diff --git a/CHANGELOG.md b/CHANGELOG.md index 0b7442bc..b9d51f40 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,6 +31,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c - [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output - [#135](https://github.com/nf-core/seqinspector/pull/135) Added index section to MultiQC reports to facilitate report navigation (#125) - [#151](https://github.com/nf-core/seqinspector/pull/151) Added a prepare_genome subworkflow to handle bwamem2 indexing +- [#156](https://github.com/nf-core/seqinspector/pull/156) Added relative sample_size and warning when a sample has less reads than desired sample_size. - [#158](https://github.com/nf-core/seqinspector/pull/158) Moved picard_collectmultiplemetrics to the subworkflow QC_BAM - [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data - [#162](https://github.com/nf-core/seqinspector/pull/162) Add tests for prepare_genome subworkflow @@ -38,11 +39,11 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c ### `Fixed` - [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided. +- [#94](https://github.com/nf-core/seqinspector/issues/94) Go through and validate test data - [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads - [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together - [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir - [#121](https://github.com/nf-core/seqinspector/pull/121) Cleanup sample naming for MultiQC report (#105) -- [#94] (https://github.com/nf-core/seqinspector/issues/94) Go through and validate test data - [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bugs in qc_bam and prepare_genome subworkflows and add tests - [#163](https://github.com/nf-core/seqinspector/pull/163) Run fastqscreen with subsampled data if available diff --git a/docs/usage.md b/docs/usage.md index 1259d7af..a3f25c90 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -98,7 +98,7 @@ genome: 'GRCh37' You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). -Optionally, the `sample_size` parameter allows you to subset a random number of reads to be analysed. Note that it refers to an absolute number. +Optionally, the `sample_size` parameter allows you to subset a random number of reads to be analysed. Both absolute numbers (e.g 100) and relative numbers (e.g 0.25) can be specified. ```bash nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results --sample_size 1000000 -profile docker diff --git a/nextflow_schema.json b/nextflow_schema.json index 1da12633..d9f197e4 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -24,9 +24,9 @@ "fa_icon": "fas fa-file-csv" }, "sample_size": { - "type": "integer", - "description": "Take this number of reads as a subset.", - "help_text": "Choose the size of the subset or 0, if no subsampling shall be performed. Note that it refers to an absolute number.", + "type": "number", + "description": "Take a subset of reads for analysis.", + "help_text": "Subset can be used as a fraction of reads (ex/ 0.20) or an absolute number of reads per sample (integer). Pipeline will still run if a sample has less reads than selected subset value.", "default": 0 }, "outdir": { diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000.main_subsample.nf.test index a62e4411..fc9da203 100644 --- a/tests/NovaSeq6000.main_subsample.nf.test +++ b/tests/NovaSeq6000.main_subsample.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test Workflow main.nf on NovaSeq6000 data sample size 90" + name "Test Workflow main.nf on NovaSeq6000 data with different sample sizes" script "../main.nf" tag "seqinspector" tag "PIPELINE" @@ -38,4 +38,77 @@ nextflow_pipeline { ) } } + + test("NovaSeq6000 data test relative sample size") { + + when { + config "./NovaSeq6000.main_subsample.nf.test.config" + params { + outdir = "$outputDir" + sample_size = 0.9 + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir( + params.outdir, + relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'] + ) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir( + params.outdir, + ignoreFile: 'tests/.nftignore' + ) + assertAll( + { assert workflow.success}, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"), + // All stable path names, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } + + test("NovaSeq6000 data test sample size exceeds available reads") { + tag "warning" + + when { + config "./NovaSeq6000.main_subsample.nf.test.config" + params { + outdir = "$outputDir" + sample_size = 120 + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir( + params.outdir, + relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'] + ) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir( + params.outdir, + ignoreFile: 'tests/.nftignore' + ) + assert workflow.success + assertAll( + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"), + // All stable path names, with a relative path + stable_name, + // All files with stable contents + stable_path, + // get all messages containing Requested sample_size (120) + filterNextflowOutput(workflow.stdout + workflow.stderr, ignore: ['Downloading plugin'], include:['Requested sample_size (120)']) + ).match() } + ) + } + } } diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap index 4b40cf01..28e919c7 100644 --- a/tests/NovaSeq6000.main_subsample.nf.test.snap +++ b/tests/NovaSeq6000.main_subsample.nf.test.snap @@ -944,6 +944,1907 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-12T10:04:43.761648394" + "timestamp": "2025-11-26T13:46:44.353118705" + }, + "NovaSeq6000 data test relative sample size": { + "content": [ + { + "BWAMEM2_MEM": { + "bwamem2": "2.2.1", + "samtools": "1.22.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "FASTQSCREEN_FASTQSCREEN": { + "fastqscreen": "0.16.0" + }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.4.0" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.22.1" + }, + "SEQFU_STATS": { + "seqfu": "1.22.3" + }, + "SEQTK_SAMPLE": { + "seqtk": "1.4-r122" + }, + "Workflow": { + "nf-core/seqinspector": "v1.0dev" + } + }, + [ + "bwamem2_index", + "bwamem2_index/bwamem2", + "bwamem2_index/bwamem2/genome.fa.0123", + "bwamem2_index/bwamem2/genome.fa.amb", + "bwamem2_index/bwamem2/genome.fa.ann", + "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64", + "bwamem2_index/bwamem2/genome.fa.pac", + "bwamem2_mem", + "bwamem2_mem/Sample1_01.bam", + "bwamem2_mem/Sample1_01.bam.bai", + "bwamem2_mem/Sample23_03.bam", + "bwamem2_mem/Sample23_03.bam.bai", + "bwamem2_mem/SampleA_02.bam", + "bwamem2_mem/SampleA_02.bam.bai", + "bwamem2_mem/Undetermined_05.bam", + "bwamem2_mem/Undetermined_05.bam.bai", + "bwamem2_mem/sampletest_04.bam", + "bwamem2_mem/sampletest_04.bam.bai", + "fastqc", + "fastqc/Sample1_01_fastqc.html", + "fastqc/Sample1_01_fastqc.zip", + "fastqc/Sample23_03_fastqc.html", + "fastqc/Sample23_03_fastqc.zip", + "fastqc/SampleA_02_fastqc.html", + "fastqc/SampleA_02_fastqc.zip", + "fastqc/Undetermined_05_fastqc.html", + "fastqc/Undetermined_05_fastqc.zip", + "fastqc/sampletest_04_fastqc.html", + "fastqc/sampletest_04_fastqc.zip", + "fastqscreen", + "fastqscreen/Sample1_01_screen.html", + "fastqscreen/Sample1_01_screen.png", + "fastqscreen/Sample1_01_screen.txt", + "fastqscreen/Sample23_03_screen.html", + "fastqscreen/Sample23_03_screen.png", + "fastqscreen/Sample23_03_screen.txt", + "fastqscreen/SampleA_02_screen.html", + "fastqscreen/SampleA_02_screen.png", + "fastqscreen/SampleA_02_screen.txt", + "fastqscreen/Undetermined_05_screen.html", + "fastqscreen/Undetermined_05_screen.png", + "fastqscreen/Undetermined_05_screen.txt", + "fastqscreen/sampletest_04_screen.html", + "fastqscreen/sampletest_04_screen.png", + "fastqscreen/sampletest_04_screen.txt", + "multiqc", + "multiqc/global_report", + "multiqc/global_report/multiqc_data", + "multiqc/global_report/multiqc_data/fastq_screen_plot.txt", + "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt", + "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", + 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"SampleA_02_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27", + "Undetermined_05_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e", + "Undetermined_05_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d", + "sampletest_04_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377", + "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2", + "Sample1_01_Sample1_S1_L001_R1_001.fastq.gz:md5,9f2f4855422bd18576efbc8af0368517", + "Sample23_03_Sample23_S3_L001_R1_001.fastq.gz:md5,036238392d51face00be9710c0c14523", + "SampleA_02_SampleA_S2_L001_R1_001.fastq.gz:md5,bcc1ed324745e894356ff3b66d023156", + "Undetermined_05_Undetermined_S0_L001_R1_001.fastq.gz:md5,2d64ba05e69ae081f95581cc8f0ffd36", + "sampletest_04_sampletest_S4_L001_R1_001.fastq.gz:md5,e81c2337941970a3bafa2c0adf8bebb1" + ], + [ + "WARN: Sample1_01: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.", + "WARN: Sample23_03: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.", + "WARN: SampleA_02: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.", + "WARN: Undetermined_05: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.", + "WARN: sampletest_04: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads." + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-12T11:09:26.248268345" } } \ No newline at end of file diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf index 4d5d8553..1d79a4f9 100644 --- a/workflows/seqinspector.nf +++ b/workflows/seqinspector.nf @@ -45,12 +45,12 @@ workflow SEQINSPECTOR { main: - ch_versions = channel.empty() - ch_multiqc_files = channel.empty() + ch_versions = channel.empty() + ch_multiqc_files = channel.empty() ch_multiqc_extra_files = channel.empty() - ch_bwamem2_mem = channel.empty() - ch_samtools_index = channel.empty() - ch_reference_fasta = fasta_file ? channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() : channel.value([[:], []]) + ch_bwamem2_mem = channel.empty() + ch_samtools_index = channel.empty() + ch_reference_fasta = fasta_file ? channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() : channel.value([[:], []]) PREPARE_GENOME( ch_reference_fasta, @@ -94,11 +94,29 @@ workflow SEQINSPECTOR { // Module: Run SeqFu stats // if (!("seqfu_stats" in skip_tools)) { - SEQFU_STATS( + ch_seqfu_stats = SEQFU_STATS( ch_samplesheet.map { meta, reads -> [[id: "seqfu", sample_id: meta.id, tags: meta.tags], reads] } ) + ch_seqfu_stats.stats + .map { meta, stats -> + { + // Parse the stats TSV file + [meta.sample_id, stats] + } + } + .splitCsv(header: true, sep: '\t') + .map { sample_id, row -> + // Check if requested sample size exceeds available reads + def sample_reads = row['#Seq'].toInteger() + if (params.sample_size > sample_reads) { + // prntln is used here instead of log.warn/log.info as nf-test captures stdout + // from 'println' but buffers log messages making them unavailable for assertion + // This message will appear in .nextflow.log file and temporarily on runtime stdout. + log.warn("${sample_id}: Requested sample_size (${params.sample_size}) is larger than available reads (${sample_reads}). Pipeline will continue with ${sample_reads} reads.") + } + } ch_multiqc_files = ch_multiqc_files.mix(SEQFU_STATS.out.multiqc) ch_versions = ch_versions.mix(SEQFU_STATS.out.versions.first()) } @@ -247,16 +265,14 @@ workflow SEQINSPECTOR { // Add index to other MultiQC reports //ch_multiqc_extra_files_global = Channel.empty() ch_multiqc_extra_files_global = ch_multiqc_extra_files.mix( - ch_tags.toList() - .map { tag_list -> - reportIndexMultiqc(tag_list) - } - .collectFile( - name: 'multiqc_index_mqc.yaml', - ) + ch_tags.toList().map { tag_list -> + reportIndexMultiqc(tag_list) + }.collectFile( + name: 'multiqc_index_mqc.yaml' + ) ) - MULTIQC_GLOBAL ( + MULTIQC_GLOBAL( ch_multiqc_files.map { _meta, file -> file }.mix(ch_multiqc_extra_files_global).collect(), ch_multiqc_config.toList(), [], @@ -266,13 +282,11 @@ workflow SEQINSPECTOR { ) ch_multiqc_extra_files_tag = ch_multiqc_extra_files.mix( - ch_tags.toList() - .map { tag_list -> - reportIndexMultiqc(tag_list, false) - } - .collectFile( - name: 'multiqc_index_mqc.yaml', - ) + ch_tags.toList().map { tag_list -> + reportIndexMultiqc(tag_list, false) + }.collectFile( + name: 'multiqc_index_mqc.yaml' + ) ) multiqc_extra_files_per_tag = ch_tags.combine(ch_multiqc_extra_files_tag)