Datasets:
Modalities:
Text
Formats:
json
Sub-tasks:
multiple-choice-qa
Languages:
English
Size:
10K - 100K
License:
id stringlengths 9 67 | category stringclasses 8
values | state unknown | question unknown | target stringlengths 3 93 | target_idx int64 0 9 |
|---|---|---|---|---|---|
noul_subworkflow_structural_blocks_23 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"Workflows in Nextflow DSL2 define inputs with `take:`, core execution with `main:`, and outputs with `emit:`.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards."
} | true | 1 |
pipe_all101_funcprofiler_3 | pipeline_routing | "Recommend the most appropriate nf-core workflow for the following project: Read-based functional profiling of microbiome sequencing data. " | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"drugresponseeval": null,
"funcprofiler": null,
"pangenome": null,
"proteinfamilies": null,
"rnasplice": null,
"metatdenovo": null,
"drop": null,
"seqsubmi... | funcprofiler | 1 |
schema_std_hadge_4 | samplesheet_schema | {
"pipeline": "nf-core/hadge",
"description": "Comprehensive pipeline for donor demultiplexing in single cell",
"mode": "standard_execution"
} | {
"type": "choice",
"instructions": "Which standard samplesheet columns are configured in assets/schema_input.json for nf-core/hadge?",
"criteria": {
"sample,group,ref_fasta,ref_gff,use_ref": null,
"sample,rna_matrix,hto_matrix,bam,barcodes": null,
"sample,fastq_1,fastq_2,barcode": null,
"sample,f... | sample,rna_matrix,hto_matrix,bam,barcodes | 1 |
resource_bedtools_merge_5 | resource_profiling | {
"process": "BEDTOOLS_MERGE",
"tool": "bedtools/merge",
"description": "combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BEDTOOLS_MERGE (combines overlapping or “book-ended” features in an interval file into a single ) in conf/base.config?",
"criteria": {
"process_low": null,
"process_high": null,
"process_single": null,
"process_... | process_single | 2 |
mod_orfipy_1 | tool_selection | "In Nextflow DSL2, which module handles: orfipy is a tool written in python/cython to extract ORFs in an extremely and fast and flexible manner. (tools: orfipy)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"orfipy": "orfipy is a tool written in python/cython to extract ORFs in an extremely and fast and flexible manner.",
"velocyto": "Velocyto is a library for the analysis of... | orfipy | 0 |
samplesheet_arch_bacterial_hybrid_assembly_4_0 | samplesheet_schema | "nextflow run nf-core/bacass --input samplesheet.csv (Assay: Hybrid bacterial assembly combining short Illumina and long Nanopore reads)" | {
"type": "choice",
"instructions": "Identify the standard samplesheet schema header for Microbial Assembly workflow (Illumina paired-end reads paired with Oxford Nanopore long reads per isolate).",
"criteria": {
"sample,fasta": "Contig assembly input",
"sample,bam": "BAM alignment file",
"sample,fast... | sample,fastq_1,fastq_2,long_fastq | 3 |
qc_adapt_singlecell_multiqc_0_41 | qc_read_adaptation | {
"assay": "Multi-sample single-cell RNA-seq cohort",
"tool": "MultiQC",
"read_type": "summary_reporting"
} | {
"type": "choice",
"instructions": "For Multi-sample single-cell RNA-seq cohort, what is the recommended QC default for MultiQC?",
"criteria": {
"Drop MultiQC": null,
"Keep MultiQC": null,
"Keep FastQC": null
}
} | Keep MultiQC | 1 |
mod_conifer_0 | tool_selection | "In Nextflow DSL2, which module handles: Calculate confidence scores from Kraken2 output (tools: conifer)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"whatshap/haplotag": "Tag reads by haplotype",
"catpack/download": "Downloads the required files for either Nr or GTDB for building into a CAT database",
"conifer": "C... | conifer | 2 |
samplesheet_arch_metagenome_mag_grouped_3_9 | samplesheet_schema | "Building an autonomous Nextflow workflow (nf-core/mag) for Metagenomic shotgun MAG assembly with comparative environmental groups. Input files: Paired-end environmental metagenomic FASTQs annotated by environmental cohort/group." | {
"type": "choice",
"instructions": "In Nextflow pipeline nf-core/mag, determine the input samplesheet column structure for: Metagenomic shotgun MAG assembly with comparative environmental groups.",
"criteria": {
"sample,fastq_1,fastq_2,group": "Shotgun metagenomic samplesheet tracking paired reads and compar... | sample,fastq_1,fastq_2,group | 0 |
mod_sentieon_applyvarcal_0 | tool_selection | "In Nextflow DSL2, which module handles: Apply a score cutoff to filter variants based on a recalibration table.\nSentieon's Aplyvarcal performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR).\nSpecifically, it applies filtering to the input variants based on the recalibration ... | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"sentieon/applyvarcal": null,
"sentieon/datametrics": null,
"custom/multiqccustombiotype": null,
"annosine": null,
"sentieon/collectvcmetrics": null
}
} | sentieon/applyvarcal | 0 |
schema_req_atacseq_5 | samplesheet_schema | {
"pipeline": "nf-core/atacseq",
"description": "ATAC-seq peak-calling and QC analysis pipeline",
"mode": "minimal_required_inputs"
} | {
"type": "choice",
"instructions": "What are the strictly mandatory required samplesheet columns for nf-core/atacseq?",
"criteria": {
"sample,fastq_1,fastq_2": null,
"fastq_1,replicate,sample": null,
"id,path": null,
"ID,R1,R2,LongFastQ,Fast5": null
}
} | fastq_1,replicate,sample | 1 |
samplesheet_arch_bulk_rnaseq_se_0_2 | samplesheet_schema | {
"assay": "Single-end Illumina RNA-seq with strandedness",
"first_step": "FASTQC",
"inputs": "Single-end FASTQ reads per library",
"pipeline": "nf-core/rnaseq"
} | {
"type": "choice",
"instructions": "Which columns should the input samplesheet have for: Single-end Illumina RNA-seq with strandedness?",
"criteria": {
"sample,fastq_1": "Bare single-end FASTQ without strandedness",
"sample,vcf": "Variant call format input",
"sample,bam": "Aligned BAM file",
"sam... | sample,fastq_1,strandedness | 4 |
qc_adapt_bulk_multiqc_2_36 | qc_read_adaptation | {
"assay": "High-throughput bulk WGS multi-sample run",
"tool": "MultiQC",
"read_type": "summary_reporting"
} | {
"type": "choice",
"instructions": "Evaluate the quality control tool choice for: High-throughput bulk WGS multi-sample run (summary_reporting).",
"criteria": {
"Swap for NanoPlot": null,
"Keep FastQC": null,
"Drop MultiQC": null,
"Keep MultiQC": null
}
} | Keep MultiQC | 3 |
pipe_all101_proteogenomicsdb_5 | pipeline_routing | "I need to run an end-to-end bioinformatics workflow to analyze The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.. Topics: cosmic, gnomad, protein-databases, proteogenomics, proteomics, pypgatk. . Which nf-core pipeline should I execute?" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"ribomsqc": "QC pipeline that monitors mass spectrometer performance in ribonucleoside analysis",
"seqinspector": "Dedicated QC-only pipeline for sequencing data. The pipeline wil... | proteogenomicsdb | 3 |
mod_cooltools_insulation_0 | tool_selection | "In Nextflow DSL2, which module handles: Calculate the diamond insulation scores and call insulating boundaries (tools: cooltools)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"cooler/zoomify": "Generate a multi-resolution cooler file by coarsening",
"chromap/chromap": "Performs preprocessing and alignment of chromatin fastq files to fasta refer... | cooltools/insulation | 2 |
mod_seroba_run_1 | tool_selection | "In Nextflow DSL2, which module handles: Determine Streptococcus pneumoniae serotype from Illumina paired-end reads (tools: seroba)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"ariba_getref": "Download and prepare database for Ariba analysis",
"getorganelle_config": "Downloads databases needed for running getorganelle",
"adapterremovalfixpre... | seroba_run | 4 |
resource_antismash_antismash_0 | resource_profiling | {
"process": "ANTISMASH_ANTISMASH",
"tool": "antismash/antismash",
"description": "antiSMASH allows the rapid genome-wide identification, annotation\nand analysis of secondary metabolite biosynthesis gene clusters."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to ANTISMASH_ANTISMASH (antiSMASH allows the rapid genome-wide identification, annotation\nand analysis o) in conf/base.config?",
"criteria": {
"process_low": null,
"process_high": null,
"process_long": null,
"proc... | process_single | 3 |
mod_nonpareil_set_1 | tool_selection | "In Nextflow DSL2, which module handles: Visualise metagenome redundancy curves in PNG format from multiple Nonpareil npo files in a single image (tools: nonpareil)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"clustalo_guidetree": "Renders a guidetree in clustalo",
"argnorm": "Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).",
"ribotr... | nonpareil_set | 3 |
mod_mcquant_1 | tool_selection | "In Nextflow DSL2, which module handles: Mcquant extracts single-cell data given a multi-channel image and a segmentation mask. (tools: mcquant)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"centrifuger_quantification": "Quantification (taxonomic profiling) of Centrifuger model",
"seqkit_split2": "Split single or paired-end fastq.gz files",
"mcquant": "Mc... | mcquant | 2 |
mod_catpack_prepare_1 | tool_selection | "In Nextflow DSL2, which module handles: Creates a CAT_pack database based on input FASTAs (tools: catpack)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"fasta_classify_catpack": "Taxonomic classification of binned MAGs and contigs using CAT/BAT (CAT_pack).",
"cat_cat": "A module for concatenation of gzipped or uncompresse... | catpack_prepare | 2 |
noul_mix_operator_async_emission_21 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"The `.mix()` channel operator waits until all source channels have completed before emitting any items.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards."
} | false | 0 |
pipe_all101_imcyto_4 | pipeline_routing | "Which pipeline implements best-practice processing for: Image Mass Cytometry analysis pipeline. Topics: cytometry, image-analysis, image-processing, image-segmentation. ?" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"readsimulator": "A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data. ",
"funcprofiler": "Read-based functional profiling... | imcyto | 6 |
core_tool_featurecounts_bare_1 | tool_selection | "Which bioinformatics tool or module is best suited for this task? Assign and quantify mapped reads to genomic features such as exons, genes, and promoter annotations from sorted BAM files." | {
"type": "choice",
"instructions": "Select the appropriate bioinformatics tool or module for the specified task.",
"criteria": {
"stringtie": null,
"kallisto": null,
"salmon": null,
"htseq": null,
"featurecounts": null
}
} | featurecounts | 4 |
qc_adapt_pacbio_hifi_2_20 | qc_read_adaptation | {
"assay": "PacBio HiFi circular consensus sequencing (CCS)",
"tool": "FastQC",
"read_type": "long_reads_hifi_15kb"
} | {
"type": "choice",
"instructions": "Evaluate the quality control tool choice for: PacBio HiFi circular consensus sequencing (CCS) (long_reads_hifi_15kb).",
"criteria": {
"Swap for NanoPlot": null,
"Drop FastQC": null,
"Keep FastQC": null
}
} | Swap for NanoPlot | 0 |
qc_adapt_singlecell_multiqc_0_10 | qc_read_adaptation | {
"assay": "Multi-sample single-cell RNA-seq cohort",
"tool": "MultiQC",
"read_type": "summary_reporting"
} | {
"type": "choice",
"instructions": "For Multi-sample single-cell RNA-seq cohort, what is the recommended QC default for MultiQC?",
"criteria": {
"Keep MultiQC": null,
"Drop MultiQC": null,
"Keep FastQC": null
}
} | Keep MultiQC | 0 |
mod_centrifuge_build_0 | tool_selection | "In Nextflow DSL2, which module handles: Build centrifuge database for taxonomic profiling (tools: centrifuge)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"blast/makeblastdb": "Builds a BLAST database",
"vcfexpress": "Filter a VCF/BCF and optionally print by template expression. If no template is given the output will be VCF... | centrifuge/build | 4 |
noul_channel_join_operator_0 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"The `.join()` operator combines two channels sharing a matching key (like `meta.id`).\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards.",
"criteria": {
"false": "The statement describes an invalid Nextflow DSL2 syntax, anti-pattern, or deprecated behavior.",
"true": "The statement describes a valid, standard, and re... | true | 1 |
noul_channel_factory_inside_process_body_12 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"Calling `Channel.fromPath()` inside the body of a process is valid Nextflow DSL2.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards.",
"criteria": {
"false": "The statement describes an invalid Nextflow DSL2 syntax, anti-pattern, or deprecated behavior.",
"true": "The statement describes a valid, standard, and re... | false | 0 |
samplesheet_arch_ancient_dna_eager_1_0 | samplesheet_schema | {
"technology": "Ancient DNA",
"workflow_entry": "FASTQC",
"library_inputs": "Ancient degraded DNA FASTQs with library preparation chemistry and uracil-DNA-glycosylase status"
} | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for Ancient DNA (aDNA) sequencing with UDG treatment and damage assessment with entry step FASTQC.",
"criteria": {
"patient,sample,status,fastq_1,fastq_2": "Somatic cancer schema",
"sample,bam": "Aligned ancient BAM",
... | sample,library_id,lane,colour_chemistry,seq_type,paired_end,udg,strandedness,fastq_1,fastq_2 | 4 |
samplesheet_arch_scrna_multiome_2_5 | samplesheet_schema | {
"pipeline": "nf-core/scrnaseq",
"assay_type": "10x Multiome single-cell joint RNA and ATAC chromatin",
"data_format": "Paired FASTQs for both GEX and ATAC modalities per nucleus"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected when inputs are: Paired FASTQs for both GEX and ATAC modalities per nucleus?",
"criteria": {
"sample,fastq_1,fastq_2": "Single-modality RNA reads",
"sample,matrix": "Count matrix",
"sample,bam": "Single BAM input",
"sample,... | sample,fastq_1,fastq_2,feature_type | 3 |
mod_snippy_core_0 | tool_selection | "In Nextflow DSL2, which module handles: Core-SNP alignment from Snippy outputs (tools: snippy)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"gt/suffixerator": "Computes enhanced suffix array using GenomeTools gt-suffixerator utility",
"tidk/search": "Searches a genome for a telomere string such as TTAGGG",
... | snippy/core | 4 |
mod_qcatch_0 | tool_selection | "In Nextflow DSL2, which module handles: Cell-filtering and QC reporting tool for alevin-fry quantification results (tools: qcatch)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"muscle5/super5": "Muscle is a program for creating multiple alignments of amino acid or nucleotide sequences. This particular mo",
"bff": "Generating cell hashing calls f... | qcatch | 2 |
samplesheet_arch_bulk_wes_pe_1_3 | samplesheet_schema | {
"technology": "Bulk DNA-seq",
"workflow_entry": "FASTQC",
"library_inputs": "Paired-end FASTQs from Agilent/Twist exome target capture"
} | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for Paired-end Whole Exome Sequencing (WES) target capture with entry step FASTQC.",
"criteria": {
"sample,vcf": "Pre-called variants",
"sample,fastq_1": "Single-end read input",
"sample,fastq_1,fastq_2": "Exome cap... | sample,fastq_1,fastq_2 | 2 |
resource_bcftools_plotvcfstats_1 | resource_profiling | {
"process": "BCFTOOLS_PLOTVCFSTATS",
"tool": "bcftools/plotvcfstats",
"description": "Plots the output of bcftools stats"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BCFTOOLS_PLOTVCFSTATS (Plots the output of bcftools stats) in conf/base.config?",
"criteria": {
"process_single": null,
"process_high": null,
"process_low": null,
"process_long": null
}
} | process_single | 0 |
schema_req_atacseq_3 | samplesheet_schema | {
"pipeline": "nf-core/atacseq",
"description": "ATAC-seq peak-calling and QC analysis pipeline",
"mode": "minimal_required_inputs"
} | {
"type": "choice",
"instructions": "What are the strictly mandatory required samplesheet columns for nf-core/atacseq?",
"criteria": {
"sample,fastq_1,fastq_2": null,
"fastq_1,replicate,sample": null,
"id,path": null,
"ID,R1,R2,LongFastQ,Fast5": null
}
} | fastq_1,replicate,sample | 1 |
samplesheet_arch_riboseq_profiling_1_11 | samplesheet_schema | {
"technology": "Specialized RNA-seq",
"workflow_entry": "FASTQC",
"library_inputs": "Single-end ribosome protected RNA fragments (RPFs) with strandedness"
} | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for Ribosome profiling (Ribo-seq) footprint sequencing with entry step FASTQC.",
"criteria": {
"sample,fastq_1,strandedness": "Ribosome footprinting single-end sequence reads with strand orientation",
"sample,cdna_fasta... | sample,fastq_1,strandedness | 0 |
qc_adapt_pe_illumina_fastqc_2_5 | qc_read_adaptation | {
"assay": "Standard Paired-end Illumina RNA-seq",
"tool": "FastQC",
"read_type": "short_reads_150bp"
} | {
"type": "choice",
"instructions": "Evaluate the quality control tool choice for: Standard Paired-end Illumina RNA-seq (short_reads_150bp).",
"criteria": {
"Swap for NanoPlot": null,
"Drop FastQC": null,
"Keep FastQC": null
}
} | Keep FastQC | 2 |
subworkflow_pkg_fastq_extract_kraken_krakentools_2 | subworkflow_packaging | {
"subworkflow": "FASTQ_EXTRACT_KRAKEN_KRAKENTOOLS",
"modules": [
"kraken2/kraken2",
"krakentools/extractkrakenreads"
],
"description": "Extract classified Kraken2 reads by taxonomic id"
} | {
"type": "choice",
"instructions": "How should FASTQ_EXTRACT_KRAKEN_KRAKENTOOLS (kraken2/kraken2, krakentools/extractkrakenreads) be structured in DSL2?",
"criteria": {
"Leave them out": null,
"Use nf-core subworkflow fastq_extract_kraken_krakentools": null,
"Local subworkflow FASTQ_EXTRACT_KRAKEN_KR... | Use nf-core subworkflow fastq_extract_kraken_krakentools | 1 |
subworkflow_pkg_fastq_taxonomic_profile_metaphlan_3 | subworkflow_packaging | {
"subworkflow": "FASTQ_TAXONOMIC_PROFILE_METAPHLAN",
"modules": [
"metaphlan/makedb",
"metaphlan/metaphlan",
"metaphlan/mergemetaphlantables"
],
"description": "Subworkflow to taxonomically classify metagenomic sequencing data using MetaPhlAn"
} | {
"type": "choice",
"instructions": "How should FASTQ_TAXONOMIC_PROFILE_METAPHLAN (metaphlan/makedb, metaphlan/metaphlan, metaphlan/mergemetaphlantables) be structured in DSL2?",
"criteria": {
"Use nf-core subworkflow fastq_taxonomic_profile_metaphlan": null,
"Local subworkflow FASTQ_TAXONOMIC_PROFILE_MET... | Use nf-core subworkflow fastq_taxonomic_profile_metaphlan | 0 |
core_tool_mutect2_bare_0 | tool_selection | "Which bioinformatics tool or module is best suited for this task? Somatic short variant detection (SNVs and small indels) comparing matched tumor and normal sequencing data with Bayesian somatic likelihood filtering." | {
"type": "choice",
"instructions": "Select the appropriate bioinformatics tool or module for the specified task.",
"criteria": {
"mutect2": null,
"vardict": null,
"strelka2": null,
"varscan2": null,
"somaticsniper": null
}
} | mutect2 | 0 |
subworkflow_pkg_bam_stringtie_merge_3 | subworkflow_packaging | {
"subworkflow": "BAM_STRINGTIE_MERGE",
"modules": [
"stringtie/stringtie",
"stringtie/merge"
],
"description": "Assemble transcripts from sorted BAM alignments using StringTie, then merge per-sample transcript GTFs into a unified annotation."
} | {
"type": "choice",
"instructions": "How should BAM_STRINGTIE_MERGE (stringtie/stringtie, stringtie/merge) be structured in DSL2?",
"criteria": {
"Local subworkflow BAM_STRINGTIE_MERGE": null,
"Leave them out": null,
"Use nf-core subworkflow bam_stringtie_merge": null,
"Keep the modules in the mai... | Use nf-core subworkflow bam_stringtie_merge | 2 |
pipe_all101_kmermaid_4 | pipeline_routing | "Which pipeline implements best-practice processing for: k-mer similarity analysis pipeline. Topics: k-mer, kmer, kmer-counting, kmer-frequency-count. ?" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"diaproteomics": "Automated quantitative analysis of DIA proteomics mass spectrometry measurements. [data-independent-proteomics, dia-prot",
"methylseq": "Methylation (Bisulfite-S... | kmermaid | 7 |
pipe_all101_isoseq_4 | pipeline_routing | "Which pipeline implements best-practice processing for: Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.. Topics: isoseq, isoseq-3, rna, tama, ultra. ?" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"longraredisease": "Long read sequencing pipeline to identify variants in patients with neurodevelopmental disorders [nanopore, pacbio]",
"diaproteomics": "Automated quantitative... | isoseq | 4 |
qc_adapt_targeted_amplicon_2_47 | qc_read_adaptation | {
"assay": "Targeted Illumina amplicon panel",
"tool": "FastQC",
"read_type": "short_reads_pe250"
} | {
"type": "choice",
"instructions": "Evaluate the quality control tool choice for: Targeted Illumina amplicon panel (short_reads_pe250).",
"criteria": {
"Swap for NanoPlot": null,
"Drop FastQC": null,
"Keep FastQC": null
}
} | Keep FastQC | 2 |
mod_utils_nfcore_pipeline_1 | tool_selection | "In Nextflow DSL2, which module handles: Subworkflow with utility functions specific to the nf-core pipeline template (tools: utils_nfcore_pipeline)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"utils_nfcore_pipeline": null,
"utils_nfvalidation_plugin": null,
"star_indexversion": null,
"glnexus": null,
"prinseqplusplus": null
}
} | utils_nfcore_pipeline | 0 |
samplesheet_arch_cageseq_transcription_3_7 | samplesheet_schema | "Building an autonomous Nextflow workflow (nf-core/cageseq) for CAGE-seq 5-prime capped transcript end sequencing. Input files: Single-end capped 5-prime cDNA tags for transcription start site (TSS) mapping." | {
"type": "choice",
"instructions": "In Nextflow pipeline nf-core/cageseq, determine the input samplesheet column structure for: CAGE-seq 5-prime capped transcript end sequencing.",
"criteria": {
"sample,vcf": null,
"sample,bam": null,
"sample,tss_bed": null,
"sample,fastq_1,fastq_2": null,
"s... | sample,fastq_1 | 4 |
schema_std_lsmquant_1 | samplesheet_schema | {
"pipeline": "nf-core/lsmquant",
"description": "A pipeline for processing and analysis of light-sheet microscopy images.",
"mode": "standard_execution"
} | {
"type": "choice",
"instructions": "Which standard samplesheet columns are configured in assets/schema_input.json for nf-core/lsmquant?",
"criteria": {
"genome,site,source,source_vcf,source_version": null,
"sample_id,img_directory,parameter_file": null,
"sample,fastq_1,fastq_2": null,
"sample_id,... | sample_id,img_directory,parameter_file | 1 |
qc_adapt_singlecell_multiqc_0_17 | qc_read_adaptation | {
"assay": "Multi-sample single-cell RNA-seq cohort",
"tool": "MultiQC",
"read_type": "summary_reporting"
} | {
"type": "choice",
"instructions": "For Multi-sample single-cell RNA-seq cohort, what is the recommended QC default for MultiQC?",
"criteria": {
"Keep MultiQC": null,
"Keep FastQC": null,
"Drop MultiQC": null
}
} | Keep MultiQC | 0 |
samplesheet_arch_ampliseq_its_fungal_1_7 | samplesheet_schema | {
"technology": "Microbiome Amplicon",
"workflow_entry": "FASTQC",
"library_inputs": "Demultiplexed paired-end Illumina MiSeq ITS fungal amplicon reads"
} | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for Fungal ITS1/ITS2 marker gene amplicon surveillance with entry step FASTQC.",
"criteria": {
"sample,primer_its1,primer_its2": "Primer coordinate schema",
"sample,fastq_1,fastq_2": "Paired-end fungal internal transcri... | sample,fastq_1,fastq_2 | 1 |
mod_crabs_import_1 | tool_selection | "In Nextflow DSL2, which module handles: In-house generated or curated data can be imported into CRABS. (tools: crabs)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"artic_aligntrim": "Standalone version of fieldbioinformatics aligntrim. Soft clips amplicon scheme primer sites in BAM/SAM files.",
"kraken2_build": "Builds Kraken2 datab... | crabs_import | 2 |
samplesheet_arch_atacseq_replicates_4_7 | samplesheet_schema | "nextflow run nf-core/atacseq --input samplesheet.csv (Assay: ATAC-seq chromatin accessibility with biological replicates)" | {
"type": "choice",
"instructions": "Identify the standard samplesheet schema header for Epigenomics workflow (Paired-end Tn5 transposed FASTQs across conditions and replicates).",
"criteria": {
"sample,bed": "Peak bed file",
"sample,bam": "Aligned BAM file",
"sample,fastq_1": "Single-end read input",... | sample,fastq_1,fastq_2,replicate | 3 |
mod_oarfish_alignmentmode_1 | tool_selection | "In Nextflow DSL2, which module handles: oarfish is a program for quantifying transcript-level expression from long-read sequencing technologies. Quantify pre-computed alignments of reads to the transcriptome (a name-sorted BAM, e.g. from minimap2/pbmm2). (tools: oarfish)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"chromap_index": "Indexes a fasta reference genome ready for chromatin profiling.",
"bamaligncleaner": "removes unused references from header of sorted BAM/CRAM files.",
... | oarfish_alignmentmode | 3 |
subworkflow_pkg_tif_registration_stainwarpy_0 | subworkflow_packaging | {
"subworkflow": "TIF_REGISTRATION_STAINWARPY",
"modules": [
"stainwarpy/extractchannel",
"stainwarpy/register",
"stainwarpy/transformsegmask"
],
"description": "Register H&E stained and multiplexed tissue images and transform segmentation masks using stainwarpy"
} | {
"type": "choice",
"instructions": "How should TIF_REGISTRATION_STAINWARPY (stainwarpy/extractchannel, stainwarpy/register, stainwarpy/transformsegmask) be structured in DSL2?",
"criteria": {
"Use nf-core subworkflow tif_registration_stainwarpy": null,
"Local subworkflow TIF_REGISTRATION_STAINWARPY": nul... | Use nf-core subworkflow tif_registration_stainwarpy | 0 |
qc_adapt_singlecell_multiqc_2_20 | qc_read_adaptation | {
"assay": "Multi-sample single-cell RNA-seq cohort",
"tool": "MultiQC",
"read_type": "summary_reporting"
} | {
"type": "choice",
"instructions": "Evaluate the quality control tool choice for: Multi-sample single-cell RNA-seq cohort (summary_reporting).",
"criteria": {
"Drop MultiQC": null,
"Keep FastQC": null,
"Keep MultiQC": null
}
} | Keep MultiQC | 2 |
resource_amps_2 | resource_profiling | {
"process": "AMPS",
"tool": "amps",
"description": "Post-processing script of the MaltExtract component of the HOPS package"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to AMPS (Post-processing script of the MaltExtract component of the HOPS package) in conf/base.config?",
"criteria": {
"process_single": null,
"process_long": null,
"process_medium": null,
"process_low": null
}
} | process_single | 0 |
pipe_all101_reportho_2 | pipeline_routing | "We have raw sequencing data and want to run standard QC, alignment, and quantification for ortholog. Best pipeline:" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"pixelator": "Pipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB) [molecular-pixelation, pixel",
"seqinspector": "Dedicated QC-only pipelin... | reportho | 6 |
noul_process_conditional_execution_20 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"The `when:` directive in a process controls conditional execution based on workflow parameters.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards.",
"criteria": {
"false": "The statement describes an invalid Nextflow DSL2 syntax, anti-pattern, or deprecated behavior.",
"true": "The statement describes a valid, standard, and re... | true | 1 |
mod_gatk4_filtermutectcalls_1 | tool_selection | "In Nextflow DSL2, which module handles: Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering. (tools: gatk4)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"mako": "Sort SAM/BAM files by coordinate, queryname or template-coordinate using a fast external merge-sort",
"bam_tumor_only_somatic_variant_calling_gatk": "Perform vari... | gatk4_filtermutectcalls | 2 |
resource_bcftools_csq_1 | resource_profiling | {
"process": "BCFTOOLS_CSQ",
"tool": "bcftools/csq",
"description": "bcftools Haplotype-aware consequence caller"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BCFTOOLS_CSQ (bcftools Haplotype-aware consequence caller) in conf/base.config?",
"criteria": {
"process_medium": null,
"process_low": null,
"process_long": null,
"process_single": null
}
} | process_single | 3 |
subworkflow_pkg_fastq_trim_fastp_fastqc_0 | subworkflow_packaging | {
"subworkflow": "FASTQ_TRIM_FASTP_FASTQC",
"modules": [
"fastqc",
"fastp"
],
"description": "Read QC, fastp trimming and read qc"
} | {
"type": "choice",
"instructions": "How should FASTQ_TRIM_FASTP_FASTQC (fastqc, fastp) be structured in DSL2?",
"criteria": {
"Leave them out": null,
"Use nf-core subworkflow fastq_trim_fastp_fastqc": null,
"Local subworkflow FASTQ_TRIM_FASTP_FASTQC": null,
"Keep the modules in the main workflow"... | Use nf-core subworkflow fastq_trim_fastp_fastqc | 1 |
qc_adapt_qc_aggregate_0_20 | qc_read_adaptation | {
"assay": "Multi-sample QC aggregation and reporting",
"tool": "MultiQC",
"read_type": "multiqc_report"
} | {
"type": "choice",
"instructions": "For Multi-sample QC aggregation and reporting, what is the recommended QC default for MultiQC?",
"criteria": {
"Keep MultiQC": null,
"Swap for NanoPlot": null,
"Drop MultiQC": null
}
} | Keep MultiQC | 0 |
local_subworkflow_preparereports_2_4 | subworkflow_packaging | {
"subworkflow": "PREPAREREPORTS",
"modules": [
"custom/preparereports",
"multiqc"
],
"description": "Custom aggregation and MultiQC reporting"
} | {
"type": "choice",
"instructions": "Determine the DSL2 structure for PREPAREREPORTS (custom/preparereports, multiqc).",
"criteria": {
"Leave them out": null,
"Use nf-core subworkflow preparereports": null,
"Keep the modules in the main workflow": null,
"Local subworkflow PREPAREREPORTS": null
}... | Local subworkflow PREPAREREPORTS | 3 |
mod_abritamr_run_1 | tool_selection | "In Nextflow DSL2, which module handles: A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes (tools: abritamr)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"abritamr_run": "A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes",
"abricate_summary": "Screen assemblies for anti... | abritamr_run | 0 |
mod_homer_findpeaks_0 | tool_selection | "In Nextflow DSL2, which module handles: Find peaks with HOMER suite (tools: homer)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"agat/spfilterbyorfsize": null,
"annotsv/installannotations": null,
"homer/findpeaks": null,
"ctatsplicing/startocancerintrons": null,
"tximeta/tximport": null... | homer/findpeaks | 2 |
mod_agat_convertbed2gff_1 | tool_selection | "In Nextflow DSL2, which module handles: Takes a bed12 file and converts to a GFF3 file (tools: agat)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"agat_convertgff2bed": "Takes a GFF3 file and converts to a bed12 file",
"agat_convertbed2gff": "Takes a bed12 file and converts to a GFF3 file",
"angsd_gl": "Calculat... | agat_convertbed2gff | 1 |
qc_adapt_ont_ultra_long_2_12 | qc_read_adaptation | {
"assay": "Ultra-long Oxford Nanopore genomic DNA reads",
"tool": "FastQC",
"read_type": "long_reads_20kb_plus"
} | {
"type": "choice",
"instructions": "Evaluate the quality control tool choice for: Ultra-long Oxford Nanopore genomic DNA reads (long_reads_20kb_plus).",
"criteria": {
"Drop FastQC": null,
"Keep FastQC": null,
"Swap for NanoPlot": null
}
} | Swap for NanoPlot | 2 |
field_constraint_bai_0_3 | samplesheet_schema | {
"field_name": "bai",
"datatype": "companion_index",
"description": "Companion BAM index file"
} | {
"type": "choice",
"instructions": "What is the JSON Schema validation constraint for samplesheet column 'bai'?",
"criteria": {
"type: boolean": "Boolean flag",
"pattern: ^\\S+\\.crai$": "CRAM index format",
"pattern: ^\\S+\\.bam\\.bai$ or ^\\S+\\.bai$": "Filename regex ensuring companion index with ... | pattern: ^\S+\.bam\.bai$ or ^\S+\.bai$ | 2 |
resource_bracken_bracken_4 | resource_profiling | {
"process": "BRACKEN_BRACKEN",
"tool": "bracken/bracken",
"description": "Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BRACKEN_BRACKEN (Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.) in conf/base.config?",
"criteria": {
"process_single": null,
"process_low": null,
"process_high": null,
"process_mediu... | process_single | 0 |
mod_fcsgx_fetchdb_0 | tool_selection | "In Nextflow DSL2, which module handles: Fetches the NCBI FCS-GX database using a provided manifest URL (tools: fcsgx)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"tabix/bgziptabix": "DEPRECATED. Use HTSLIB/BGZIPTABIX instead. bgzip a sorted tab-delimited genome file and then create tabix inde",
"hamronization/summarize": "Tool to s... | fcsgx/fetchdb | 3 |
mod_angsd_dosaf_1 | tool_selection | "In Nextflow DSL2, which module handles: Estimate site allele frequencies from BAM files. (tools: angsd)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"fastx_collapser": "Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts)",
"angsd_gl": "Calculated genotype likelihoods ... | angsd_dosaf | 3 |
mod_fastq_remove_rrna_0 | tool_selection | "In Nextflow DSL2, which module handles: Remove ribosomal RNA reads from FASTQ files using SortMeRNA, RiboDetector, or Bowtie2 (tools: fastq_remove_rrna)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"fastq_remove_rrna": "Remove ribosomal RNA reads from FASTQ files using SortMeRNA, RiboDetector, or Bowtie2",
"shinyngs/staticexploratory": "Make exploratory plots for ana... | fastq_remove_rrna | 0 |
pipe_all101_eager_5 | pipeline_routing | "I need to run an end-to-end bioinformatics workflow to analyze A fully reproducible and state-of-the-art ancient DNA analysis pipeline. Topics: adna, ancient-dna-analysis, ancientdna, genome, metagenomics, pathogen-genomics. . Which nf-core pipeline should I execute?" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"airrflow": "B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framewo",
"multiplesequencealign": "A pipeline to run... | eager | 7 |
noul_modifying_channel_meta_inside_bash_script_block_7 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"You can modify the properties of a channel's `meta` map directly inside the process `script:` section using Groovy syntax.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards."
} | false | 0 |
noul_channel_operator_map_14 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"The `.map { meta, reads -> [ meta, reads ] }` channel operator transforms channel emissions synchronously.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards.",
"criteria": {
"false": "The statement describes an invalid Nextflow DSL2 syntax, anti-pattern, or deprecated behavior.",
"true": "The statement describes a valid, standard, and re... | true | 1 |
pipe_all101_kmermaid_3 | pipeline_routing | "Recommend the most appropriate nf-core workflow for the following project: k-mer similarity analysis pipeline. Topics: k-mer, kmer, kmer-counting, kmer-frequency-count. " | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"kmermaid": null,
"longraredisease": null,
"nanoseq": null,
"hadge": null,
"stableexpression": null,
"viralrecon": null,
"mnaseseq": null,
"variantbenchmar... | kmermaid | 0 |
mod_fasta_index_methylseq_1 | tool_selection | "In Nextflow DSL2, which module handles: Generate index files from reference fasta for bismark, bwameth and bwamem aligners (tools: fasta_index_methylseq)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"bismark_deduplicate": null,
"centrifuger_build": null,
"bismark_methylationextractor": null,
"fasta_index_methylseq": null,
"truvari_segment": null
}
} | fasta_index_methylseq | 3 |
mod_drep_dereplicate_1 | tool_selection | "In Nextflow DSL2, which module handles: Dereplicates a genome set by identifying highly similar genomes and choose the best representative genome (tools: drep)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"agat_convertspgff2gtf": "Converts a GFF/GTF file into a proper GTF file",
"abyss_abysspe": "ABySS is a de novo sequence assembler intended for short paired-end reads and ... | drep_dereplicate | 3 |
pipe_core10_taxprofiler_1_described | pipeline_routing | "Which released nf-core pipeline is specifically built for this assay? Shotgun metagenomic profiling combining multiple taxonomic classifiers into harmonized multi-sample reports." | {
"type": "choice",
"instructions": "Select the released nf-core pipeline designed for this assay.",
"criteria": {
"eager": "A fully reproducible and state-of-the-art ancient DNA analysis pipeline (adna, ancient-dna-analysis, ancientdna, genome)",
"viralrecon": "Assembly and intrahost/low-frequency varian... | taxprofiler | 7 |
mod_bcftools_split_0 | tool_selection | "In Nextflow DSL2, which module handles: Split a vcf file into files per chromosome (tools: bcftools)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"bcftools/split": "Split a vcf file into files per chromosome",
"rseqc/splitbam": "Split BAM file based on gene list in BED format",
"atlas/call": "generate VCF file f... | bcftools/split | 0 |
resource_atlas_pmd_4 | resource_profiling | {
"process": "ATLAS_PMD",
"tool": "atlas/pmd",
"description": "Estimate the post-mortem damage patterns of DNA"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to ATLAS_PMD (Estimate the post-mortem damage patterns of DNA) in conf/base.config?",
"criteria": {
"process_long": null,
"process_medium": null,
"process_high": null,
"process_single": null
}
} | process_single | 3 |
mod_deeptools_plotheatmap_0 | tool_selection | "In Nextflow DSL2, which module handles: plots values produced by deeptools_computematrix as a heatmap (tools: deeptools)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"rundbcan/easysubstrate": "Substrate annotation module for the dbcan pipeline. This module is used to annotate carbohydrate-active enzyme",
"krona/ktimporttaxonomy": "Kron... | deeptools/plotheatmap | 2 |
samplesheet_arch_mira_influenza_sc2_0_10 | samplesheet_schema | {
"assay": "Custom MIRA-NF Influenza and SARS-CoV-2 targeted consensus pipeline",
"first_step": "INPUT_CHECK",
"inputs": "Paired-end surveillance FASTQs from respiratory pathogen panels",
"pipeline": "custom/mira-nf"
} | {
"type": "choice",
"instructions": "Which columns should the input samplesheet have for: Custom MIRA-NF Influenza and SARS-CoV-2 targeted consensus pipeline?",
"criteria": {
"sample,fastq_1,fastq_2": null,
"sample,fastq_1": null,
"sample,bam": null,
"sample,vcf": null,
"sample,reference_segme... | sample,fastq_1,fastq_2 | 0 |
qc_adapt_bulk_multiqc_2_42 | qc_read_adaptation | {
"assay": "High-throughput bulk WGS multi-sample run",
"tool": "MultiQC",
"read_type": "summary_reporting"
} | {
"type": "choice",
"instructions": "Evaluate the quality control tool choice for: High-throughput bulk WGS multi-sample run (summary_reporting).",
"criteria": {
"Keep MultiQC": null,
"Keep FastQC": null,
"Swap for NanoPlot": null,
"Drop MultiQC": null
}
} | Keep MultiQC | 0 |
qc_adapt_pacbio_hifi_0_6 | qc_read_adaptation | {
"assay": "PacBio HiFi circular consensus sequencing (CCS)",
"tool": "FastQC",
"read_type": "long_reads_hifi_15kb"
} | {
"type": "choice",
"instructions": "For PacBio HiFi circular consensus sequencing (CCS), what is the recommended QC default for FastQC?",
"criteria": {
"Keep FastQC": null,
"Swap for NanoPlot": null,
"Drop FastQC": null
}
} | Swap for NanoPlot | 1 |
mod_pigz_compress_0 | tool_selection | "In Nextflow DSL2, which module handles: Compresses files with pigz. (tools: pigz)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"pigz/compress": "Compresses files with pigz.",
"tabix/bgzip": "DEPRECATED. Use HTSLIB/BGZIPTABIX instead. Compresses/decompresses files",
"maltextract": "Tool for eva... | pigz/compress | 0 |
pipe_all101_mcmicro_0 | pipeline_routing | "I need to run an end-to-end bioinformatics workflow to analyze An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.. Topics: bioformats, image-analysis, image-processing, microscopy, multiplexed-imaging, ome-tiff. . Which nf-core pipeline should I execute?" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"lsmquant": null,
"mcmicro": null,
"rnasplice": null,
"magmap": null,
"hicar": null
}
} | mcmicro | 1 |
mod_svdb_query_0 | tool_selection | "In Nextflow DSL2, which module handles: Query a structural variant database, using a vcf file as query (tools: svdb)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"svdb/query": "Query a structural variant database, using a vcf file as query",
"caddsv/run": "Score structural variants with CADD-SV.",
"tmb/pytmb": "This module calc... | svdb/query | 0 |
samplesheet_arch_proteomics_dia_0_9 | samplesheet_schema | {
"assay": "Data-Independent Acquisition (DIA) quantitative mass spectrometry",
"first_step": "INPUT_CHECK",
"inputs": "Thermo / Bruker RAW or mzML mass spectrometry runs across biological conditions",
"pipeline": "nf-core/diaproteomics"
} | {
"type": "choice",
"instructions": "Which columns should the input samplesheet have for: Data-Independent Acquisition (DIA) quantitative mass spectrometry?",
"criteria": {
"sample,peptides_tsv": "Processed peptide intensity table",
"sample,mzml": "mzML file without biological group assignment",
"samp... | sample,raw_file,condition | 4 |
subworkflow_pkg_bam_dedup_stats_samtools_umitools_2 | subworkflow_packaging | {
"subworkflow": "BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS",
"modules": [
"umitools/dedup",
"samtools/index",
"samtools/view",
"samtools/stats",
"samtools/idxstats",
"samtools/flagstat",
"bam_stats_samtools"
],
"description": "UMI-tools dedup, index BAM file and run samtools stats, flagstat... | {
"type": "choice",
"instructions": "How should BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS (umitools/dedup, samtools/index, samtools/view, samtools/stats, samtools/idxstats, samtools/flagstat, bam_stats_samtools) be structured in DSL2?",
"criteria": {
"Keep the modules in the main workflow": null,
"Leave them out"... | Use nf-core subworkflow bam_dedup_stats_samtools_umitools | 3 |
samplesheet_arch_viral_ont_single_0_8 | samplesheet_schema | {
"assay": "Viral genome sequencing on Oxford Nanopore MinION / GridION",
"first_step": "NANOPLOT",
"inputs": "Demultiplexed single-end long reads from tiled viral amplicons",
"pipeline": "nf-core/viralrecon"
} | {
"type": "choice",
"instructions": "Which columns should the input samplesheet have for: Viral genome sequencing on Oxford Nanopore MinION / GridION?",
"criteria": {
"sample,bam": "Aligned BAM files",
"sample,fasta": "Assembled viral genome",
"sample,vcf": "Variant list",
"sample,fastq_1": "Singl... | sample,fastq_1 | 3 |
samplesheet_arch_epigenomics_hic_2_10 | samplesheet_schema | {
"pipeline": "nf-core/hic",
"assay_type": "Hi-C chromosome conformation capture mapping",
"data_format": "Paired-end proximity ligation FASTQs with restriction enzyme digestion specification"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected when inputs are: Paired-end proximity ligation FASTQs with restriction enzyme digestion specification?",
"criteria": {
"sample,fastq_1,fastq_2": "Hi-C proximity ligation paired-end FASTQ sequencing reads",
"sample,bed": "Restrictio... | sample,fastq_1,fastq_2 | 0 |
resource_bwa_index_3 | resource_profiling | {
"process": "BWA_INDEX",
"tool": "bwa/index",
"description": "Create BWA index for reference genome"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BWA_INDEX (Create BWA index for reference genome) in conf/base.config?",
"criteria": {
"process_single": null,
"process_high": null,
"process_low": null,
"process_long": null
}
} | process_high | 1 |
samplesheet_arch_spatial_visium_2_2 | samplesheet_schema | {
"pipeline": "nf-core/spatialaxe",
"assay_type": "10x Visium spatial transcriptomics with histology image",
"data_format": "Spatial cDNA FASTQs paired with high-resolution brightfield tissue image and slide coordinates"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected when inputs are: Spatial cDNA FASTQs paired with high-resolution brightfield tissue image and slide coordinates?",
"criteria": {
"sample,bam": "Aligned BAM file",
"sample,image": "Image file only without sequencing data",
"samp... | sample,fastq_1,fastq_2,image,slide,area | 2 |
field_constraint_sample_3_2 | samplesheet_schema | {
"schema_target": "assets/schema_input.json",
"field": "sample",
"validation_type": "unique_identifier"
} | {
"type": "choice",
"instructions": "Select the appropriate draft-07 JSON Schema property specification for 'sample'.",
"criteria": {
"type: integer": "Numeric integer constraint",
"enum: [0, 1]": "Binary integer enum",
"pattern: ^\\S+$ (no whitespace, unique)": "String without whitespace serving as u... | pattern: ^\S+$ (no whitespace, unique) | 2 |
resource_arcashla_extract_5 | resource_profiling | {
"process": "ARCASHLA_EXTRACT",
"tool": "arcashla/extract",
"description": "Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to ARCASHLA_EXTRACT (Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alterna) in conf/base.config?",
"criteria": {
"process_low": null,
"process_high": null,
"process_single": null,
"proces... | process_single | 2 |
mod_toulligqc_0 | tool_selection | "In Nextflow DSL2, which module handles: A post sequencing QC tool for Oxford Nanopore sequencers (tools: toulligqc)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"toulligqc": "A post sequencing QC tool for Oxford Nanopore sequencers",
"seqfu/derep": "Dereplicate FASTX sequences, removing duplicate sequences and printing the number ... | toulligqc | 0 |
mod_pridepy_fetchsdrf_0 | tool_selection | "In Nextflow DSL2, which module handles: Fetch an SDRF file from the PRIDE Archive for a given project accession. (tools: pridepy)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"diamond/cluster": "calculate clusters of highly similar sequences",
"pridepy/fetchsdrf": "Fetch an SDRF file from the PRIDE Archive for a given project accession.",
"... | pridepy/fetchsdrf | 1 |
field_constraint_phenotype_1_3 | samplesheet_schema | {
"column": "phenotype",
"purpose": "Affection status in clinical trio / family analysis"
} | {
"type": "choice",
"instructions": "Determine the schema validation rule for field 'phenotype' (Affection status in clinical trio / family analysis).",
"criteria": {
"enum: [normal, tumor]": null,
"enum: [0, 1, 2, -9] (1=unaffected, 2=affected)": null,
"type: string free-text": null,
"format: fil... | enum: [0, 1, 2, -9] (1=unaffected, 2=affected) | 1 |
samplesheet_arch_taxprofiler_shotgun_1_8 | samplesheet_schema | {
"technology": "Metagenomics Profiling",
"workflow_entry": "FASTQC",
"library_inputs": "Short or long reads with run accession and library instrument platform"
} | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for Multi-taxonomic profiling of complex metagenomic shotgun reads with entry step FASTQC.",
"criteria": {
"sample,run_accession,instrument_platform,fastq_1,fastq_2": "Taxonomic profiling samplesheet tracking sample, run ac... | sample,run_accession,instrument_platform,fastq_1,fastq_2 | 0 |
pipe_all101_kmermaid_1 | pipeline_routing | "User query: What is the official nf-core pipeline for k-mer analysis? Specific context: k-mer similarity analysis pipeline. Topics: k-mer, kmer, kmer-counting, kmer-frequency-count. " | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"funcprofiler": "Read-based functional profiling of microbiome sequencing data",
"lsmquant": "A pipeline for processing and analysis of light-sheet microscopy images. [3dunet, ima... | kmermaid | 4 |
End of preview. Expand in Data Studio
📊 nf-pilot-decisions (Primeomicx/nf-pilot-decisions)
The Ground-Truth Decision Dataset for Nextflow DSL2 & nf-core Architecture
nf-pilot-decisions is a standardized, multi-task decision-layer dataset for training autonomous Nextflow co-pilots and System-1 fast routing engines across the complete nf-core bioinformatics ecosystem.
📊 Dataset Structure & Pillar Breakdown
Contains 11,654 curated decision records across 8 core architectural pillars:
| Pillar | Records | Description |
|---|---|---|
| Tool & Module Selection | 4,426 | Disambiguation across 2,153 official nf-core modules and BioContainers. |
| Samplesheet Schema & Headers | 1,950 | JSON Schema draft-07 types, enums, regex patterns, and formats for samplesheet fields. |
| QC Read Length Adaptation | 1,500 | Quality control tool selection across Illumina short-reads, PacBio HiFi, and ONT long-reads. |
| Resource Profiling & Directives | 1,500 | Memory, CPU, time, and dynamic retry/error-strategy directive rules for pipeline processes. |
| DSL2 Syntax & Best Practices | 800 | Nextflow channel emitting patterns, publishDir policies, and anti-pattern filtering. |
| Pipeline Routing | 656 | Matching user biological assay descriptions to official nf-core pipelines. |
| Subworkflow Packaging | 622 | Determining when to wrap multi-process chains into reusable subworkflows. |
| Task Intent Routing | 200 | Categorizing user intent across synthesis, debugging, parameter tuning, and execution. |
🗂️ Split Information
| Split | Records | Percentage | File Path |
|---|---|---|---|
| Train | 9,324 | 80.0% | data/train.jsonl |
| Validation | 1,165 | 10.0% | data/validation.jsonl |
| Test | 1,165 | 10.0% | data/test.jsonl |
| Total | 11,654 | 100.0% |
🚀 Quickstart
from datasets import load_dataset
dataset = load_dataset("Primeomicx/nf-pilot-decisions")
print(dataset)
🤖 Trained Model
This dataset powers Primeomicx/nf-pilot, the autonomous System-1 Nextflow co-pilot.
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