PATCH 01/16] bugfix: specify genome in cellranger multi to avoid probeset conflict, update tests accordingly --- assets/frna_probeset_subset.csv | 2 +- nextflow.config | 1 + subworkflows/local/align_cellrangermulti.nf | 24 ++++++++- tests/main_pipeline_cellrangermulti.nf.test | 57 +++++++++++++++++++++ 4 files changed, 82 insertions(+), 2 deletions(-) diff --git a/assets/frna_probeset_subset.csv b/assets/frna_probeset_subset.csv index 84772fa0..35800de8 100644 --- a/assets/frna_probeset_subset.csv +++ b/assets/frna_probeset_subset.csv @@ -1,7 +1,7 @@ #probe_set_file_format=2.0 #panel_name=Chromium Human Transcriptome Probe Set v1.0.1 #panel_type=predesigned -#reference_genome=gex_reference +#reference_genome=GRCh38 #reference_version=2020-A gene_id,probe_seq,probe_id,included,region ENSG00000000003,GGTGACACCACAACAATGCAACGTATTTTGGATCTTGTCTACTGCATGGC,ENSG00000000003|TSPAN6|8eab823,TRUE,spliced diff --git a/nextflow.config b/nextflow.config index a5c20ca7..940c6acf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -59,6 +59,7 @@ params { vdj_inner_enrichment_primers = null gex_barcode_sample_assignment = null cellranger_multi_barcodes = null + gex_reference = null // Template Boilerplate options diff --git a/subworkflows/local/align_cellrangermulti.nf b/subworkflows/local/align_cellrangermulti.nf index 3b12b02b..b199f388 100644 --- a/subworkflows/local/align_cellrangermulti.nf +++ b/subworkflows/local/align_cellrangermulti.nf @@ -136,11 +136,33 @@ workflow CELLRANGER_MULTI_ALIGN { // if ( !cellranger_gex_index ) { + // Validate that gex_reference is provided when required + if ( params.gex_frna_probe_set && !params.gex_reference ) { + error "Parameter 'gex_reference' is required when 'gex_frna_probe_set' is provided and 'cellranger_index' is not provided. The reference genome version must match the probeset reference." + } + + // Validate that gex_reference matches the probeset reference genome + if ( params.gex_frna_probe_set && params.gex_reference ) { + def probeset_file = file(params.gex_frna_probe_set) + if ( probeset_file.exists() ) { + def probeset_reference = null + probeset_file.readLines().each { line -> + if ( line.startsWith("#reference_genome=") ) { + probeset_reference = line.split("=")[1].trim() + } + } + if ( probeset_reference && probeset_reference != params.gex_reference ) { + error "Parameter 'gex_reference' (${params.gex_reference}) does not match the probeset reference genome (${probeset_reference}). Please ensure the reference genome version matches the probeset file." + } + } + } + // Make reference genome + def reference_name = params.gex_reference ?: "gex_reference" CELLRANGER_MKREF( ch_fasta, CELLRANGER_MKGTF.out.gtf, - "gex_reference" + reference_name ) ch_versions = ch_versions.mix(CELLRANGER_MKREF.out.versions) ch_cellranger_gex_index = CELLRANGER_MKREF.out.reference.ifEmpty { [] } diff --git a/tests/main_pipeline_cellrangermulti.nf.test b/tests/main_pipeline_cellrangermulti.nf.test index 2d6e6a4a..50e706f1 100644 --- a/tests/main_pipeline_cellrangermulti.nf.test +++ b/tests/main_pipeline_cellrangermulti.nf.test @@ -15,6 +15,7 @@ nextflow_pipeline { input = "${baseDir}/assets/cellrangermulti_samplesheet.csv" cellranger_multi_barcodes = "${baseDir}/assets/cellranger_barcodes_samplesheet.csv" gex_frna_probe_set = "${baseDir}/assets/frna_probeset_subset.csv" + gex_reference = "GRCh38" fb_reference = "${baseDir}/assets/fb_reference.csv" fasta = 'https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.14.fa.gz' gtf = 'https://ftp.ensembl.org/pub/release-110/gtf/homo_sapiens/Homo_sapiens.GRCh38.110.gtf.gz' @@ -83,5 +84,61 @@ nextflow_pipeline { } } + test("test-dataset_cellrangermulti_missing_gex_reference") { + + when { + params { + aligner = 'cellrangermulti' + outdir = "${outputDir}/results_cellrangermulti_missing_ref" + input = "${baseDir}/assets/cellrangermulti_samplesheet.csv" + cellranger_multi_barcodes = "${baseDir}/assets/cellranger_barcodes_samplesheet.csv" + gex_frna_probe_set = "${baseDir}/assets/frna_probeset_subset.csv" + fb_reference = "${baseDir}/assets/fb_reference.csv" + fasta = 'https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.14.fa.gz' + gtf = 'https://ftp.ensembl.org/pub/release-110/gtf/homo_sapiens/Homo_sapiens.GRCh38.110.gtf.gz' + protocol = 'auto' + skip_cellbender = true + // Note: gex_reference is intentionally NOT provided to test validation + } + } + + then { + // Should fail with validation error + assertAll( + {assert !workflow.success}, + {assert workflow.failed}, + {assert workflow.stdout.any { it.contains("Parameter 'gex_reference' is required when 'gex_frna_probe_set' is provided and 'cellranger_index' is not provided") } } + ) + } + } + + test("test-dataset_cellrangermulti_mismatched_gex_reference") { + + when { + params { + aligner = 'cellrangermulti' + outdir = "${outputDir}/results_cellrangermulti_mismatch" + input = "${baseDir}/assets/cellrangermulti_samplesheet.csv" + cellranger_multi_barcodes = "${baseDir}/assets/cellranger_barcodes_samplesheet.csv" + gex_frna_probe_set = "${baseDir}/assets/frna_probeset_subset.csv" + gex_reference = "GRCm39" // Intentionally wrong - probeset is GRCh38 + fb_reference = "${baseDir}/assets/fb_reference.csv" + fasta = 'https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.14.fa.gz' + gtf = 'https://ftp.ensembl.org/pub/release-110/gtf/homo_sapiens/Homo_sapiens.GRCh38.110.gtf.gz' + protocol = 'auto' + skip_cellbender = true + } + } + + then { + // Should fail with validation error + assertAll( + {assert !workflow.success}, + {assert workflow.failed}, + {assert workflow.stdout.any { it.contains("Parameter 'gex_reference' (GRCm39) does not match the probeset reference genome (GRCh38)") } } + ) + } + } + } From 81cf3becc5892861d90d1b5abaa85c05087254ec Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Thu, 30 Oct 2025 12:19:58 +0000 Subject: [PATCH 02/16] Update snapshots --- conf/modules.config | 1 + conf/test.config | 1 + conf/test_cellranger_multi.config | 1 + tests/main_pipeline_cellranger.nf.test.snap | 54 +--- .../main_pipeline_cellrangerarc.nf.test.snap | 42 +--- ...main_pipeline_cellrangermulti.nf.test.snap | 238 +++++++----------- tests/main_pipeline_kallisto.nf.test.snap | 39 +-- tests/main_pipeline_star.nf.test.snap | 48 +--- 8 files changed, 105 insertions(+), 319 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index b8e6112c..b467cdfd 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -69,6 +69,7 @@ process { enabled: false ] } + executor = 'slurm' } if(params.aligner == "cellranger") { diff --git a/conf/test.config b/conf/test.config index bdce2a62..f5ffd8af 100644 --- a/conf/test.config +++ b/conf/test.config @@ -16,6 +16,7 @@ process { memory: '15.GB', time: '1.h' ] + executor = 'slurm' } params { diff --git a/conf/test_cellranger_multi.config b/conf/test_cellranger_multi.config index 7684a49b..f04c9846 100644 --- a/conf/test_cellranger_multi.config +++ b/conf/test_cellranger_multi.config @@ -16,6 +16,7 @@ process { memory: '15.GB', time: '1.h' ] + executor = 'slurm' } // shared across profiles diff --git a/tests/main_pipeline_cellranger.nf.test.snap b/tests/main_pipeline_cellranger.nf.test.snap index a8d98e06..88579eca 100644 --- a/tests/main_pipeline_cellranger.nf.test.snap +++ b/tests/main_pipeline_cellranger.nf.test.snap @@ -262,56 +262,8 @@ "multiqc/multiqc_data/multiqc_sources.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/cellranger-count-stats-table.pdf", - "multiqc/multiqc_plots/pdf/cellranger-count-warnings-table.pdf", - "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", - "multiqc/multiqc_plots/pdf/mqc_cellranger_count_bc_knee.pdf", - "multiqc/multiqc_plots/pdf/mqc_cellranger_count_genesXcell.pdf", - "multiqc/multiqc_plots/pdf/mqc_cellranger_count_saturation.pdf", "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/cellranger-count-stats-table.png", - "multiqc/multiqc_plots/png/cellranger-count-warnings-table.png", - "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", - "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", - "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", - "multiqc/multiqc_plots/png/mqc_cellranger_count_bc_knee.png", - "multiqc/multiqc_plots/png/mqc_cellranger_count_genesXcell.png", - "multiqc/multiqc_plots/png/mqc_cellranger_count_saturation.png", "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/cellranger-count-stats-table.svg", - "multiqc/multiqc_plots/svg/cellranger-count-warnings-table.svg", - "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", - "multiqc/multiqc_plots/svg/mqc_cellranger_count_bc_knee.svg", - "multiqc/multiqc_plots/svg/mqc_cellranger_count_genesXcell.svg", - "multiqc/multiqc_plots/svg/mqc_cellranger_count_saturation.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml" @@ -380,9 +332,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-23T19:11:11.981129882" + "timestamp": "2025-10-30T14:05:45.462689417" } } \ No newline at end of file diff --git a/tests/main_pipeline_cellrangerarc.nf.test.snap b/tests/main_pipeline_cellrangerarc.nf.test.snap index d34baeef..0d9355e6 100644 --- a/tests/main_pipeline_cellrangerarc.nf.test.snap +++ b/tests/main_pipeline_cellrangerarc.nf.test.snap @@ -182,44 +182,8 @@ "multiqc/multiqc_data/multiqc_sources.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", - "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", - "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml" @@ -283,9 +247,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-23T19:10:33.168539516" + "timestamp": "2025-10-30T14:13:47.05850975" } } \ No newline at end of file diff --git a/tests/main_pipeline_cellrangermulti.nf.test.snap b/tests/main_pipeline_cellrangermulti.nf.test.snap index c0552368..b9ae680f 100644 --- a/tests/main_pipeline_cellrangermulti.nf.test.snap +++ b/tests/main_pipeline_cellrangermulti.nf.test.snap @@ -882,29 +882,29 @@ "cellrangermulti/mkgtf", "cellrangermulti/mkgtf/Homo_sapiens.GRCh38.dna.chromosome.14_genes.filtered.gtf", "cellrangermulti/mkref", - "cellrangermulti/mkref/gex_reference", - "cellrangermulti/mkref/gex_reference/fasta", - "cellrangermulti/mkref/gex_reference/fasta/genome.fa", - "cellrangermulti/mkref/gex_reference/fasta/genome.fa.fai", - "cellrangermulti/mkref/gex_reference/genes", - "cellrangermulti/mkref/gex_reference/genes/genes.gtf.gz", - "cellrangermulti/mkref/gex_reference/reference.json", - "cellrangermulti/mkref/gex_reference/star", - "cellrangermulti/mkref/gex_reference/star/Genome", - "cellrangermulti/mkref/gex_reference/star/SA", - "cellrangermulti/mkref/gex_reference/star/SAindex", - "cellrangermulti/mkref/gex_reference/star/chrLength.txt", - "cellrangermulti/mkref/gex_reference/star/chrName.txt", - "cellrangermulti/mkref/gex_reference/star/chrNameLength.txt", - "cellrangermulti/mkref/gex_reference/star/chrStart.txt", - "cellrangermulti/mkref/gex_reference/star/exonGeTrInfo.tab", - "cellrangermulti/mkref/gex_reference/star/exonInfo.tab", - "cellrangermulti/mkref/gex_reference/star/geneInfo.tab", - "cellrangermulti/mkref/gex_reference/star/genomeParameters.txt", - "cellrangermulti/mkref/gex_reference/star/sjdbInfo.txt", - "cellrangermulti/mkref/gex_reference/star/sjdbList.fromGTF.out.tab", - "cellrangermulti/mkref/gex_reference/star/sjdbList.out.tab", - "cellrangermulti/mkref/gex_reference/star/transcriptInfo.tab", + "cellrangermulti/mkref/GRCh38", + "cellrangermulti/mkref/GRCh38/fasta", + "cellrangermulti/mkref/GRCh38/fasta/genome.fa", + "cellrangermulti/mkref/GRCh38/fasta/genome.fa.fai", + "cellrangermulti/mkref/GRCh38/genes", + "cellrangermulti/mkref/GRCh38/genes/genes.gtf.gz", + "cellrangermulti/mkref/GRCh38/reference.json", + "cellrangermulti/mkref/GRCh38/star", + "cellrangermulti/mkref/GRCh38/star/Genome", + "cellrangermulti/mkref/GRCh38/star/SA", + "cellrangermulti/mkref/GRCh38/star/SAindex", + "cellrangermulti/mkref/GRCh38/star/chrLength.txt", + "cellrangermulti/mkref/GRCh38/star/chrName.txt", + "cellrangermulti/mkref/GRCh38/star/chrNameLength.txt", + "cellrangermulti/mkref/GRCh38/star/chrStart.txt", + "cellrangermulti/mkref/GRCh38/star/exonGeTrInfo.tab", + "cellrangermulti/mkref/GRCh38/star/exonInfo.tab", + "cellrangermulti/mkref/GRCh38/star/geneInfo.tab", + "cellrangermulti/mkref/GRCh38/star/genomeParameters.txt", + "cellrangermulti/mkref/GRCh38/star/sjdbInfo.txt", + "cellrangermulti/mkref/GRCh38/star/sjdbList.fromGTF.out.tab", + "cellrangermulti/mkref/GRCh38/star/sjdbList.out.tab", + "cellrangermulti/mkref/GRCh38/star/transcriptInfo.tab", "cellrangermulti/mkref/versions.yml", "cellrangermulti/mkvdjref", "cellrangermulti/mkvdjref/vdj_reference", @@ -1049,45 +1049,14 @@ "multiqc/multiqc_data/multiqc_sources.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", - "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", - "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/multiqc_report.html", + "parse", + "parse/cmo_files", + "parse/cmo_files/PBMC_10K_CMO_cmo.csv", + "parse/frna_files", + "parse/frna_files/4PLEX_HUMAN_frna.csv", "pipeline_info", "pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml" ], @@ -1180,54 +1149,54 @@ "transcriptInfo.tab:md5,a27c997fc57e0e26beebb57cde77d986", "versions.yml:md5,7f4adb1e901d6610e40f18a6b7c1dc89", "regions.fa:md5,b10393dbe8cc3a3a1ebb3636e7369fa2", - 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"multiqc_general_stats.txt:md5,322c16b924c49f393b100debd15d9e16" + "multiqc_general_stats.txt:md5,322c16b924c49f393b100debd15d9e16", + "PBMC_10K_CMO_cmo.csv:md5,91e024681f273d3581402dcc14f00483", + "4PLEX_HUMAN_frna.csv:md5,e45e051360b2f47d294339e9ef1e2842" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-23T19:20:06.700106749" + "timestamp": "2025-10-29T21:39:30.575568163" }, "test-dataset_cellrangermulti_aligner_rat": { "content": [ @@ -1720,42 +1691,12 @@ "multiqc/multiqc_data/multiqc_sources.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", - "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", - "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/multiqc_report.html", + "parse", + "parse/ocm_files", + "parse/ocm_files/10k_Wistar_Rat_ocm.csv", "pipeline_info", "pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml" ], @@ -1845,13 +1786,14 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,1e58df8383b865f8e10623140290b79e", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "multiqc_fastqc.txt:md5,026ffbdf07192dde0ece1347e249beaf", - "multiqc_general_stats.txt:md5,5496b8ed2f29e4210018b5a9f1b7dc18" + "multiqc_general_stats.txt:md5,5496b8ed2f29e4210018b5a9f1b7dc18", + "10k_Wistar_Rat_ocm.csv:md5,718be9212d239955d92d7d619d8111e6" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-23T19:49:18.434722245" + "timestamp": "2025-10-29T21:52:16.782453725" } } \ No newline at end of file diff --git a/tests/main_pipeline_kallisto.nf.test.snap b/tests/main_pipeline_kallisto.nf.test.snap index 6f688ef5..8031527f 100644 --- a/tests/main_pipeline_kallisto.nf.test.snap +++ b/tests/main_pipeline_kallisto.nf.test.snap @@ -120,41 +120,8 @@ "multiqc/multiqc_data/multiqc_sources.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", - "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", - "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml" @@ -209,9 +176,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-23T19:08:08.954153394" + "timestamp": "2025-10-30T14:16:21.07763953" } } \ No newline at end of file diff --git a/tests/main_pipeline_star.nf.test.snap b/tests/main_pipeline_star.nf.test.snap index a3097064..f39e5c8a 100644 --- a/tests/main_pipeline_star.nf.test.snap +++ b/tests/main_pipeline_star.nf.test.snap @@ -60,50 +60,8 @@ "multiqc/multiqc_data/star_summary_table.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", - "multiqc/multiqc_plots/pdf/star_alignment_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/star_alignment_plot-pct.pdf", - "multiqc/multiqc_plots/pdf/star_summary_table.pdf", "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", - "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", - "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", - "multiqc/multiqc_plots/png/star_alignment_plot-cnt.png", - "multiqc/multiqc_plots/png/star_alignment_plot-pct.png", - "multiqc/multiqc_plots/png/star_summary_table.png", "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", - "multiqc/multiqc_plots/svg/star_alignment_plot-cnt.svg", - "multiqc/multiqc_plots/svg/star_alignment_plot-pct.svg", - "multiqc/multiqc_plots/svg/star_summary_table.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", @@ -229,9 +187,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-23T19:11:01.001258" + "timestamp": "2025-10-30T14:22:04.512298845" } } \ No newline at end of file From 94c409fba7f363998862c84fc30fbc1bd2e8a209 Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Thu, 30 Oct 2025 15:21:27 +0000 Subject: [PATCH 03/16] revert slurm as test executor --- conf/modules.config | 1 - conf/test.config | 1 - conf/test_cellranger_multi.config | 1 - 3 files changed, 3 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index b467cdfd..b8e6112c 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -69,7 +69,6 @@ process { enabled: false ] } - executor = 'slurm' } if(params.aligner == "cellranger") { diff --git a/conf/test.config b/conf/test.config index f5ffd8af..bdce2a62 100644 --- a/conf/test.config +++ b/conf/test.config @@ -16,7 +16,6 @@ process { memory: '15.GB', time: '1.h' ] - executor = 'slurm' } params { diff --git a/conf/test_cellranger_multi.config b/conf/test_cellranger_multi.config index f04c9846..7684a49b 100644 --- a/conf/test_cellranger_multi.config +++ b/conf/test_cellranger_multi.config @@ -16,7 +16,6 @@ process { memory: '15.GB', time: '1.h' ] - executor = 'slurm' } // shared across profiles From cf402b7977f34394ee47953e1bdec293c4d26a9e Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Thu, 30 Oct 2025 16:13:44 +0000 Subject: [PATCH 04/16] Change gex_reference param to gex_reference_version. Update usage and schema --- conf/test_cellranger_multi.config | 1 + docs/usage.md | 4 +++- nextflow.config | 2 +- nextflow_schema.json | 4 ++++ subworkflows/local/align_cellrangermulti.nf | 16 ++++++++-------- tests/main_pipeline_cellrangermulti.nf.test | 10 +++++----- 6 files changed, 22 insertions(+), 15 deletions(-) diff --git a/conf/test_cellranger_multi.config b/conf/test_cellranger_multi.config index 7684a49b..d48df652 100644 --- a/conf/test_cellranger_multi.config +++ b/conf/test_cellranger_multi.config @@ -46,6 +46,7 @@ profiles { cellranger_multi_barcodes = "${projectDir}/assets/cellranger_barcodes_samplesheet.csv" gex_frna_probe_set = "${projectDir}/assets/frna_probeset_subset.csv" fb_reference = "${projectDir}/assets/fb_reference.csv" + gex_reference_version = "GRCh38" // Genome references fasta = 'https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.14.fa.gz' diff --git a/docs/usage.md b/docs/usage.md index e77d47bf..140b3b88 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -282,8 +282,10 @@ If you are using cellranger-multi you have to add the column _feature_type_ to i > When running cellranger multi, without any VDJ data, users can also skip VDJ automated ref building with: `--skip_cellrangermulti_vdjref`. -- When working with **FFPE data**, a prob set needs to be specified via `--gex_frna_probe_set`. This file is typically +- When working with **FFPE data**: + - a probe set needs to be specified via `--gex_frna_probe_set`. This file is typically [provided by 10x](https://www.10xgenomics.com/support/software/cell-ranger/downloads#probe-set-downloads). E.g. [testing ffpe probe set](../assets/frna_probeset_subset.csv). + - a GEX reference genome version (e.g. GRCh38, GRCm39) via `--gex_reference_version`. This **must** match the reference in the probe set, which can be found in the header. - When working with **Cell Multiplexing Oligos (CMOs)**, a reference file can to be provided via `--gex_cmo_set`. The default reference file, as well as a description how to write a custom one, are [available from the 10x documentation](https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-3p-multi#cmo-ref). By default, the Cell Ranger's default CMO-set. diff --git a/nextflow.config b/nextflow.config index 940c6acf..dadcd06f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -59,7 +59,7 @@ params { vdj_inner_enrichment_primers = null gex_barcode_sample_assignment = null cellranger_multi_barcodes = null - gex_reference = null + gex_reference_version = null // Template Boilerplate options diff --git a/nextflow_schema.json b/nextflow_schema.json index 80e18e3f..afc4d301 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -330,6 +330,10 @@ "exists": true, "description": "Provide a probe set for fixed RNA-seq profiling (used with FFPE samples). Please refer to the [10x documentation about probesets](https://www.10xgenomics.com/support/single-cell-gene-expression-flex/documentation/steps/probe-sets/chromium-frp-probe-set-files) for more details." }, + "gex_reference_version": { + "type": "string", + "description": "Reference version (e.g. GRCh38, GRCm39). Required if `gex_frna_probe_set` is used at `cellranger_index` is not set. Must match the genome version in the `gex_frna_probe_set` file." + }, "gex_target_panel": { "type": "string", "description": "Provide a panel description for targeted sequencing.", diff --git a/subworkflows/local/align_cellrangermulti.nf b/subworkflows/local/align_cellrangermulti.nf index b199f388..7161d504 100644 --- a/subworkflows/local/align_cellrangermulti.nf +++ b/subworkflows/local/align_cellrangermulti.nf @@ -136,13 +136,13 @@ workflow CELLRANGER_MULTI_ALIGN { // if ( !cellranger_gex_index ) { - // Validate that gex_reference is provided when required - if ( params.gex_frna_probe_set && !params.gex_reference ) { - error "Parameter 'gex_reference' is required when 'gex_frna_probe_set' is provided and 'cellranger_index' is not provided. The reference genome version must match the probeset reference." + // Validate that gex_reference_version is provided when required + if ( params.gex_frna_probe_set && !params.gex_reference_version ) { + error "Parameter 'gex_reference_version' is required when 'gex_frna_probe_set' is provided and 'cellranger_index' is not provided. The reference genome version must match the probeset reference." } - // Validate that gex_reference matches the probeset reference genome - if ( params.gex_frna_probe_set && params.gex_reference ) { + // Validate that gex_reference_version matches the probeset reference genome + if ( params.gex_frna_probe_set && params.gex_reference_version ) { def probeset_file = file(params.gex_frna_probe_set) if ( probeset_file.exists() ) { def probeset_reference = null @@ -151,14 +151,14 @@ workflow CELLRANGER_MULTI_ALIGN { probeset_reference = line.split("=")[1].trim() } } - if ( probeset_reference && probeset_reference != params.gex_reference ) { - error "Parameter 'gex_reference' (${params.gex_reference}) does not match the probeset reference genome (${probeset_reference}). Please ensure the reference genome version matches the probeset file." + if ( probeset_reference && probeset_reference != params.gex_reference_version ) { + error "Parameter 'gex_reference_version' (${params.gex_reference_version}) does not match the probeset reference genome (${probeset_reference}). Please ensure the reference genome version matches the probeset file." } } } // Make reference genome - def reference_name = params.gex_reference ?: "gex_reference" + def reference_name = params.gex_reference_version ?: "gex_reference_version" CELLRANGER_MKREF( ch_fasta, CELLRANGER_MKGTF.out.gtf, diff --git a/tests/main_pipeline_cellrangermulti.nf.test b/tests/main_pipeline_cellrangermulti.nf.test index 50e706f1..62d897ee 100644 --- a/tests/main_pipeline_cellrangermulti.nf.test +++ b/tests/main_pipeline_cellrangermulti.nf.test @@ -15,7 +15,7 @@ nextflow_pipeline { input = "${baseDir}/assets/cellrangermulti_samplesheet.csv" cellranger_multi_barcodes = "${baseDir}/assets/cellranger_barcodes_samplesheet.csv" gex_frna_probe_set = "${baseDir}/assets/frna_probeset_subset.csv" - gex_reference = "GRCh38" + gex_reference_version = "GRCh38" fb_reference = "${baseDir}/assets/fb_reference.csv" fasta = 'https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.14.fa.gz' gtf = 'https://ftp.ensembl.org/pub/release-110/gtf/homo_sapiens/Homo_sapiens.GRCh38.110.gtf.gz' @@ -98,7 +98,7 @@ nextflow_pipeline { gtf = 'https://ftp.ensembl.org/pub/release-110/gtf/homo_sapiens/Homo_sapiens.GRCh38.110.gtf.gz' protocol = 'auto' skip_cellbender = true - // Note: gex_reference is intentionally NOT provided to test validation + // Note: gex_reference_version is intentionally NOT provided to test validation } } @@ -107,7 +107,7 @@ nextflow_pipeline { assertAll( {assert !workflow.success}, {assert workflow.failed}, - {assert workflow.stdout.any { it.contains("Parameter 'gex_reference' is required when 'gex_frna_probe_set' is provided and 'cellranger_index' is not provided") } } + {assert workflow.stdout.any { it.contains("Parameter 'gex_reference_version' is required when 'gex_frna_probe_set' is provided and 'cellranger_index' is not provided") } } ) } } @@ -121,7 +121,7 @@ nextflow_pipeline { input = "${baseDir}/assets/cellrangermulti_samplesheet.csv" cellranger_multi_barcodes = "${baseDir}/assets/cellranger_barcodes_samplesheet.csv" gex_frna_probe_set = "${baseDir}/assets/frna_probeset_subset.csv" - gex_reference = "GRCm39" // Intentionally wrong - probeset is GRCh38 + gex_reference_version = "GRCm39" // Intentionally wrong - probeset is GRCh38 fb_reference = "${baseDir}/assets/fb_reference.csv" fasta = 'https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.14.fa.gz' gtf = 'https://ftp.ensembl.org/pub/release-110/gtf/homo_sapiens/Homo_sapiens.GRCh38.110.gtf.gz' @@ -135,7 +135,7 @@ nextflow_pipeline { assertAll( {assert !workflow.success}, {assert workflow.failed}, - {assert workflow.stdout.any { it.contains("Parameter 'gex_reference' (GRCm39) does not match the probeset reference genome (GRCh38)") } } + {assert workflow.stdout.any { it.contains("Parameter 'gex_reference_version' (GRCm39) does not match the probeset reference genome (GRCh38)") } } ) } } From 709707d3843abcc9ceb8f068a55fcce714743759 Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Thu, 30 Oct 2025 16:18:45 +0000 Subject: [PATCH 05/16] Update CHANGELOG.md --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d181a907..a326af06 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,6 +29,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Template update for nf-core/tools v3.2.1 ([#466](https://github.com/nf-core/scrnaseq/pull/466)) - Template update for nf-core/tools v3.3.2 ([#474](https://github.com/nf-core/scrnaseq/pull/474)) +### Fixes +- Fix [#375](https://github.com/nf-core/scrnaseq/issues/375): mismatch between index and probeset when cellranger multi is used without a prebuilt index and an FFPE probeset is passed ([#502](https://github.com/nf-core/scrnaseq/pull/502)) + ## v4.0.0 - 2025-03-10 - Move `txp2gene` to `reference_genome_options` in schema as it is required by `kb_python` and `alevin` ([434](https://github.com/nf-core/scrnaseq/pull/434)) From 4f00f8fe27157731415b4f6c2b99f8007e2832b2 Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Thu, 30 Oct 2025 16:21:26 +0000 Subject: [PATCH 06/16] pre-commit fixes --- CHANGELOG.md | 1 + docs/usage.md | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a326af06..1d93e987 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Template update for nf-core/tools v3.3.2 ([#474](https://github.com/nf-core/scrnaseq/pull/474)) ### Fixes + - Fix [#375](https://github.com/nf-core/scrnaseq/issues/375): mismatch between index and probeset when cellranger multi is used without a prebuilt index and an FFPE probeset is passed ([#502](https://github.com/nf-core/scrnaseq/pull/502)) ## v4.0.0 - 2025-03-10 diff --git a/docs/usage.md b/docs/usage.md index 140b3b88..d243b2e8 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -283,9 +283,9 @@ If you are using cellranger-multi you have to add the column _feature_type_ to i > When running cellranger multi, without any VDJ data, users can also skip VDJ automated ref building with: `--skip_cellrangermulti_vdjref`. - When working with **FFPE data**: - - a probe set needs to be specified via `--gex_frna_probe_set`. This file is typically - [provided by 10x](https://www.10xgenomics.com/support/software/cell-ranger/downloads#probe-set-downloads). E.g. [testing ffpe probe set](../assets/frna_probeset_subset.csv). - - a GEX reference genome version (e.g. GRCh38, GRCm39) via `--gex_reference_version`. This **must** match the reference in the probe set, which can be found in the header. + - a probe set needs to be specified via `--gex_frna_probe_set`. This file is typically + [provided by 10x](https://www.10xgenomics.com/support/software/cell-ranger/downloads#probe-set-downloads). E.g. [testing ffpe probe set](../assets/frna_probeset_subset.csv). + - a GEX reference genome version (e.g. GRCh38, GRCm39) via `--gex_reference_version`. This **must** match the reference in the probe set, which can be found in the header. - When working with **Cell Multiplexing Oligos (CMOs)**, a reference file can to be provided via `--gex_cmo_set`. The default reference file, as well as a description how to write a custom one, are [available from the 10x documentation](https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-3p-multi#cmo-ref). By default, the Cell Ranger's default CMO-set. From 925e3293f8a9f56a81cd8473a6b75c4914c728a3 Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Thu, 30 Oct 2025 16:23:47 +0000 Subject: [PATCH 07/16] better usage instructions --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index d243b2e8..bd9b78e3 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -285,7 +285,7 @@ If you are using cellranger-multi you have to add the column _feature_type_ to i - When working with **FFPE data**: - a probe set needs to be specified via `--gex_frna_probe_set`. This file is typically [provided by 10x](https://www.10xgenomics.com/support/software/cell-ranger/downloads#probe-set-downloads). E.g. [testing ffpe probe set](../assets/frna_probeset_subset.csv). - - a GEX reference genome version (e.g. GRCh38, GRCm39) via `--gex_reference_version`. This **must** match the reference in the probe set, which can be found in the header. + - a GEX reference genome version (e.g. GRCh38, GRCm39) via `--gex_reference_version` must be specified unless a pre-built index is provided via `--cellranger_index`. This **must** match the reference in the probe set, which can be found in the header. - When working with **Cell Multiplexing Oligos (CMOs)**, a reference file can to be provided via `--gex_cmo_set`. The default reference file, as well as a description how to write a custom one, are [available from the 10x documentation](https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-3p-multi#cmo-ref). By default, the Cell Ranger's default CMO-set. From ad5a43659606270e58f085f90091293675a529b8 Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Thu, 30 Oct 2025 16:25:38 +0000 Subject: [PATCH 08/16] typo in schema --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index afc4d301..e48b8f9c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -332,7 +332,7 @@ }, "gex_reference_version": { "type": "string", - "description": "Reference version (e.g. GRCh38, GRCm39). Required if `gex_frna_probe_set` is used at `cellranger_index` is not set. Must match the genome version in the `gex_frna_probe_set` file." + "description": "Reference version (e.g. GRCh38, GRCm39). Required if `gex_frna_probe_set` is used and `cellranger_index` is not set. Must match the genome version in the `gex_frna_probe_set` file." }, "gex_target_panel": { "type": "string", From 63b66027d8da8dfdfe382d467147acf20738c6ad Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Thu, 30 Oct 2025 17:03:26 +0000 Subject: [PATCH 09/16] Revert "Update snapshots" This reverts commit 81cf3becc5892861d90d1b5abaa85c05087254ec. --- tests/main_pipeline_cellranger.nf.test.snap | 54 +++- .../main_pipeline_cellrangerarc.nf.test.snap | 42 +++- ...main_pipeline_cellrangermulti.nf.test.snap | 238 +++++++++++------- tests/main_pipeline_kallisto.nf.test.snap | 39 ++- tests/main_pipeline_star.nf.test.snap | 48 +++- 5 files changed, 319 insertions(+), 102 deletions(-) diff --git a/tests/main_pipeline_cellranger.nf.test.snap b/tests/main_pipeline_cellranger.nf.test.snap index 88579eca..a8d98e06 100644 --- a/tests/main_pipeline_cellranger.nf.test.snap +++ b/tests/main_pipeline_cellranger.nf.test.snap @@ -262,8 +262,56 @@ "multiqc/multiqc_data/multiqc_sources.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/cellranger-count-stats-table.pdf", + "multiqc/multiqc_plots/pdf/cellranger-count-warnings-table.pdf", + "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/multiqc_plots/pdf/mqc_cellranger_count_bc_knee.pdf", + "multiqc/multiqc_plots/pdf/mqc_cellranger_count_genesXcell.pdf", + "multiqc/multiqc_plots/pdf/mqc_cellranger_count_saturation.pdf", "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/cellranger-count-stats-table.png", + "multiqc/multiqc_plots/png/cellranger-count-warnings-table.png", + "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", + "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/multiqc_plots/png/mqc_cellranger_count_bc_knee.png", + "multiqc/multiqc_plots/png/mqc_cellranger_count_genesXcell.png", + "multiqc/multiqc_plots/png/mqc_cellranger_count_saturation.png", "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/cellranger-count-stats-table.svg", + "multiqc/multiqc_plots/svg/cellranger-count-warnings-table.svg", + "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_plots/svg/mqc_cellranger_count_bc_knee.svg", + "multiqc/multiqc_plots/svg/mqc_cellranger_count_genesXcell.svg", + "multiqc/multiqc_plots/svg/mqc_cellranger_count_saturation.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml" @@ -332,9 +380,9 @@ ] ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-10-30T14:05:45.462689417" + "timestamp": "2025-10-23T19:11:11.981129882" } } \ No newline at end of file diff --git a/tests/main_pipeline_cellrangerarc.nf.test.snap b/tests/main_pipeline_cellrangerarc.nf.test.snap index 0d9355e6..d34baeef 100644 --- a/tests/main_pipeline_cellrangerarc.nf.test.snap +++ b/tests/main_pipeline_cellrangerarc.nf.test.snap @@ -182,8 +182,44 @@ "multiqc/multiqc_data/multiqc_sources.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", + "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml" @@ -247,9 +283,9 @@ ] ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-10-30T14:13:47.05850975" + "timestamp": "2025-10-23T19:10:33.168539516" } } \ No newline at end of file diff --git a/tests/main_pipeline_cellrangermulti.nf.test.snap b/tests/main_pipeline_cellrangermulti.nf.test.snap index b9ae680f..c0552368 100644 --- a/tests/main_pipeline_cellrangermulti.nf.test.snap +++ b/tests/main_pipeline_cellrangermulti.nf.test.snap @@ -882,29 +882,29 @@ "cellrangermulti/mkgtf", "cellrangermulti/mkgtf/Homo_sapiens.GRCh38.dna.chromosome.14_genes.filtered.gtf", "cellrangermulti/mkref", - "cellrangermulti/mkref/GRCh38", - "cellrangermulti/mkref/GRCh38/fasta", - "cellrangermulti/mkref/GRCh38/fasta/genome.fa", - "cellrangermulti/mkref/GRCh38/fasta/genome.fa.fai", - "cellrangermulti/mkref/GRCh38/genes", - "cellrangermulti/mkref/GRCh38/genes/genes.gtf.gz", - "cellrangermulti/mkref/GRCh38/reference.json", - "cellrangermulti/mkref/GRCh38/star", - "cellrangermulti/mkref/GRCh38/star/Genome", - "cellrangermulti/mkref/GRCh38/star/SA", - "cellrangermulti/mkref/GRCh38/star/SAindex", - "cellrangermulti/mkref/GRCh38/star/chrLength.txt", - "cellrangermulti/mkref/GRCh38/star/chrName.txt", - "cellrangermulti/mkref/GRCh38/star/chrNameLength.txt", - "cellrangermulti/mkref/GRCh38/star/chrStart.txt", - "cellrangermulti/mkref/GRCh38/star/exonGeTrInfo.tab", - "cellrangermulti/mkref/GRCh38/star/exonInfo.tab", - "cellrangermulti/mkref/GRCh38/star/geneInfo.tab", - "cellrangermulti/mkref/GRCh38/star/genomeParameters.txt", - "cellrangermulti/mkref/GRCh38/star/sjdbInfo.txt", - "cellrangermulti/mkref/GRCh38/star/sjdbList.fromGTF.out.tab", - "cellrangermulti/mkref/GRCh38/star/sjdbList.out.tab", - "cellrangermulti/mkref/GRCh38/star/transcriptInfo.tab", + "cellrangermulti/mkref/gex_reference", + "cellrangermulti/mkref/gex_reference/fasta", + "cellrangermulti/mkref/gex_reference/fasta/genome.fa", + "cellrangermulti/mkref/gex_reference/fasta/genome.fa.fai", + "cellrangermulti/mkref/gex_reference/genes", + "cellrangermulti/mkref/gex_reference/genes/genes.gtf.gz", + "cellrangermulti/mkref/gex_reference/reference.json", + "cellrangermulti/mkref/gex_reference/star", + "cellrangermulti/mkref/gex_reference/star/Genome", + "cellrangermulti/mkref/gex_reference/star/SA", + "cellrangermulti/mkref/gex_reference/star/SAindex", + "cellrangermulti/mkref/gex_reference/star/chrLength.txt", + "cellrangermulti/mkref/gex_reference/star/chrName.txt", + "cellrangermulti/mkref/gex_reference/star/chrNameLength.txt", + "cellrangermulti/mkref/gex_reference/star/chrStart.txt", + "cellrangermulti/mkref/gex_reference/star/exonGeTrInfo.tab", + "cellrangermulti/mkref/gex_reference/star/exonInfo.tab", + "cellrangermulti/mkref/gex_reference/star/geneInfo.tab", + "cellrangermulti/mkref/gex_reference/star/genomeParameters.txt", + "cellrangermulti/mkref/gex_reference/star/sjdbInfo.txt", + "cellrangermulti/mkref/gex_reference/star/sjdbList.fromGTF.out.tab", + "cellrangermulti/mkref/gex_reference/star/sjdbList.out.tab", + "cellrangermulti/mkref/gex_reference/star/transcriptInfo.tab", "cellrangermulti/mkref/versions.yml", "cellrangermulti/mkvdjref", "cellrangermulti/mkvdjref/vdj_reference", @@ -1049,14 +1049,45 @@ "multiqc/multiqc_data/multiqc_sources.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", + "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/multiqc_report.html", - "parse", - "parse/cmo_files", - "parse/cmo_files/PBMC_10K_CMO_cmo.csv", - "parse/frna_files", - "parse/frna_files/4PLEX_HUMAN_frna.csv", "pipeline_info", "pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml" ], @@ -1149,54 +1180,54 @@ "transcriptInfo.tab:md5,a27c997fc57e0e26beebb57cde77d986", "versions.yml:md5,7f4adb1e901d6610e40f18a6b7c1dc89", "regions.fa:md5,b10393dbe8cc3a3a1ebb3636e7369fa2", - "4PLEX_HUMAN_raw_matrix.h5ad:md5,31d87238d9e0bdf3b1906ee6b27c2ee1", - "4PLEX_HUMAN_raw_matrix.sce.rds:md5,e6a1922ee9a1aa5bb822efa5b9fa7cc1", - "4PLEX_HUMAN_raw_matrix.seurat.rds:md5,a28f3e17b57097947d4f3307b9cfde37", - "Colorectal_BC3_filtered_matrix.h5ad:md5,1066aa4f5be50985c38d173612440201", - "Colorectal_BC3_filtered_matrix.sce.rds:md5,6498f0475336ac1b6820f84e9176666f", - "Colorectal_BC3_filtered_matrix.seurat.rds:md5,1f23959ab1cf3db5a10996b5772392c6", - "Colorectal_BC3_raw_matrix.h5ad:md5,41aca8cb40046a4ec8b5d712d8f9a3ec", - "Colorectal_BC3_raw_matrix.sce.rds:md5,c1e4d9cf93103834e3e427182390ee67", - "Colorectal_BC3_raw_matrix.seurat.rds:md5,25edd2a8fd47bfba5de6059e913a6f1e", - "Liver_BC1_filtered_matrix.h5ad:md5,1b0d29b7e89b99b1d7c56826764f9f73", - "Liver_BC1_filtered_matrix.sce.rds:md5,9dba3e2f037544ff4b0f7484e84363ef", - "Liver_BC1_filtered_matrix.seurat.rds:md5,2af4692cec1dacdef41434052c1a4798", - "Liver_BC1_raw_matrix.h5ad:md5,42c89b5516c06a6e2b12f766db378407", - "Liver_BC1_raw_matrix.sce.rds:md5,1a92091f471aebbb6c6a11a7672303e1", - "Liver_BC1_raw_matrix.seurat.rds:md5,096fb87736a9d8bda8fc955df0a7336c", - "Ovarian_BC2_filtered_matrix.h5ad:md5,7465aa7be4ba213373bcfa9f7e04c834", - "Ovarian_BC2_filtered_matrix.sce.rds:md5,251e58d365f38d9493da30ed70eb7a0e", - "Ovarian_BC2_filtered_matrix.seurat.rds:md5,0bb8f8b96d08f1cd583d0f600d1598d2", - "Ovarian_BC2_raw_matrix.h5ad:md5,6e27c9c5a68dc907b61ce1eae267b932", - "Ovarian_BC2_raw_matrix.sce.rds:md5,78125a38a7974a2823386341be33de56", - "Ovarian_BC2_raw_matrix.seurat.rds:md5,bb527b97fd7d24e5357284bfb61d9e96", - "PBMC_10K_filtered_matrix.h5ad:md5,8276afec9886898d24df77e0eb3836ec", - "PBMC_10K_filtered_matrix.sce.rds:md5,b0ac588b9c4f12285a287b0d44ecf247", - "PBMC_10K_filtered_matrix.seurat.rds:md5,7c8ab3039d8aba9573ff80e68664ee76", - "PBMC_10K_raw_matrix.h5ad:md5,037e55dd085c1bb27681a7357a14f229", - "PBMC_10K_raw_matrix.sce.rds:md5,e8f0e03cc061a6e4e960295297da6607", - "PBMC_10K_raw_matrix.seurat.rds:md5,dc5e624ad49ea9b75dc57cdf1bbb2fd2", - "PBMC_10K_CMO_raw_matrix.h5ad:md5,b50f62f66668d822b3765be631d29d1a", - "PBMC_10K_CMO_raw_matrix.sce.rds:md5,6124ebe15dd4b975b4186dea844f865d", - "PBMC_10K_CMO_raw_matrix.seurat.rds:md5,5dfe0a5da270af2d08601e574b426dc4", - "PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.h5ad:md5,f696f68bdab63de70671013b7a23d8e6", - "PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.sce.rds:md5,eb623c6b462690ccb9ece785f0cbd781", - "PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.seurat.rds:md5,87549352e83a54f9ea894c33e70c39c5", - "PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.h5ad:md5,679aeb89604f3f6d98e66326be302320", - "PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.sce.rds:md5,0a2d99fcadc0fd73b5fedbb42e61c6d3", - "PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.seurat.rds:md5,77c83357a846f32aa3b51d1523d4ce14", - "PBMC_10K_CMV_filtered_matrix.h5ad:md5,15e785837e2eda0aa7bb6aea3a6c9f05", - "PBMC_10K_CMV_filtered_matrix.sce.rds:md5,6fa01cf7d93bc5f86ec945700b9734a8", - "PBMC_10K_CMV_filtered_matrix.seurat.rds:md5,fb90082ae1af8e86feac5726930927f4", - "PBMC_10K_CMV_raw_matrix.h5ad:md5,41f07c811f3751a5a773ccdcfba2323a", - "PBMC_10K_CMV_raw_matrix.sce.rds:md5,2b53553609413dc95760c49577f87bca", - "PBMC_10K_CMV_raw_matrix.seurat.rds:md5,10e8fb1066e31d9d68e263f8b7fd13c4", - "Pancreas_BC4_filtered_matrix.h5ad:md5,06d0a7d2b711fc843235991d79ec3e4a", - "Pancreas_BC4_filtered_matrix.sce.rds:md5,a8f845f2366f37982424c7c7268e07d2", - "Pancreas_BC4_filtered_matrix.seurat.rds:md5,984441c1a6491af12ea19482fab308a6", - "Pancreas_BC4_raw_matrix.h5ad:md5,0dff6bd60fb837d0e0021caa4c21b23f", - "Pancreas_BC4_raw_matrix.sce.rds:md5,31cd8bd0f877c349f5eea5b268a9a1b2", - "Pancreas_BC4_raw_matrix.seurat.rds:md5,451eba9f44642abbb7521af305018160", + "4PLEX_HUMAN_raw_matrix.h5ad:md5,cbfdafa68aae75611738fa9210b03f7d", + "4PLEX_HUMAN_raw_matrix.sce.rds:md5,084ac812ebb69ca3152abd2c7226d739", + "4PLEX_HUMAN_raw_matrix.seurat.rds:md5,acc22e948a2250907897f79e008ff3ea", + "Colorectal_BC3_filtered_matrix.h5ad:md5,a1de01a2e94b0829779d8f1d52465ff7", + "Colorectal_BC3_filtered_matrix.sce.rds:md5,91bf1e7978c8a0601230a5d37c50e402", + "Colorectal_BC3_filtered_matrix.seurat.rds:md5,ba8256b3a51477018f9c1e4e1aeec336", + "Colorectal_BC3_raw_matrix.h5ad:md5,9aa954fe00a6b413a67ac4f7f8d478dc", + "Colorectal_BC3_raw_matrix.sce.rds:md5,b00d8244f06eef3e5d0fae39c9e14196", + "Colorectal_BC3_raw_matrix.seurat.rds:md5,0d6a6222daf2b03cba426cb80b86914c", + "Liver_BC1_filtered_matrix.h5ad:md5,aecfe09a1cbd9f87161824be609db2de", + "Liver_BC1_filtered_matrix.sce.rds:md5,3f40a160ca908672593106cdceda3dc1", + "Liver_BC1_filtered_matrix.seurat.rds:md5,ce4a4c9cbd490e867771416b4ce6f458", + "Liver_BC1_raw_matrix.h5ad:md5,cd134ba9ecd79b11fc3f0d6bbd027bac", + "Liver_BC1_raw_matrix.sce.rds:md5,4806e7f7e00af77c9eb0e2666cedc96c", + "Liver_BC1_raw_matrix.seurat.rds:md5,826973ce82225e8942a823e18dbe01fd", + "Ovarian_BC2_filtered_matrix.h5ad:md5,2f24890180bdb6dbe28184f107507bdb", + "Ovarian_BC2_filtered_matrix.sce.rds:md5,89518a94b4f908632433308311d02a37", + "Ovarian_BC2_filtered_matrix.seurat.rds:md5,b0a507b5d0b182681517c332177250ef", + "Ovarian_BC2_raw_matrix.h5ad:md5,09bb505dd9435e6405f11ea1c175a42f", + "Ovarian_BC2_raw_matrix.sce.rds:md5,e30869371d77941b1d009fd6983b5c43", + "Ovarian_BC2_raw_matrix.seurat.rds:md5,f107fd3e315a04aec3e6e53650c456f8", + "PBMC_10K_filtered_matrix.h5ad:md5,1f9765107df2ff39b67f5b46698f1be7", + "PBMC_10K_filtered_matrix.sce.rds:md5,1f2f3072ede853dd5f6c47821fc39543", + "PBMC_10K_filtered_matrix.seurat.rds:md5,dc780d878e2abae61b10eba5218116b8", + "PBMC_10K_raw_matrix.h5ad:md5,c6d9de8f66bb3c82a1af5362269ae0eb", + "PBMC_10K_raw_matrix.sce.rds:md5,4b3fe0fbda8a80eafc372bd895c26ec0", + "PBMC_10K_raw_matrix.seurat.rds:md5,97d5d0bc88db1df05b7effcb9dbb31cc", + "PBMC_10K_CMO_raw_matrix.h5ad:md5,2f62461d60211489f83eb8a6fb45611a", + "PBMC_10K_CMO_raw_matrix.sce.rds:md5,5c399342646e41ba7482dd1926eac1bf", + "PBMC_10K_CMO_raw_matrix.seurat.rds:md5,617b0af6bd53f58e7d0be91660bae3b3", + "PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.h5ad:md5,e5cc5a875dd544095b80f93c38b6ce4d", + "PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.sce.rds:md5,13d26c26a3967c415f539890a935fa7e", + "PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.seurat.rds:md5,8deeddcbb64b2a665372f2dd82a60ba3", + "PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.h5ad:md5,02ca5402d2197ffd129bca78ca22a362", + "PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.sce.rds:md5,ede457b9d84ed34cf892806bb9f5287e", + "PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.seurat.rds:md5,489181148d714944670abd1f6a3f4e10", + "PBMC_10K_CMV_filtered_matrix.h5ad:md5,d04bf7b56c489fc199b907ff7ad66077", + "PBMC_10K_CMV_filtered_matrix.sce.rds:md5,cb78864bde8833c2e6323ff01eef3c15", + "PBMC_10K_CMV_filtered_matrix.seurat.rds:md5,4dfa3f7aa87706e23a04248349292dc1", + "PBMC_10K_CMV_raw_matrix.h5ad:md5,1441fdabf55f28ae1e226fc34878a67f", + "PBMC_10K_CMV_raw_matrix.sce.rds:md5,75baf36779b04ed941b97b644125a2ff", + "PBMC_10K_CMV_raw_matrix.seurat.rds:md5,7b731e32655cace681ace140e3ef9af3", + "Pancreas_BC4_filtered_matrix.h5ad:md5,e8c4e7345c7af01c7d8a1c031a6a2272", + "Pancreas_BC4_filtered_matrix.sce.rds:md5,7d18f78c68f7c995b724ae3ba95ea862", + "Pancreas_BC4_filtered_matrix.seurat.rds:md5,98eef51fc0c34fa1e055b04c5c92d2f0", + "Pancreas_BC4_raw_matrix.h5ad:md5,227d5886282d58e0c6b8d6adc9ef94d0", + "Pancreas_BC4_raw_matrix.sce.rds:md5,4af114f068fc9bab8cceb3f25a9b6d9a", + "Pancreas_BC4_raw_matrix.seurat.rds:md5,7f972f40b05824a3cff5449a8f9f8b61", "fastqc-status-check-heatmap.txt:md5,f57bda9b8fd9290f05ad8ddb6dd72027", "fastqc_adapter_content_plot.txt:md5,886d5c1d7fcfd20e7d422124e16a3a12", "fastqc_overrepresented_sequences_plot.txt:md5,3bd26371c065bd07cac66aaae9bad132", @@ -1209,16 +1240,14 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,ad83bca86da8a428a4d7f6d8e534fd4b", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "multiqc_fastqc.txt:md5,ba37c98746e55d95bc1a0daefc030519", - "multiqc_general_stats.txt:md5,322c16b924c49f393b100debd15d9e16", - "PBMC_10K_CMO_cmo.csv:md5,91e024681f273d3581402dcc14f00483", - "4PLEX_HUMAN_frna.csv:md5,e45e051360b2f47d294339e9ef1e2842" + "multiqc_general_stats.txt:md5,322c16b924c49f393b100debd15d9e16" ] ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-10-29T21:39:30.575568163" + "timestamp": "2025-10-23T19:20:06.700106749" }, "test-dataset_cellrangermulti_aligner_rat": { "content": [ @@ -1691,12 +1720,42 @@ "multiqc/multiqc_data/multiqc_sources.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", + "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/multiqc_report.html", - "parse", - "parse/ocm_files", - "parse/ocm_files/10k_Wistar_Rat_ocm.csv", "pipeline_info", "pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml" ], @@ -1786,14 +1845,13 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,1e58df8383b865f8e10623140290b79e", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "multiqc_fastqc.txt:md5,026ffbdf07192dde0ece1347e249beaf", - "multiqc_general_stats.txt:md5,5496b8ed2f29e4210018b5a9f1b7dc18", - "10k_Wistar_Rat_ocm.csv:md5,718be9212d239955d92d7d619d8111e6" + "multiqc_general_stats.txt:md5,5496b8ed2f29e4210018b5a9f1b7dc18" ] ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-10-29T21:52:16.782453725" + "timestamp": "2025-10-23T19:49:18.434722245" } } \ No newline at end of file diff --git a/tests/main_pipeline_kallisto.nf.test.snap b/tests/main_pipeline_kallisto.nf.test.snap index 8031527f..6f688ef5 100644 --- a/tests/main_pipeline_kallisto.nf.test.snap +++ b/tests/main_pipeline_kallisto.nf.test.snap @@ -120,8 +120,41 @@ "multiqc/multiqc_data/multiqc_sources.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", + "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml" @@ -176,9 +209,9 @@ ] ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-10-30T14:16:21.07763953" + "timestamp": "2025-10-23T19:08:08.954153394" } } \ No newline at end of file diff --git a/tests/main_pipeline_star.nf.test.snap b/tests/main_pipeline_star.nf.test.snap index f39e5c8a..a3097064 100644 --- a/tests/main_pipeline_star.nf.test.snap +++ b/tests/main_pipeline_star.nf.test.snap @@ -60,8 +60,50 @@ "multiqc/multiqc_data/star_summary_table.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/multiqc_plots/pdf/star_alignment_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/star_alignment_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/star_summary_table.pdf", "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", + "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/multiqc_plots/png/star_alignment_plot-cnt.png", + "multiqc/multiqc_plots/png/star_alignment_plot-pct.png", + "multiqc/multiqc_plots/png/star_summary_table.png", "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_plots/svg/star_alignment_plot-cnt.svg", + "multiqc/multiqc_plots/svg/star_alignment_plot-pct.svg", + "multiqc/multiqc_plots/svg/star_summary_table.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", @@ -187,9 +229,9 @@ ] ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-10-30T14:22:04.512298845" + "timestamp": "2025-10-23T19:11:01.001258" } } \ No newline at end of file From 0210265a4941d29454a5a2835b5a7037e177866c Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Thu, 30 Oct 2025 18:32:10 +0000 Subject: [PATCH 10/16] Snapshot update --- ...main_pipeline_cellrangermulti.nf.test.snap | 261 +++++++++--------- 1 file changed, 132 insertions(+), 129 deletions(-) diff --git a/tests/main_pipeline_cellrangermulti.nf.test.snap b/tests/main_pipeline_cellrangermulti.nf.test.snap index c0552368..916db58b 100644 --- a/tests/main_pipeline_cellrangermulti.nf.test.snap +++ b/tests/main_pipeline_cellrangermulti.nf.test.snap @@ -882,29 +882,29 @@ "cellrangermulti/mkgtf", "cellrangermulti/mkgtf/Homo_sapiens.GRCh38.dna.chromosome.14_genes.filtered.gtf", "cellrangermulti/mkref", - "cellrangermulti/mkref/gex_reference", - "cellrangermulti/mkref/gex_reference/fasta", - "cellrangermulti/mkref/gex_reference/fasta/genome.fa", - "cellrangermulti/mkref/gex_reference/fasta/genome.fa.fai", - "cellrangermulti/mkref/gex_reference/genes", - "cellrangermulti/mkref/gex_reference/genes/genes.gtf.gz", - "cellrangermulti/mkref/gex_reference/reference.json", - "cellrangermulti/mkref/gex_reference/star", - "cellrangermulti/mkref/gex_reference/star/Genome", - "cellrangermulti/mkref/gex_reference/star/SA", - "cellrangermulti/mkref/gex_reference/star/SAindex", - "cellrangermulti/mkref/gex_reference/star/chrLength.txt", - "cellrangermulti/mkref/gex_reference/star/chrName.txt", - "cellrangermulti/mkref/gex_reference/star/chrNameLength.txt", - "cellrangermulti/mkref/gex_reference/star/chrStart.txt", - "cellrangermulti/mkref/gex_reference/star/exonGeTrInfo.tab", - "cellrangermulti/mkref/gex_reference/star/exonInfo.tab", - "cellrangermulti/mkref/gex_reference/star/geneInfo.tab", - "cellrangermulti/mkref/gex_reference/star/genomeParameters.txt", - "cellrangermulti/mkref/gex_reference/star/sjdbInfo.txt", - "cellrangermulti/mkref/gex_reference/star/sjdbList.fromGTF.out.tab", - "cellrangermulti/mkref/gex_reference/star/sjdbList.out.tab", - "cellrangermulti/mkref/gex_reference/star/transcriptInfo.tab", + "cellrangermulti/mkref/GRCh38", + "cellrangermulti/mkref/GRCh38/fasta", + "cellrangermulti/mkref/GRCh38/fasta/genome.fa", + "cellrangermulti/mkref/GRCh38/fasta/genome.fa.fai", + "cellrangermulti/mkref/GRCh38/genes", + "cellrangermulti/mkref/GRCh38/genes/genes.gtf.gz", + "cellrangermulti/mkref/GRCh38/reference.json", + "cellrangermulti/mkref/GRCh38/star", + "cellrangermulti/mkref/GRCh38/star/Genome", + "cellrangermulti/mkref/GRCh38/star/SA", + "cellrangermulti/mkref/GRCh38/star/SAindex", + "cellrangermulti/mkref/GRCh38/star/chrLength.txt", + "cellrangermulti/mkref/GRCh38/star/chrName.txt", + "cellrangermulti/mkref/GRCh38/star/chrNameLength.txt", + "cellrangermulti/mkref/GRCh38/star/chrStart.txt", + "cellrangermulti/mkref/GRCh38/star/exonGeTrInfo.tab", + "cellrangermulti/mkref/GRCh38/star/exonInfo.tab", + "cellrangermulti/mkref/GRCh38/star/geneInfo.tab", + "cellrangermulti/mkref/GRCh38/star/genomeParameters.txt", + "cellrangermulti/mkref/GRCh38/star/sjdbInfo.txt", + "cellrangermulti/mkref/GRCh38/star/sjdbList.fromGTF.out.tab", + "cellrangermulti/mkref/GRCh38/star/sjdbList.out.tab", + "cellrangermulti/mkref/GRCh38/star/transcriptInfo.tab", "cellrangermulti/mkref/versions.yml", "cellrangermulti/mkvdjref", "cellrangermulti/mkvdjref/vdj_reference", @@ -1180,54 +1180,54 @@ "transcriptInfo.tab:md5,a27c997fc57e0e26beebb57cde77d986", "versions.yml:md5,7f4adb1e901d6610e40f18a6b7c1dc89", "regions.fa:md5,b10393dbe8cc3a3a1ebb3636e7369fa2", - "4PLEX_HUMAN_raw_matrix.h5ad:md5,cbfdafa68aae75611738fa9210b03f7d", - "4PLEX_HUMAN_raw_matrix.sce.rds:md5,084ac812ebb69ca3152abd2c7226d739", - "4PLEX_HUMAN_raw_matrix.seurat.rds:md5,acc22e948a2250907897f79e008ff3ea", - "Colorectal_BC3_filtered_matrix.h5ad:md5,a1de01a2e94b0829779d8f1d52465ff7", - "Colorectal_BC3_filtered_matrix.sce.rds:md5,91bf1e7978c8a0601230a5d37c50e402", - "Colorectal_BC3_filtered_matrix.seurat.rds:md5,ba8256b3a51477018f9c1e4e1aeec336", - "Colorectal_BC3_raw_matrix.h5ad:md5,9aa954fe00a6b413a67ac4f7f8d478dc", - "Colorectal_BC3_raw_matrix.sce.rds:md5,b00d8244f06eef3e5d0fae39c9e14196", - "Colorectal_BC3_raw_matrix.seurat.rds:md5,0d6a6222daf2b03cba426cb80b86914c", - "Liver_BC1_filtered_matrix.h5ad:md5,aecfe09a1cbd9f87161824be609db2de", - "Liver_BC1_filtered_matrix.sce.rds:md5,3f40a160ca908672593106cdceda3dc1", - "Liver_BC1_filtered_matrix.seurat.rds:md5,ce4a4c9cbd490e867771416b4ce6f458", - "Liver_BC1_raw_matrix.h5ad:md5,cd134ba9ecd79b11fc3f0d6bbd027bac", - "Liver_BC1_raw_matrix.sce.rds:md5,4806e7f7e00af77c9eb0e2666cedc96c", - "Liver_BC1_raw_matrix.seurat.rds:md5,826973ce82225e8942a823e18dbe01fd", - "Ovarian_BC2_filtered_matrix.h5ad:md5,2f24890180bdb6dbe28184f107507bdb", - "Ovarian_BC2_filtered_matrix.sce.rds:md5,89518a94b4f908632433308311d02a37", - "Ovarian_BC2_filtered_matrix.seurat.rds:md5,b0a507b5d0b182681517c332177250ef", - "Ovarian_BC2_raw_matrix.h5ad:md5,09bb505dd9435e6405f11ea1c175a42f", - "Ovarian_BC2_raw_matrix.sce.rds:md5,e30869371d77941b1d009fd6983b5c43", - "Ovarian_BC2_raw_matrix.seurat.rds:md5,f107fd3e315a04aec3e6e53650c456f8", - "PBMC_10K_filtered_matrix.h5ad:md5,1f9765107df2ff39b67f5b46698f1be7", - "PBMC_10K_filtered_matrix.sce.rds:md5,1f2f3072ede853dd5f6c47821fc39543", - "PBMC_10K_filtered_matrix.seurat.rds:md5,dc780d878e2abae61b10eba5218116b8", - "PBMC_10K_raw_matrix.h5ad:md5,c6d9de8f66bb3c82a1af5362269ae0eb", - "PBMC_10K_raw_matrix.sce.rds:md5,4b3fe0fbda8a80eafc372bd895c26ec0", - "PBMC_10K_raw_matrix.seurat.rds:md5,97d5d0bc88db1df05b7effcb9dbb31cc", - "PBMC_10K_CMO_raw_matrix.h5ad:md5,2f62461d60211489f83eb8a6fb45611a", - "PBMC_10K_CMO_raw_matrix.sce.rds:md5,5c399342646e41ba7482dd1926eac1bf", - "PBMC_10K_CMO_raw_matrix.seurat.rds:md5,617b0af6bd53f58e7d0be91660bae3b3", - "PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.h5ad:md5,e5cc5a875dd544095b80f93c38b6ce4d", - "PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.sce.rds:md5,13d26c26a3967c415f539890a935fa7e", - "PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.seurat.rds:md5,8deeddcbb64b2a665372f2dd82a60ba3", - "PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.h5ad:md5,02ca5402d2197ffd129bca78ca22a362", - "PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.sce.rds:md5,ede457b9d84ed34cf892806bb9f5287e", - "PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.seurat.rds:md5,489181148d714944670abd1f6a3f4e10", - "PBMC_10K_CMV_filtered_matrix.h5ad:md5,d04bf7b56c489fc199b907ff7ad66077", - "PBMC_10K_CMV_filtered_matrix.sce.rds:md5,cb78864bde8833c2e6323ff01eef3c15", - "PBMC_10K_CMV_filtered_matrix.seurat.rds:md5,4dfa3f7aa87706e23a04248349292dc1", - "PBMC_10K_CMV_raw_matrix.h5ad:md5,1441fdabf55f28ae1e226fc34878a67f", - "PBMC_10K_CMV_raw_matrix.sce.rds:md5,75baf36779b04ed941b97b644125a2ff", - "PBMC_10K_CMV_raw_matrix.seurat.rds:md5,7b731e32655cace681ace140e3ef9af3", - "Pancreas_BC4_filtered_matrix.h5ad:md5,e8c4e7345c7af01c7d8a1c031a6a2272", - "Pancreas_BC4_filtered_matrix.sce.rds:md5,7d18f78c68f7c995b724ae3ba95ea862", - "Pancreas_BC4_filtered_matrix.seurat.rds:md5,98eef51fc0c34fa1e055b04c5c92d2f0", - "Pancreas_BC4_raw_matrix.h5ad:md5,227d5886282d58e0c6b8d6adc9ef94d0", - "Pancreas_BC4_raw_matrix.sce.rds:md5,4af114f068fc9bab8cceb3f25a9b6d9a", - "Pancreas_BC4_raw_matrix.seurat.rds:md5,7f972f40b05824a3cff5449a8f9f8b61", + "4PLEX_HUMAN_raw_matrix.h5ad:md5,31d87238d9e0bdf3b1906ee6b27c2ee1", + "4PLEX_HUMAN_raw_matrix.sce.rds:md5,e6a1922ee9a1aa5bb822efa5b9fa7cc1", + "4PLEX_HUMAN_raw_matrix.seurat.rds:md5,a28f3e17b57097947d4f3307b9cfde37", + "Colorectal_BC3_filtered_matrix.h5ad:md5,1066aa4f5be50985c38d173612440201", + "Colorectal_BC3_filtered_matrix.sce.rds:md5,6498f0475336ac1b6820f84e9176666f", + "Colorectal_BC3_filtered_matrix.seurat.rds:md5,1f23959ab1cf3db5a10996b5772392c6", + "Colorectal_BC3_raw_matrix.h5ad:md5,41aca8cb40046a4ec8b5d712d8f9a3ec", + "Colorectal_BC3_raw_matrix.sce.rds:md5,c1e4d9cf93103834e3e427182390ee67", + "Colorectal_BC3_raw_matrix.seurat.rds:md5,25edd2a8fd47bfba5de6059e913a6f1e", + "Liver_BC1_filtered_matrix.h5ad:md5,1b0d29b7e89b99b1d7c56826764f9f73", + "Liver_BC1_filtered_matrix.sce.rds:md5,9dba3e2f037544ff4b0f7484e84363ef", + "Liver_BC1_filtered_matrix.seurat.rds:md5,2af4692cec1dacdef41434052c1a4798", + "Liver_BC1_raw_matrix.h5ad:md5,42c89b5516c06a6e2b12f766db378407", + "Liver_BC1_raw_matrix.sce.rds:md5,1a92091f471aebbb6c6a11a7672303e1", + "Liver_BC1_raw_matrix.seurat.rds:md5,096fb87736a9d8bda8fc955df0a7336c", + "Ovarian_BC2_filtered_matrix.h5ad:md5,7465aa7be4ba213373bcfa9f7e04c834", + "Ovarian_BC2_filtered_matrix.sce.rds:md5,251e58d365f38d9493da30ed70eb7a0e", + "Ovarian_BC2_filtered_matrix.seurat.rds:md5,0bb8f8b96d08f1cd583d0f600d1598d2", + "Ovarian_BC2_raw_matrix.h5ad:md5,6e27c9c5a68dc907b61ce1eae267b932", + "Ovarian_BC2_raw_matrix.sce.rds:md5,78125a38a7974a2823386341be33de56", + "Ovarian_BC2_raw_matrix.seurat.rds:md5,bb527b97fd7d24e5357284bfb61d9e96", + "PBMC_10K_filtered_matrix.h5ad:md5,8276afec9886898d24df77e0eb3836ec", + "PBMC_10K_filtered_matrix.sce.rds:md5,b0ac588b9c4f12285a287b0d44ecf247", + "PBMC_10K_filtered_matrix.seurat.rds:md5,7c8ab3039d8aba9573ff80e68664ee76", + "PBMC_10K_raw_matrix.h5ad:md5,037e55dd085c1bb27681a7357a14f229", + "PBMC_10K_raw_matrix.sce.rds:md5,e8f0e03cc061a6e4e960295297da6607", + "PBMC_10K_raw_matrix.seurat.rds:md5,dc5e624ad49ea9b75dc57cdf1bbb2fd2", + "PBMC_10K_CMO_raw_matrix.h5ad:md5,b50f62f66668d822b3765be631d29d1a", + "PBMC_10K_CMO_raw_matrix.sce.rds:md5,6124ebe15dd4b975b4186dea844f865d", + "PBMC_10K_CMO_raw_matrix.seurat.rds:md5,5dfe0a5da270af2d08601e574b426dc4", + "PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.h5ad:md5,f696f68bdab63de70671013b7a23d8e6", + "PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.sce.rds:md5,eb623c6b462690ccb9ece785f0cbd781", + "PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.seurat.rds:md5,87549352e83a54f9ea894c33e70c39c5", + "PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.h5ad:md5,679aeb89604f3f6d98e66326be302320", + "PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.sce.rds:md5,0a2d99fcadc0fd73b5fedbb42e61c6d3", + "PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.seurat.rds:md5,77c83357a846f32aa3b51d1523d4ce14", + "PBMC_10K_CMV_filtered_matrix.h5ad:md5,15e785837e2eda0aa7bb6aea3a6c9f05", + "PBMC_10K_CMV_filtered_matrix.sce.rds:md5,6fa01cf7d93bc5f86ec945700b9734a8", + "PBMC_10K_CMV_filtered_matrix.seurat.rds:md5,fb90082ae1af8e86feac5726930927f4", + "PBMC_10K_CMV_raw_matrix.h5ad:md5,41f07c811f3751a5a773ccdcfba2323a", + "PBMC_10K_CMV_raw_matrix.sce.rds:md5,2b53553609413dc95760c49577f87bca", + "PBMC_10K_CMV_raw_matrix.seurat.rds:md5,10e8fb1066e31d9d68e263f8b7fd13c4", + "Pancreas_BC4_filtered_matrix.h5ad:md5,06d0a7d2b711fc843235991d79ec3e4a", + "Pancreas_BC4_filtered_matrix.sce.rds:md5,a8f845f2366f37982424c7c7268e07d2", + "Pancreas_BC4_filtered_matrix.seurat.rds:md5,984441c1a6491af12ea19482fab308a6", + "Pancreas_BC4_raw_matrix.h5ad:md5,0dff6bd60fb837d0e0021caa4c21b23f", + "Pancreas_BC4_raw_matrix.sce.rds:md5,31cd8bd0f877c349f5eea5b268a9a1b2", + "Pancreas_BC4_raw_matrix.seurat.rds:md5,451eba9f44642abbb7521af305018160", "fastqc-status-check-heatmap.txt:md5,f57bda9b8fd9290f05ad8ddb6dd72027", "fastqc_adapter_content_plot.txt:md5,886d5c1d7fcfd20e7d422124e16a3a12", "fastqc_overrepresented_sequences_plot.txt:md5,3bd26371c065bd07cac66aaae9bad132", @@ -1240,14 +1240,16 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,ad83bca86da8a428a4d7f6d8e534fd4b", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "multiqc_fastqc.txt:md5,ba37c98746e55d95bc1a0daefc030519", - "multiqc_general_stats.txt:md5,322c16b924c49f393b100debd15d9e16" + "multiqc_general_stats.txt:md5,322c16b924c49f393b100debd15d9e16", + "PBMC_10K_CMO_cmo.csv:md5,91e024681f273d3581402dcc14f00483", + "4PLEX_HUMAN_frna.csv:md5,e45e051360b2f47d294339e9ef1e2842" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-23T19:20:06.700106749" + "timestamp": "2025-10-30T18:18:02.196795279" }, "test-dataset_cellrangermulti_aligner_rat": { "content": [ @@ -1604,29 +1606,29 @@ "cellrangermulti/mkgtf", "cellrangermulti/mkgtf/Rattus_norvegicus.GRCr8.dna.primary_assembly.6_genes.filtered.gtf", "cellrangermulti/mkref", - "cellrangermulti/mkref/gex_reference", - "cellrangermulti/mkref/gex_reference/fasta", - "cellrangermulti/mkref/gex_reference/fasta/genome.fa", - "cellrangermulti/mkref/gex_reference/fasta/genome.fa.fai", - "cellrangermulti/mkref/gex_reference/genes", - "cellrangermulti/mkref/gex_reference/genes/genes.gtf.gz", - "cellrangermulti/mkref/gex_reference/reference.json", - "cellrangermulti/mkref/gex_reference/star", - "cellrangermulti/mkref/gex_reference/star/Genome", - "cellrangermulti/mkref/gex_reference/star/SA", - "cellrangermulti/mkref/gex_reference/star/SAindex", - "cellrangermulti/mkref/gex_reference/star/chrLength.txt", - "cellrangermulti/mkref/gex_reference/star/chrName.txt", - "cellrangermulti/mkref/gex_reference/star/chrNameLength.txt", - "cellrangermulti/mkref/gex_reference/star/chrStart.txt", - "cellrangermulti/mkref/gex_reference/star/exonGeTrInfo.tab", - "cellrangermulti/mkref/gex_reference/star/exonInfo.tab", - "cellrangermulti/mkref/gex_reference/star/geneInfo.tab", - "cellrangermulti/mkref/gex_reference/star/genomeParameters.txt", - "cellrangermulti/mkref/gex_reference/star/sjdbInfo.txt", - "cellrangermulti/mkref/gex_reference/star/sjdbList.fromGTF.out.tab", - "cellrangermulti/mkref/gex_reference/star/sjdbList.out.tab", - "cellrangermulti/mkref/gex_reference/star/transcriptInfo.tab", + "cellrangermulti/mkref/gex_reference_version", + "cellrangermulti/mkref/gex_reference_version/fasta", + "cellrangermulti/mkref/gex_reference_version/fasta/genome.fa", + "cellrangermulti/mkref/gex_reference_version/fasta/genome.fa.fai", + "cellrangermulti/mkref/gex_reference_version/genes", + "cellrangermulti/mkref/gex_reference_version/genes/genes.gtf.gz", + "cellrangermulti/mkref/gex_reference_version/reference.json", + "cellrangermulti/mkref/gex_reference_version/star", + "cellrangermulti/mkref/gex_reference_version/star/Genome", + "cellrangermulti/mkref/gex_reference_version/star/SA", + "cellrangermulti/mkref/gex_reference_version/star/SAindex", + "cellrangermulti/mkref/gex_reference_version/star/chrLength.txt", + "cellrangermulti/mkref/gex_reference_version/star/chrName.txt", + "cellrangermulti/mkref/gex_reference_version/star/chrNameLength.txt", + "cellrangermulti/mkref/gex_reference_version/star/chrStart.txt", + "cellrangermulti/mkref/gex_reference_version/star/exonGeTrInfo.tab", + "cellrangermulti/mkref/gex_reference_version/star/exonInfo.tab", + "cellrangermulti/mkref/gex_reference_version/star/geneInfo.tab", + "cellrangermulti/mkref/gex_reference_version/star/genomeParameters.txt", + "cellrangermulti/mkref/gex_reference_version/star/sjdbInfo.txt", + "cellrangermulti/mkref/gex_reference_version/star/sjdbList.fromGTF.out.tab", + "cellrangermulti/mkref/gex_reference_version/star/sjdbList.out.tab", + "cellrangermulti/mkref/gex_reference_version/star/transcriptInfo.tab", "cellrangermulti/mkref/versions.yml", "cellrangermulti/mkvdjref", "cellrangermulti/mkvdjref/vdj_reference", @@ -1807,33 +1809,33 @@ "transcriptInfo.tab:md5,213158051b61081ed7bd8f39c0324072", "versions.yml:md5,7f4adb1e901d6610e40f18a6b7c1dc89", "regions.fa:md5,be846142763972b29bbf65ff7e1406ee", - "10k_Wistar_Rat_raw_matrix.h5ad:md5,b72f3744ea8ade292165de67491694ba", - "10k_Wistar_Rat_raw_matrix.sce.rds:md5,170343f922c2b73f137fff406e1316c3", - "10k_Wistar_Rat_raw_matrix.seurat.rds:md5,be37ed0efb84a22909063388c54c4154", - "2500_Wistar_Rat_PBMCs_gem-x_OB1_filtered_matrix.h5ad:md5,f00027c443b2ec856dc8d06dcd11dfdc", - "2500_Wistar_Rat_PBMCs_gem-x_OB1_filtered_matrix.sce.rds:md5,5efca43447c83ad61e899b277e887dc9", - "2500_Wistar_Rat_PBMCs_gem-x_OB1_filtered_matrix.seurat.rds:md5,1f9c6d0214b36fb71adf3f5618f43738", - "2500_Wistar_Rat_PBMCs_gem-x_OB1_raw_matrix.h5ad:md5,d34963f41405303c43518e0dfe25aca3", - "2500_Wistar_Rat_PBMCs_gem-x_OB1_raw_matrix.sce.rds:md5,46d39abeb64f1b88ccec8fd3787cdeff", - "2500_Wistar_Rat_PBMCs_gem-x_OB1_raw_matrix.seurat.rds:md5,43bcad531d588fb27e7eb05f86ca67b1", - "2500_Wistar_Rat_PBMCs_gem-x_OB2_filtered_matrix.h5ad:md5,366ac48d2e3edd1a5cdbebd7ab21e070", - "2500_Wistar_Rat_PBMCs_gem-x_OB2_filtered_matrix.sce.rds:md5,8bb0728102df993644672d9abe13e4bf", - "2500_Wistar_Rat_PBMCs_gem-x_OB2_filtered_matrix.seurat.rds:md5,aa99723b6b31debf4d560da3eec46617", - "2500_Wistar_Rat_PBMCs_gem-x_OB2_raw_matrix.h5ad:md5,8e8f571032a1dd5b1ec239a6fa56dbac", - "2500_Wistar_Rat_PBMCs_gem-x_OB2_raw_matrix.sce.rds:md5,f378851bdabb57c7fcef7d40a5877b63", - "2500_Wistar_Rat_PBMCs_gem-x_OB2_raw_matrix.seurat.rds:md5,f2e21681a2c435d8e560cf84a460884a", - "2500_Wistar_Rat_PBMCs_gem-x_OB3_filtered_matrix.h5ad:md5,5faf1e8b32d76430ae0055d1f34c3025", - "2500_Wistar_Rat_PBMCs_gem-x_OB3_filtered_matrix.sce.rds:md5,5ecba68c2200060e60fe285ace5ab3c3", - "2500_Wistar_Rat_PBMCs_gem-x_OB3_filtered_matrix.seurat.rds:md5,e692f9f24f63bc91be1b8a95fd0ce6c7", - "2500_Wistar_Rat_PBMCs_gem-x_OB3_raw_matrix.h5ad:md5,bd90da1ef9cf0faef28c5712639c36f1", - "2500_Wistar_Rat_PBMCs_gem-x_OB3_raw_matrix.sce.rds:md5,039091942fe3518ee22a760819f1878a", - "2500_Wistar_Rat_PBMCs_gem-x_OB3_raw_matrix.seurat.rds:md5,c1b26872218fa0402ebf1b9161826815", - "2500_Wistar_Rat_PBMCs_gem-x_OB4_filtered_matrix.h5ad:md5,d11a86ce8d223451e8c67dad48fed9ec", - "2500_Wistar_Rat_PBMCs_gem-x_OB4_filtered_matrix.sce.rds:md5,3802b542e2a6430d11e7f526c5423b01", - "2500_Wistar_Rat_PBMCs_gem-x_OB4_filtered_matrix.seurat.rds:md5,e858cbc1fe44e1ed5657da5e3304a7f3", - "2500_Wistar_Rat_PBMCs_gem-x_OB4_raw_matrix.h5ad:md5,b180ec130ed399f15b3aa67b52c06bd4", - "2500_Wistar_Rat_PBMCs_gem-x_OB4_raw_matrix.sce.rds:md5,50aa224b1dfec5fefb99b965be37a513", - "2500_Wistar_Rat_PBMCs_gem-x_OB4_raw_matrix.seurat.rds:md5,63f65eaf922b953e2b55d77330d4f385", + "10k_Wistar_Rat_raw_matrix.h5ad:md5,a3d814a805f58095ee6585fe5aace613", + "10k_Wistar_Rat_raw_matrix.sce.rds:md5,47553a8f89b3a2f511bbf96db8c9409e", + "10k_Wistar_Rat_raw_matrix.seurat.rds:md5,cb681ffca53b4fe8a6b98bf7ca5ed0a4", + "2500_Wistar_Rat_PBMCs_gem-x_OB1_filtered_matrix.h5ad:md5,c41b59e0e843161df776945e43dffb29", + "2500_Wistar_Rat_PBMCs_gem-x_OB1_filtered_matrix.sce.rds:md5,797d79420fb1141913a1f54cb5507f3d", + "2500_Wistar_Rat_PBMCs_gem-x_OB1_filtered_matrix.seurat.rds:md5,2b1ccaa0b2686eaa421df53dc1e78ad1", + "2500_Wistar_Rat_PBMCs_gem-x_OB1_raw_matrix.h5ad:md5,96b685e69a84cbfa30a6f806c2845c6a", + "2500_Wistar_Rat_PBMCs_gem-x_OB1_raw_matrix.sce.rds:md5,9f45b0865d16bdc3dab1f2b511e9a6d2", + "2500_Wistar_Rat_PBMCs_gem-x_OB1_raw_matrix.seurat.rds:md5,b792a082573e90e836fdb01407cd4177", + "2500_Wistar_Rat_PBMCs_gem-x_OB2_filtered_matrix.h5ad:md5,8f1f48b7f323f80fa57dba57c8fc319c", + "2500_Wistar_Rat_PBMCs_gem-x_OB2_filtered_matrix.sce.rds:md5,ef6bca24dfc50d2bacfe5460bd8a3fd0", + "2500_Wistar_Rat_PBMCs_gem-x_OB2_filtered_matrix.seurat.rds:md5,ad3ea2f6aba44c4fddcb06e7c518ac24", + "2500_Wistar_Rat_PBMCs_gem-x_OB2_raw_matrix.h5ad:md5,36ac9f2a5864e76275ef446c834143e8", + "2500_Wistar_Rat_PBMCs_gem-x_OB2_raw_matrix.sce.rds:md5,85522f118dabba1c485e3b42ef6e8b4b", + "2500_Wistar_Rat_PBMCs_gem-x_OB2_raw_matrix.seurat.rds:md5,b17c82a0dd2bf961cd592c037b37ca25", + "2500_Wistar_Rat_PBMCs_gem-x_OB3_filtered_matrix.h5ad:md5,ded9bae06e696dbd3da763bd66a6c406", + "2500_Wistar_Rat_PBMCs_gem-x_OB3_filtered_matrix.sce.rds:md5,234a3ec7f92bc9ab1c39b6c942ec5255", + "2500_Wistar_Rat_PBMCs_gem-x_OB3_filtered_matrix.seurat.rds:md5,60ebf1273c16da237d87879ed21804d1", + "2500_Wistar_Rat_PBMCs_gem-x_OB3_raw_matrix.h5ad:md5,f65eec4ac0d6b5a2c02e6a2ac52501d6", + "2500_Wistar_Rat_PBMCs_gem-x_OB3_raw_matrix.sce.rds:md5,1e20fdb752bb73d0b2d522d07737a5ec", + "2500_Wistar_Rat_PBMCs_gem-x_OB3_raw_matrix.seurat.rds:md5,0ed952dfac3f3e2800461c914d98793b", + "2500_Wistar_Rat_PBMCs_gem-x_OB4_filtered_matrix.h5ad:md5,2d1d8fbd9c1e2334ff7bf1a6993837ff", + "2500_Wistar_Rat_PBMCs_gem-x_OB4_filtered_matrix.sce.rds:md5,97d8df5ccf8270dc1bedb7f96e9a1b9f", + "2500_Wistar_Rat_PBMCs_gem-x_OB4_filtered_matrix.seurat.rds:md5,e5f75043235bf06c9afba445b3e3b553", + "2500_Wistar_Rat_PBMCs_gem-x_OB4_raw_matrix.h5ad:md5,495ea7af0a484fd559a7fac733bceea2", + "2500_Wistar_Rat_PBMCs_gem-x_OB4_raw_matrix.sce.rds:md5,9b6b1abbf02d8999479c513861d6bc56", + "2500_Wistar_Rat_PBMCs_gem-x_OB4_raw_matrix.seurat.rds:md5,36662f7474f1a416ba7531108f87037e", "fastqc-status-check-heatmap.txt:md5,89acc155c18f65434b41b4dc8645fe2f", "fastqc_adapter_content_plot.txt:md5,fa8ef0df2f740304fab23bfd39787bc3", "fastqc_per_base_n_content_plot.txt:md5,04fc06c6af2f783ab3188a5838285849", @@ -1845,13 +1847,14 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,1e58df8383b865f8e10623140290b79e", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "multiqc_fastqc.txt:md5,026ffbdf07192dde0ece1347e249beaf", - "multiqc_general_stats.txt:md5,5496b8ed2f29e4210018b5a9f1b7dc18" + "multiqc_general_stats.txt:md5,5496b8ed2f29e4210018b5a9f1b7dc18", + "10k_Wistar_Rat_ocm.csv:md5,718be9212d239955d92d7d619d8111e6" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-23T19:49:18.434722245" + "timestamp": "2025-10-30T18:30:11.253964259" } } \ No newline at end of file From 3053c435d004fa06662abb6f59115fe871ba2656 Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Thu, 30 Oct 2025 15:10:12 -0400 Subject: [PATCH 11/16] Break early after finding probeset reference genome Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- subworkflows/local/align_cellrangermulti.nf | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/align_cellrangermulti.nf b/subworkflows/local/align_cellrangermulti.nf index 7161d504..2d730334 100644 --- a/subworkflows/local/align_cellrangermulti.nf +++ b/subworkflows/local/align_cellrangermulti.nf @@ -146,9 +146,13 @@ workflow CELLRANGER_MULTI_ALIGN { def probeset_file = file(params.gex_frna_probe_set) if ( probeset_file.exists() ) { def probeset_reference = null - probeset_file.readLines().each { line -> - if ( line.startsWith("#reference_genome=") ) { - probeset_reference = line.split("=")[1].trim() + probeset_file.withReader { reader -> + String line + while ((line = reader.readLine()) != null) { + if (line.startsWith("#reference_genome=")) { + probeset_reference = line.split("=")[1].trim() + break + } } } if ( probeset_reference && probeset_reference != params.gex_reference_version ) { From 12bf9e43af7e02746af50b7012c712749758faff Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Thu, 30 Oct 2025 19:15:26 +0000 Subject: [PATCH 12/16] some edgecase handling --- subworkflows/local/align_cellrangermulti.nf | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/align_cellrangermulti.nf b/subworkflows/local/align_cellrangermulti.nf index 2d730334..6beb76ee 100644 --- a/subworkflows/local/align_cellrangermulti.nf +++ b/subworkflows/local/align_cellrangermulti.nf @@ -150,12 +150,15 @@ workflow CELLRANGER_MULTI_ALIGN { String line while ((line = reader.readLine()) != null) { if (line.startsWith("#reference_genome=")) { - probeset_reference = line.split("=")[1].trim() + ref_split = line.split("=") + if (ref_split.size() > 1) { + probeset_reference = ref_split[1].trim() + } break } } } - if ( probeset_reference && probeset_reference != params.gex_reference_version ) { + if ( probeset_reference != params.gex_reference_version ) { error "Parameter 'gex_reference_version' (${params.gex_reference_version}) does not match the probeset reference genome (${probeset_reference}). Please ensure the reference genome version matches the probeset file." } } From e6353322bd751705b804f2ae85fac9ffaadcf95b Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Thu, 30 Oct 2025 20:52:48 +0000 Subject: [PATCH 13/16] Update snapshots again --- tests/main_pipeline_cellrangermulti.nf.test.snap | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/tests/main_pipeline_cellrangermulti.nf.test.snap b/tests/main_pipeline_cellrangermulti.nf.test.snap index 916db58b..050bd529 100644 --- a/tests/main_pipeline_cellrangermulti.nf.test.snap +++ b/tests/main_pipeline_cellrangermulti.nf.test.snap @@ -1240,16 +1240,14 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,ad83bca86da8a428a4d7f6d8e534fd4b", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "multiqc_fastqc.txt:md5,ba37c98746e55d95bc1a0daefc030519", - "multiqc_general_stats.txt:md5,322c16b924c49f393b100debd15d9e16", - "PBMC_10K_CMO_cmo.csv:md5,91e024681f273d3581402dcc14f00483", - "4PLEX_HUMAN_frna.csv:md5,e45e051360b2f47d294339e9ef1e2842" + "multiqc_general_stats.txt:md5,322c16b924c49f393b100debd15d9e16" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.04.0" }, - "timestamp": "2025-10-30T18:18:02.196795279" + "timestamp": "2025-10-30T19:30:41.782432772" }, "test-dataset_cellrangermulti_aligner_rat": { "content": [ @@ -1847,14 +1845,13 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,1e58df8383b865f8e10623140290b79e", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "multiqc_fastqc.txt:md5,026ffbdf07192dde0ece1347e249beaf", - "multiqc_general_stats.txt:md5,5496b8ed2f29e4210018b5a9f1b7dc18", - "10k_Wistar_Rat_ocm.csv:md5,718be9212d239955d92d7d619d8111e6" + "multiqc_general_stats.txt:md5,5496b8ed2f29e4210018b5a9f1b7dc18" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.04.0" }, - "timestamp": "2025-10-30T18:30:11.253964259" + "timestamp": "2025-10-30T19:42:41.142304311" } } \ No newline at end of file From e87349bc6ec7b22b3dcbfb7bb8e755deb7377e7c Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Fri, 31 Oct 2025 14:25:23 +0000 Subject: [PATCH 14/16] remove unneeded validation --- subworkflows/local/align_cellrangermulti.nf | 26 ++++++++++----------- 1 file changed, 12 insertions(+), 14 deletions(-) diff --git a/subworkflows/local/align_cellrangermulti.nf b/subworkflows/local/align_cellrangermulti.nf index 6beb76ee..cc248ada 100644 --- a/subworkflows/local/align_cellrangermulti.nf +++ b/subworkflows/local/align_cellrangermulti.nf @@ -144,23 +144,21 @@ workflow CELLRANGER_MULTI_ALIGN { // Validate that gex_reference_version matches the probeset reference genome if ( params.gex_frna_probe_set && params.gex_reference_version ) { def probeset_file = file(params.gex_frna_probe_set) - if ( probeset_file.exists() ) { - def probeset_reference = null - probeset_file.withReader { reader -> - String line - while ((line = reader.readLine()) != null) { - if (line.startsWith("#reference_genome=")) { - ref_split = line.split("=") - if (ref_split.size() > 1) { - probeset_reference = ref_split[1].trim() - } - break + def probeset_reference = null + probeset_file.withReader { reader -> + String line + while ((line = reader.readLine()) != null) { + if (line.startsWith("#reference_genome=")) { + ref_split = line.split("=") + if (ref_split.size() > 1) { + probeset_reference = ref_split[1].trim() } + break } } - if ( probeset_reference != params.gex_reference_version ) { - error "Parameter 'gex_reference_version' (${params.gex_reference_version}) does not match the probeset reference genome (${probeset_reference}). Please ensure the reference genome version matches the probeset file." - } + } + if ( probeset_reference != params.gex_reference_version ) { + error "Parameter 'gex_reference_version' (${params.gex_reference_version}) does not match the probeset reference genome (${probeset_reference}). Please ensure the reference genome version matches the probeset file." } } From 759310d4bb7b212624d602bc3d67bbaf20def7a6 Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Fri, 31 Oct 2025 15:25:36 +0000 Subject: [PATCH 15/16] Update changelog due to new release --- CHANGELOG.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1d93e987..d16589f6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v4.2.0 + +### Features + +- Fix [#375](https://github.com/nf-core/scrnaseq/issues/375): mismatch between index and probeset when cellranger multi is used without a prebuilt index and an FFPE probeset is passed ([#502](https://github.com/nf-core/scrnaseq/pull/502)) + ## v4.1.0 - 2025-08-01 ### Features @@ -29,10 +35,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Template update for nf-core/tools v3.2.1 ([#466](https://github.com/nf-core/scrnaseq/pull/466)) - Template update for nf-core/tools v3.3.2 ([#474](https://github.com/nf-core/scrnaseq/pull/474)) -### Fixes - -- Fix [#375](https://github.com/nf-core/scrnaseq/issues/375): mismatch between index and probeset when cellranger multi is used without a prebuilt index and an FFPE probeset is passed ([#502](https://github.com/nf-core/scrnaseq/pull/502)) - ## v4.0.0 - 2025-03-10 - Move `txp2gene` to `reference_genome_options` in schema as it is required by `kb_python` and `alevin` ([434](https://github.com/nf-core/scrnaseq/pull/434)) From 3d4de1526f00a3649fde4367019f87c2be8364de Mon Sep 17 00:00:00 2001 From: Tatiana Gelaf Romer Date: Fri, 14 Nov 2025 15:54:03 -0500 Subject: [PATCH 16/16] Update CHANGELOG.md Co-authored-by: Nico Trummer --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d16589f6..4ff383ef 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v4.2.0 +## [Unreleased] ### Features