Datasets:

Primeomicx
/

nfcore-laya-decisions

id stringlengths 9 67	category stringclasses 8 values	state unknown	question unknown	target stringlengths 3 73	target_idx int64 0 9
qc_adapt_targeted_amplicon_1_48	qc_read_adaptation	{ "assay": "Targeted Illumina amplicon panel", "tool": "FastQC", "read_type": "short_reads_pe250" }	{ "type": "choice", "instructions": "How should QC step FastQC be configured given sequencing characteristics: short_reads_pe250?", "criteria": { "Keep FastQC": null, "Swap for NanoPlot": null, "Drop FastQC": null } }	Keep FastQC	0
resource_angsd_realsfs_3	resource_profiling	{ "process": "ANGSD_REALSFS", "tool": "angsd/realsfs", "description": "Estimate site frequency spectrum from site allele frequencies" }	{ "type": "choice", "instructions": "What resource profile label should be assigned to ANGSD_REALSFS (Estimate site frequency spectrum from site allele frequencies) in conf/base.config?", "criteria": { "process_single": null, "process_low": null, "process_high": null, "process_medium": null } }	process_single	0
subworkflow_pkg_fasta_consensus_autocycler_2	subworkflow_packaging	{ "subworkflow": "FASTA_CONSENSUS_AUTOCYCLER", "modules": [ "autocycler/compress", "autocycler/cluster", "autocycler/trim", "autocycler/resolve", "autocycler/combine" ], "description": "Generate consensus assemblies and assembly graphs from grouped contig FASTA files using autocycler" }	{ "type": "choice", "instructions": "How should FASTA_CONSENSUS_AUTOCYCLER (autocycler/compress, autocycler/cluster, autocycler/trim, autocycler/resolve, autocycler/combine) be structured in DSL2?", "criteria": { "Leave them out": null, "Local subworkflow FASTA_CONSENSUS_AUTOCYCLER": null, "Use nf-cor...	Use nf-core subworkflow fasta_consensus_autocycler	2
samplesheet_scrna_10x_0_44	samplesheet_schema	{ "assay": "Single-cell 10x Genomics 3-prime gene expression", "first_step": "CELLRANGER", "inputs": "Cellular barcode FASTQ pairs" }	{ "type": "choice", "instructions": "Which columns should the input samplesheet have for: Single-cell 10x Genomics 3-prime gene expression?", "criteria": { "sample,barcode,fastq": null, "sample,features": null, "sample,bam": null, "sample,fastq_1": null, "sample,fastq_1,fastq_2": null } }	sample,fastq_1,fastq_2	4
qc_adapt_ont_nanoplot_0_2	qc_read_adaptation	{ "assay": "Direct RNA sequencing on Oxford Nanopore PromethION", "tool": "FastQC", "read_type": "long_reads_direct_rna" }	{ "type": "choice", "instructions": "For Direct RNA sequencing on Oxford Nanopore PromethION, what is the recommended QC default for FastQC?", "criteria": { "Drop FastQC": null, "Keep FastQC": null, "Swap for NanoPlot": null } }	Swap for NanoPlot	2
mod_arriba_download_0	tool_selection	"In Nextflow DSL2, which module handles: Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. (tools: arriba)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "parabricks/starfusion": "This tool uses the GPU to perform fusion calling for RNA-Seq samples, utilizing the STAR-Fusion algorithm. Thi", "igv/js": "igv.js is an embeddab...	arriba/download	4
samplesheet_atacseq_pe_2_45	samplesheet_schema	{ "assay": "Paired-end ATAC-seq chromatin accessibility", "first_step": "FASTQC", "inputs": "Paired-end Tn5 transposed FASTQs" }	{ "type": "choice", "instructions": "What samplesheet CSV header schema is expected when inputs are: Paired-end Tn5 transposed FASTQs?", "criteria": { "sample,fastq_1": null, "sample,bam": null, "sample,fastq_1,fastq_2": null, "sample,vcf": null, "sample,bed": null } }	sample,fastq_1,fastq_2	2
mod_vsearch_fastqfilter_0	tool_selection	"In Nextflow DSL2, which module handles: Performs quality filtering and / or conversion of a FASTQ file to FASTA format. (tools: vsearch)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "sentieon/dnamodelapply": null, "vsearch/cluster": null, "vsearch/fastqfilter": null, "vsearch/sintax": null, "catpack/summarise": null } }	vsearch/fastqfilter	2
mod_gatk4_calculatecontamination_1	tool_selection	"In Nextflow DSL2, which module handles: Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls. (tools: gatk4)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "gatk4_applyvqsr": "Apply a score cutoff to filter variants based on a recalibration table.\nAplyVQSR performs the second pass in a", "gatk4_calculatecontamination": "Calc...	gatk4_calculatecontamination	1
samplesheet_mag_grouped_2_46	samplesheet_schema	{ "assay": "Metagenomic MAG assembly with comparative groups", "first_step": "FASTQC", "inputs": "template: nf-core/mag" }	{ "type": "choice", "instructions": "What samplesheet CSV header schema is expected when inputs are: template: nf-core/mag?", "criteria": { "sample,fastq_1,fastq_2,group": null, "sample,group,short_reads": null, "sample,fastq_1,fastq_2": null, "sample,bam": null, "sample,fastq_1": null } }	sample,fastq_1,fastq_2,group	0
resource_basicpy_2	resource_profiling	{ "process": "BASICPY", "tool": "basicpy", "description": "BaSiCPy is a python package for background and shading correction of optical microscopy images. It is developed based on the Matlab version of BaSiC tool with major improvements in the algorithm." }	{ "type": "choice", "instructions": "What resource profile label should be assigned to BASICPY (BaSiCPy is a python package for background and shading correction of optical mic) in conf/base.config?", "criteria": { "process_long": null, "process_low": null, "process_single": null, "process_medium"...	process_single	2
local_subworkflow_checkirma_2_1	subworkflow_packaging	{ "subworkflow": "CHECKIRMA", "modules": [ "custom/checkirma" ], "description": "Custom validation of assembly output" }	{ "type": "choice", "instructions": "Determine the DSL2 structure for CHECKIRMA (custom/checkirma).", "criteria": { "Leave them out": null, "Local subworkflow CHECKIRMA": null, "Use nf-core subworkflow checkirma": null, "Keep the modules in the main workflow": null } }	Local subworkflow CHECKIRMA	1
mod_cnvkit_reference_0	tool_selection	"In Nextflow DSL2, which module handles: Compile a coverage reference from the given files (normal samples). (tools: cnvkit)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "ilastik/multicut": "Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells", "cnvkit/export": "Convert copy number...	cnvkit/reference	2
pipe_all101_oncoanalyser_1	pipeline_routing	"User query: What is the official nf-core pipeline for cancer analysis? Specific context: A comprehensive cancer DNA/RNA analysis and reporting pipeline. Topics: cancer, clinical, ctdna, dna, exome, longitudinal. "	{ "type": "choice", "instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.", "criteria": { "taxprofiler": "Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data [classification, illumina", "oncoanalyser": "A comprehensive cancer ...	oncoanalyser	1
noul_channel_factory_inside_process_body_7	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." }	false	0
resource_bedtools_unionbedg_2	resource_profiling	{ "process": "BEDTOOLS_UNIONBEDG", "tool": "bedtools/unionbedg", "description": "Combines multiple BedGraph files into a single file" }	{ "type": "choice", "instructions": "What resource profile label should be assigned to BEDTOOLS_UNIONBEDG (Combines multiple BedGraph files into a single file) in conf/base.config?", "criteria": { "process_single": null, "process_medium": null, "process_long": null, "process_high": null } }	process_single	0
mod_huggingface_download_0	tool_selection	"In Nextflow DSL2, which module handles: Download a file from a Hugging Face Hub repository using the `hf` CLI (tools: huggingface_hub)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "blast/updateblastdb": "Downloads a BLAST database from NCBI", "jvarkit/vcf2table": "Convert VCF to a user friendly table", "picard/collecthsmetrics": "Collects hybrid...	huggingface/download	3
resource_artic_minion_2	resource_profiling	{ "process": "ARTIC_MINION", "tool": "artic/minion", "description": "Run the alignment/variant-call/consensus logic of the artic pipeline" }	{ "type": "choice", "instructions": "What resource profile label should be assigned to ARTIC_MINION (Run the alignment/variant-call/consensus logic of the artic pipeline) in conf/base.config?", "criteria": { "process_long": null, "process_single": null, "process_medium": null, "process_low": null ...	process_single	1
mod_cooler_merge_1	tool_selection	"In Nextflow DSL2, which module handles: Merge multiple coolers with identical axes (tools: cooler)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "biobambam_bammerge": null, "seqkit_seq": null, "cooler_merge": null, "fmhfunprofiler": null, "concoct_extractfastabins": null } }	cooler_merge	2
subworkflow_pkg_vcf_annotate_snpeff_0	subworkflow_packaging	{ "subworkflow": "VCF_ANNOTATE_SNPEFF", "modules": [ "snpeff", "snpeff/snpeff", "htslib/bgziptabix" ], "description": "Perform annotation with snpEff and bgzip + tabix index the resulting VCF file" }	{ "type": "choice", "instructions": "How should VCF_ANNOTATE_SNPEFF (snpeff, snpeff/snpeff, htslib/bgziptabix) be structured in DSL2?", "criteria": { "Keep the modules in the main workflow": null, "Local subworkflow VCF_ANNOTATE_SNPEFF": null, "Leave them out": null, "Use nf-core subworkflow vcf_a...	Use nf-core subworkflow vcf_annotate_snpeff	3
samplesheet_ont_pcr_amplicon_2_2	samplesheet_schema	{ "assay": "Viral amplicon sequencing on Oxford Nanopore (ARTIC)", "first_step": "NANOPLOT", "inputs": "Single-end FASTQ reads" }	{ "type": "choice", "instructions": "What samplesheet CSV header schema is expected when inputs are: Single-end FASTQ reads?", "criteria": { "sample,primer_bed": null, "sample,bam": null, "sample,fastq_1,fastq_2": null, "sample,fastq_1": null, "sample,vcf": null } }	sample,fastq_1	3
resource_bismark_summary_1	resource_profiling	{ "process": "BISMARK_SUMMARY", "tool": "bismark/summary", "description": "Uses Bismark report files of several samples in a run folder to generate a graphical summary HTML report." }	{ "type": "choice", "instructions": "What resource profile label should be assigned to BISMARK_SUMMARY (Uses Bismark report files of several samples in a run folder to generate a graph) in conf/base.config?", "criteria": { "process_medium": null, "process_high": null, "process_low": null, "process...	process_single	3
samplesheet_chipseq_ctrl_0_55	samplesheet_schema	{ "assay": "ChIP-seq with antibody and input controls", "first_step": "TRIMGALORE", "inputs": "Paired-end FASTQ with controls" }	{ "type": "choice", "instructions": "Which columns should the input samplesheet have for: ChIP-seq with antibody and input controls?", "criteria": { "sample,vcf": null, "sample,bam": null, "sample,fastq_1,antibody": null, "sample,fastq_1,fastq_2,antibody,control": null, "sample,fastq_1,fastq_2...	sample,fastq_1,fastq_2,antibody,control	3
resource_artic_guppyplex_4	resource_profiling	{ "process": "ARTIC_GUPPYPLEX", "tool": "artic/guppyplex", "description": "Aggregates fastq files with demultiplexed reads" }	{ "type": "choice", "instructions": "What resource profile label should be assigned to ARTIC_GUPPYPLEX (Aggregates fastq files with demultiplexed reads) in conf/base.config?", "criteria": { "process_medium": null, "process_single": null, "process_long": null, "process_high": null } }	process_single	1
mod_fq_lint_0	tool_selection	"In Nextflow DSL2, which module handles: fq lint is a FASTQ file pair validator. (tools: fq)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "ariba/getref": "Download and prepare database for Ariba analysis", "vsearch/fastqfilter": "Performs quality filtering and / or conversion of a FASTQ file to FASTA format....	fq/lint	4
noul_exit_code_137_cause_18	dsl2_rules	"Is this statement accurate according to standard Nextflow DSL2 behavior? \"An exit code of 137 in a containerized Nextflow task is typically caused by a missing shell command.\""	{ "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
mod_simpleaf_index_1	tool_selection	"In Nextflow DSL2, which module handles: Indexing of transcriptome for gene expression quantification using SimpleAF (tools: simpleaf)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "mmseqs_createindex": "Creates sequence index for mmseqs database", "ganon_buildcustom": "Build ganon database using custom reference sequences.", "hmmer_eslsfetchinde...	simpleaf_index	4
subworkflow_pkg_fastq_align_dedup_bismark_3	subworkflow_packaging	{ "subworkflow": "FASTQ_ALIGN_DEDUP_BISMARK", "modules": [ "bismark/align", "samtools/sort", "samtools/index", "bismark/deduplicate", "bismark/methylationextractor", "bismark/coverage2cytosine", "bismark/report", "bismark/summary" ], "description": "Align BS-Seq reads to a refere...	{ "type": "choice", "instructions": "How should FASTQ_ALIGN_DEDUP_BISMARK (bismark/align, samtools/sort, samtools/index, bismark/deduplicate, bismark/methylationextractor, bismark/coverage2cytosine, bismark/report, bismark/summary) be structured in DSL2?", "criteria": { "Local subworkflow FASTQ_ALIGN_DEDUP_BI...	Use nf-core subworkflow fastq_align_dedup_bismark	3
noul_named_process_output_emits_3	dsl2_rules	"Is this statement accurate according to standard Nextflow DSL2 behavior? \"Nextflow DSL2 supports multi-channel emission from processes using named emit blocks: `path '*.bam', emit: bam`.\""	{ "type": "noul", "instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards." }	true	1
subworkflow_pkg_fastq_align_hisat2_0	subworkflow_packaging	{ "subworkflow": "FASTQ_ALIGN_HISAT2", "modules": [ "hisat2/align", "samtools/stats", "samtools/idxstats", "samtools/flagstat", "bam_sort_stats_samtools" ], "description": "Align reads to a reference genome using hisat2 then sort with samtools" }	{ "type": "choice", "instructions": "How should FASTQ_ALIGN_HISAT2 (hisat2/align, samtools/stats, samtools/idxstats, samtools/flagstat, bam_sort_stats_samtools) be structured in DSL2?", "criteria": { "Local subworkflow FASTQ_ALIGN_HISAT2": null, "Keep the modules in the main workflow": null, "Use nf-c...	Use nf-core subworkflow fastq_align_hisat2	2
qc_adapt_pacbio_hifi_2_10	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": { "Keep FastQC": null, "Swap for NanoPlot": null, "Drop FastQC": null } }	Swap for NanoPlot	1
resource_arcashla_extract_2	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_medium": null, "process_single": null, "process_high": null, "pro...	process_single	1
subworkflow_pkg_bam_variant_calling_sort_freebayes_bcftools_0	subworkflow_packaging	{ "subworkflow": "BAM_VARIANT_CALLING_SORT_FREEBAYES_BCFTOOLS", "modules": [ "freebayes", "bcftools/sort" ], "description": "Call variants using freebayes, then sort and index" }	{ "type": "choice", "instructions": "How should BAM_VARIANT_CALLING_SORT_FREEBAYES_BCFTOOLS (freebayes, bcftools/sort) be structured in DSL2?", "criteria": { "Keep the modules in the main workflow": null, "Use nf-core subworkflow bam_variant_calling_sort_freebayes_bcftools": null, "Leave them out": nu...	Use nf-core subworkflow bam_variant_calling_sort_freebayes_bcftools	1
mod_hpsuissero_0	tool_selection	"In Nextflow DSL2, which module handles: Serotype prediction of Haemophilus parasuis assemblies (tools: hpsuissero)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "hpsuissero": "Serotype prediction of Haemophilus parasuis assemblies", "abricate/summary": "Screen assemblies for antimicrobial resistance against multiple databases", ...	hpsuissero	0
pipe_all101_rnaseq_4	pipeline_routing	"Which pipeline implements best-practice processing for: RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.. Topics: rna, rna-seq. ?"	{ "type": "choice", "instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.", "criteria": { "scrnaseq": "Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligner", "viralmetagenome": "A nf-core pipeline for ...	rnaseq	2
intent_ask_question_24	intent_routing	"Classify this user request: \"How does the .mix() operator differ from .combine() in Nextflow?\""	{ "type": "choice", "instructions": "Classify the user intent into one category.", "criteria": { "debug_error": "User is reporting a runtime error, exit code (137, 127), task failure, or pipeline crash", "prepare_data": "User needs help creating a samplesheet, parsing FASTQ/BAM filenames, or staging refer...	ask_question	3
mod_idemux_1	tool_selection	"In Nextflow DSL2, which module handles: Demultiplex paired-end FASTQ files from QuantSeq-Pool (tools: idemux)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "bases2fastq": "Demultiplex Element Biosciences bases files", "dshbio_exportsegments": "Export assembly segment sequences in GFA 1.0 format to FASTA format", "qcat": "...	idemux	3
resource_backsub_4	resource_profiling	{ "process": "BACKSUB", "tool": "backsub", "description": "Pixel-by-pixel channel subtraction tool for multiplexed immunofluorescence data." }	{ "type": "choice", "instructions": "What resource profile label should be assigned to BACKSUB (Pixel-by-pixel channel subtraction tool for multiplexed immunofluorescence data.) in conf/base.config?", "criteria": { "process_single": null, "process_long": null, "process_medium": null, "process_low"...	process_single	0
samplesheet_bam_variant_1_38	samplesheet_schema	{ "assay": "Pre-aligned BAM variant calling pipeline", "first_step": "GATK_HAPLOTYPECALLER", "inputs": "Aligned BAM files" }	{ "type": "choice", "instructions": "Define the required samplesheet columns for Pre-aligned BAM variant calling pipeline with entry step GATK_HAPLOTYPECALLER.", "criteria": { "sample,bam,bai": null, "sample,fastq_1": null, "sample,bam": null, "sample,vcf": null, "sample,fastq_1,fastq_2": null...	sample,bam,bai	0
resource_bbmap_bbsplit_2	resource_profiling	{ "process": "BBMAP_BBSPLIT", "tool": "bbmap/bbsplit", "description": "Split sequencing reads by mapping them to multiple references simultaneously" }	{ "type": "choice", "instructions": "What resource profile label should be assigned to BBMAP_BBSPLIT (Split sequencing reads by mapping them to multiple references simultaneously) in conf/base.config?", "criteria": { "process_single": null, "process_medium": null, "process_low": null, "process_lon...	process_single	0
samplesheet_amplicon_16s_2_56	samplesheet_schema	{ "assay": "Amplicon 16S microbiome profiling", "first_step": "DADA2", "inputs": "Paired-end 16S amplicon FASTQs" }	{ "type": "choice", "instructions": "What samplesheet CSV header schema is expected when inputs are: Paired-end 16S amplicon FASTQs?", "criteria": { "sample,bam": null, "sample,vcf": null, "sample,fastq_1,fastq_2": null, "sample,fastq_1": null, "sample,fasta": null } }	sample,fastq_1,fastq_2	2
mod_cdhit_cdhitest_1	tool_selection	"In Nextflow DSL2, which module handles: Cluster nucleotide sequences using sequence similarity (tools: cdhit)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "cdhit_cdhitest": "Cluster nucleotide sequences using sequence similarity", "galah": "Cluster genome FASTA files by average nucleotide identity", "paraclu": "Paraclu f...	cdhit_cdhitest	0
samplesheet_chipseq_ctrl_2_64	samplesheet_schema	{ "assay": "ChIP-seq with antibody and input controls", "first_step": "TRIMGALORE", "inputs": "Paired-end FASTQ with controls" }	{ "type": "choice", "instructions": "What samplesheet CSV header schema is expected when inputs are: Paired-end FASTQ with controls?", "criteria": { "sample,fastq_1,fastq_2": null, "sample,bam": null, "sample,fastq_1,antibody": null, "sample,vcf": null, "sample,fastq_1,fastq_2,antibody,control...	sample,fastq_1,fastq_2,antibody,control	4
mod_atlas_splitmerge_1	tool_selection	"In Nextflow DSL2, which module handles: split single end read groups by length and merge paired end reads (tools: atlas)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "bcftools_pluginsplit": "Split VCF by sample, creating single- or multi-sample VCFs.", "irescue": "Quantification of transposable elements expression in scRNA-seq", "f...	atlas_splitmerge	4
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_realsfs": "Estimate site frequency spe...	angsd_dosaf	3
mod_gatk4_annotateintervals_0	tool_selection	"In Nextflow DSL2, which module handles: Annotates intervals with GC content, mappability, and segmental-duplication content (tools: gatk4)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "faa_seqfu_seqkit": null, "agat/spfilterbyorfsize": null, "annotsv/annotsv": null, "gatk4/annotateintervals": null, "motus/merge": null } }	gatk4/annotateintervals	3
qc_adapt_ont_ultra_long_0_9	qc_read_adaptation	{ "assay": "Ultra-long Oxford Nanopore genomic DNA reads", "tool": "FastQC", "read_type": "long_reads_20kb_plus" }	{ "type": "choice", "instructions": "For Ultra-long Oxford Nanopore genomic DNA reads, what is the recommended QC default for FastQC?", "criteria": { "Swap for NanoPlot": null, "Keep FastQC": null, "Drop FastQC": null } }	Swap for NanoPlot	0
resource_angsd_realsfs_4	resource_profiling	{ "process": "ANGSD_REALSFS", "tool": "angsd/realsfs", "description": "Estimate site frequency spectrum from site allele frequencies" }	{ "type": "choice", "instructions": "What resource profile label should be assigned to ANGSD_REALSFS (Estimate site frequency spectrum from site allele frequencies) in conf/base.config?", "criteria": { "process_low": null, "process_high": null, "process_long": null, "process_single": null } }	process_single	3
noul_subworkflow_structural_blocks_14	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.", "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_viralconsensus_0	tool_selection	"In Nextflow DSL2, which module handles: Fast and memory-efficient viral consensus genome sequence generation from read alignments (tools: viralconsensus)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "mmseqs/createtaxdb": "Adds taxonomy information to an existing MMseqs2 database", "checkv/updatedatabase": "Construct the database necessary for checkv's quality assessme...	viralconsensus	4
pipe_all101_funcprofiler_5	pipeline_routing	"I need to run an end-to-end bioinformatics workflow to analyze Read-based functional profiling of microbiome sequencing data. . Which nf-core pipeline should I execute?"	{ "type": "choice", "instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.", "criteria": { "raredisease": "Call and score variants from WGS/WES of rare disease patients. [diagnostics, rare-disease, snv]", "viralintegration": "Analysis pipeline for the identification of ...	funcprofiler	7
mod_sentieon_readwriter_1	tool_selection	"In Nextflow DSL2, which module handles: Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file. (tools: sentieon)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "bcftools_merge": "Merge VCF files", "concoct_extractfastabins": "Creates a FASTA file for each new cluster assigned by CONCOCT", "sentieon_readwriter": "Merges BAM fi...	sentieon_readwriter	2
mod_tiddit_sv_1	tool_selection	"In Nextflow DSL2, which module handles: Identify chromosomal rearrangements. (tools: sv)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "tiddit_sv": null, "minimac4_compressref": null, "octopusv_correct": null, "checkm2_predict": null, "rtgtools_svdecompose": null } }	tiddit_sv	0
samplesheet_scrna_10x_0_14	samplesheet_schema	{ "assay": "Single-cell 10x Genomics 3-prime gene expression", "first_step": "CELLRANGER", "inputs": "Cellular barcode FASTQ pairs" }	{ "type": "choice", "instructions": "Which columns should the input samplesheet have for: Single-cell 10x Genomics 3-prime gene expression?", "criteria": { "sample,fastq_1,fastq_2": null, "sample,fastq_1": null, "sample,bam": null, "sample,features": null, "sample,barcode,fastq": null } }	sample,fastq_1,fastq_2	0
samplesheet_mag_grouped_0_15	samplesheet_schema	{ "assay": "Metagenomic MAG assembly with comparative groups", "first_step": "FASTQC", "inputs": "template: nf-core/mag" }	{ "type": "choice", "instructions": "Which columns should the input samplesheet have for: Metagenomic MAG assembly with comparative groups?", "criteria": { "sample,fastq_1,fastq_2,group": null, "sample,bam": null, "sample,fastq_1,fastq_2": null, "sample,fastq_1": null, "sample,group,short_read...	sample,fastq_1,fastq_2,group	0
mod_nucmer_1	tool_selection	"In Nextflow DSL2, which module handles: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences. (tools: nucmer)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "ampcombi2_parsetables": "A submodule that parses and standardizes the results from various antimicrobial peptide identification tools.", "ampcombi2_complete": "A submodul...	nucmer	3
mod_parabricks_fq2bam_0	tool_selection	"In Nextflow DSL2, which module handles: NVIDIA Clara Parabricks GPU-accelerated alignment, sorting, BQSR calculation, and duplicate marking. Note this nf-core module requires files to be copied into the working directory and not symlinked. (tools: parabricks)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "gzrt": "gzrecover is a program that will attempt to extract any readable data out of a gzip file that has been corrupt", "ampcombi2/cluster": "A submodule that clusters t...	parabricks/fq2bam	4
intent_build_pipeline_18	intent_routing	"Classify this user request: \"Write a Nextflow DSL2 workflow that takes raw ONT FASTQ files and runs Flye assembly followed by Medaka polishing.\""	{ "type": "choice", "instructions": "Classify the user intent into one category.", "criteria": { "debug_error": "User is reporting a runtime error, exit code (137, 127), task failure, or pipeline crash", "prepare_data": "User needs help creating a samplesheet, parsing FASTQ/BAM filenames, or staging refer...	build_pipeline	3
qc_adapt_ont_nanoplot_1_4	qc_read_adaptation	{ "assay": "Direct RNA sequencing on Oxford Nanopore PromethION", "tool": "FastQC", "read_type": "long_reads_direct_rna" }	{ "type": "choice", "instructions": "How should QC step FastQC be configured given sequencing characteristics: long_reads_direct_rna?", "criteria": { "Swap for NanoPlot": null, "Keep FastQC": null, "Drop FastQC": null } }	Swap for NanoPlot	0
mod_genometester4_glistmaker_1	tool_selection	"In Nextflow DSL2, which module handles: Create and count k-mer lists from nucelotide sequences. (tools: genometester4)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "blast_updateblastdb": "Downloads a BLAST database from NCBI", "hypo": "Assembly polisher using short (and long) reads", "merqury_hapmers": "A script to generate hap-m...	genometester4_glistmaker	4
noul_channel_factory_inside_process_body_6	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
subworkflow_pkg_vcf_annotate_ensemblvep_snpeff_3	subworkflow_packaging	{ "subworkflow": "VCF_ANNOTATE_ENSEMBLVEP_SNPEFF", "modules": [ "ensemblvep/download", "ensemblvep/vep", "snpeff/download", "snpeff/snpeff", "htslib/bgziptabix", "bcftools/pluginscatter", "bcftools/concat", "bcftools/sort" ], "description": "Perform annotation with ensemblvep and...	{ "type": "choice", "instructions": "How should VCF_ANNOTATE_ENSEMBLVEP_SNPEFF (ensemblvep/download, ensemblvep/vep, snpeff/download, snpeff/snpeff, htslib/bgziptabix, bcftools/pluginscatter, bcftools/concat, bcftools/sort) be structured in DSL2?", "criteria": { "Leave them out": null, "Local subworkflow ...	Use nf-core subworkflow vcf_annotate_ensemblvep_snpeff	2
pipe_all101_nascent_0	pipeline_routing	"I need to run an end-to-end bioinformatics workflow to analyze Nascent Transcription Processing Pipeline. Topics: gro-seq, nascent, pro-seq, rna, transcription, tss. . Which nf-core pipeline should I execute?"	{ "type": "choice", "instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.", "criteria": { "marsseq": null, "variantbenchmarking": null, "viralrecon": null, "reportho": null, "nascent": null, "nanoseq": null, "multiplesequencealign": null, "pixel...	nascent	4
qc_adapt_singlecell_multiqc_0_40	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 FastQC": null, "Drop MultiQC": null, "Keep MultiQC": null } }	Keep MultiQC	2
subworkflow_pkg_bam_dedup_umi_0	subworkflow_packaging	{ "subworkflow": "BAM_DEDUP_UMI", "modules": [ "umitools/prepareforrsem", "samtools/sort", "bam_dedup_stats_samtools_umicollapse", "bam_dedup_stats_samtools_umitools", "bam_sort_stats_samtools" ], "description": "BAM deduplication with UMI processing for both genome and transcriptome alignme...	{ "type": "choice", "instructions": "How should BAM_DEDUP_UMI (umitools/prepareforrsem, samtools/sort, bam_dedup_stats_samtools_umicollapse, bam_dedup_stats_samtools_umitools, bam_sort_stats_samtools) be structured in DSL2?", "criteria": { "Leave them out": null, "Local subworkflow BAM_DEDUP_UMI": null, ...	Use nf-core subworkflow bam_dedup_umi	2
mod_apbs_0	tool_selection	"In Nextflow DSL2, which module handles: Compute biomolecular electrostatics by solving the Poisson-Boltzmann equation\nusing APBS (Adaptive Poisson-Boltzmann Solver). Produces electrostatic potential\nmaps and solvation energy values for large biomolecular assemblages. (tools: apbs)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "gemmi/cif2json": "Convert macromolecular structure files from mmCIF format to JSON format using gemmi.", "bacphlip": "A bacteriophage lifestyle prediction tool", "vco...	apbs	3
mod_pureclip_1	tool_selection	"In Nextflow DSL2, which module handles: PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP. (tools: pureclip)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "clippy": "Runs the Clippy CLIP peak caller", "pureclip": "PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as ",...	pureclip	1
samplesheet_bam_variant_1_59	samplesheet_schema	{ "assay": "Pre-aligned BAM variant calling pipeline", "first_step": "GATK_HAPLOTYPECALLER", "inputs": "Aligned BAM files" }	{ "type": "choice", "instructions": "Define the required samplesheet columns for Pre-aligned BAM variant calling pipeline with entry step GATK_HAPLOTYPECALLER.", "criteria": { "sample,fastq_1,fastq_2": null, "sample,vcf": null, "sample,bam,bai": null, "sample,fastq_1": null, "sample,bam": null...	sample,bam,bai	2
mod_annotsv_installannotations_1	tool_selection	"In Nextflow DSL2, which module handles: Install the AnnotSV annotations (tools: annotsv)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "paragraph_vcf2paragraph": "Convert a VCF file to a JSON graph", "bakta_bakta": "Annotation of bacterial genomes (isolates, MAGs) and plasmids", "annosine": "Accelerat...	annotsv_installannotations	3
mod_fgbio_callmolecularconsensusreads_1	tool_selection	"In Nextflow DSL2, which module handles: Calls consensus sequences from reads with the same unique molecular tag. (tools: fgbio)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "fgumi_downsample": null, "ganon_buildcustom": null, "elprep_merge": null, "fgumi_dedup": null, "fgbio_callmolecularconsensusreads": null } }	fgbio_callmolecularconsensusreads	4
mod_samtools_calmd_1	tool_selection	"In Nextflow DSL2, which module handles: calculates MD and NM tags (tools: samtoolscalmd)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "atlas_splitmerge": null, "controlfreec_freec2circos": null, "abra2": null, "samtools_calmd": null, "blast_blastdbcmd": null } }	samtools_calmd	3
resource_ampcombi2_complete_0	resource_profiling	{ "process": "AMPCOMBI2_COMPLETE", "tool": "ampcombi2/complete", "description": "A submodule that merges all output summary tables from ampcombi/parsetables in one summary file." }	{ "type": "choice", "instructions": "What resource profile label should be assigned to AMPCOMBI2_COMPLETE (A submodule that merges all output summary tables from ampcombi/parsetables in o) in conf/base.config?", "criteria": { "process_medium": null, "process_low": null, "process_long": null, "proc...	process_single	3
mod_regenie_step2_0	tool_selection	"In Nextflow DSL2, which module handles: Run REGENIE step 2 association testing from precomputed step 1 predictions (tools: regenie)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "longstitch": "\"A genome assembly correction and scaffolding pipeline using long reads, consisting of up to three steps:\n - ", "regenie/step1": "Run REGENIE step 1 to f...	regenie/step2	3
pipe_all101_cageseq_0	pipeline_routing	"I need to run an end-to-end bioinformatics workflow to analyze CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.. Topics: cage, cage-seq, cageseq-data, gene-expression, rna. . Which nf-core pipeline should I execute?"	{ "type": "choice", "instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.", "criteria": { "riboseq": null, "rnaseq": null, "demo": null, "cageseq": null, "slamseq": null, "nanoseq": null, "bacass": null, "pangenome": null } }	cageseq	3
intent_ask_question_0	intent_routing	"Classify this user request: \"How does the .mix() operator differ from .combine() in Nextflow?\""	{ "type": "choice", "instructions": "Classify the user intent into one category.", "criteria": { "ask_question": "User is asking for an explanation, conceptual difference, documentation, or Nextflow syntax rules", "prepare_data": "User needs help creating a samplesheet, parsing FASTQ/BAM filenames, or sta...	ask_question	0
mod_gtdbtk_classifywf_0	tool_selection	"In Nextflow DSL2, which module handles: GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. (tools: gtdbtk)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "gatk4/getpileupsummaries": "Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be", "popscle/dscpileup": "Softwar...	gtdbtk/classifywf	2
subworkflow_pkg_fasta_index_bismark_bwameth_2	subworkflow_packaging	{ "subworkflow": "FASTA_INDEX_BISMARK_BWAMETH", "modules": [ "untar", "gunzip", "bismark/genomepreparation", "bwameth/index", "samtools/faidx" ], "description": "Generate index files from reference fasta for bismark and bwameth" }	{ "type": "choice", "instructions": "How should FASTA_INDEX_BISMARK_BWAMETH (untar, gunzip, bismark/genomepreparation, bwameth/index, samtools/faidx) be structured in DSL2?", "criteria": { "Use nf-core subworkflow fasta_index_bismark_bwameth": null, "Local subworkflow FASTA_INDEX_BISMARK_BWAMETH": null, ...	Use nf-core subworkflow fasta_index_bismark_bwameth	0
noul_dynamic_resource_allocation_1	dsl2_rules	"Is this statement accurate according to standard Nextflow DSL2 behavior? \"Process directive `cpus { check_max( 4 * task.attempt, 'cpus' ) }` allows dynamic resource scaling on task retry.\""	{ "type": "noul", "instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards." }	true	1
mod_khmer_normalizebymedian_0	tool_selection	"In Nextflow DSL2, which module handles: Module that calls normalize-by-median.py from khmer. The module can take a mix of paired end (interleaved) and single end reads. If both types are provided, only a single file with single ends is possible. (tools: khmer)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "seq2hla": "Precision HLA typing and expression from RNA-seq data using seq2HLA", "khmer/trimlowabund": "Removes low abundance k-mers from FASTA/FASTQ files", "khmer/n...	khmer/normalizebymedian	2
mod_repeatmodeler_repeatmodeler_1	tool_selection	"In Nextflow DSL2, which module handles: Performs de novo transposable element (TE) family identification with RepeatModeler (tools: repeatmodeler)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "repeatmodeler_repeatmodeler": "Performs de novo transposable element (TE) family identification with RepeatModeler", "topas_gencons": "Create fasta consensus with TOPAS t...	repeatmodeler_repeatmodeler	0
mod_expansionhunter_1	tool_selection	"In Nextflow DSL2, which module handles: Estimate repeat sizes using NGS data (tools: expansionhunter)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "expansionhunter": "Estimate repeat sizes using NGS data", "gatk4_indexfeaturefile": "Creates an index for a feature file, e.g. VCF or BED file.", "hipstr": "Genotype ...	expansionhunter	0
mod_bamutil_trimbam_0	tool_selection	"In Nextflow DSL2, which module handles: trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping (tools: bamutil)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "fgumi/duplexmetrics": "Collects a suite of metrics to QC duplex sequencing data", "bamclipper": "This module is used to clip primer sequences from your alignments.", ...	bamutil/trimbam	2
core_tool_cellranger_described_0	tool_selection	"Which bioinformatics tool or module is best suited for this task? Demultiplexing, barcode processing, alignment, and UMI counting for 10x Genomics single-cell RNA-seq libraries."	{ "type": "choice", "instructions": "Select the appropriate bioinformatics tool or module for the specified task.", "criteria": { "starsolo": "STAR single-cell mode", "seurat": "R analysis package", "kallisto_bustools": "Single-cell quantifier", "alevin": "Salmon single-cell", "cellranger": "S...	cellranger	4
mod_modkit_repair_0	tool_selection	"In Nextflow DSL2, which module handles: Repair the MM/ML tags on trimmed or hard-clipped ONT reads using untrimmed ONT reads. (tools: modkit)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "bismark/report": null, "bwamem3/mem": null, "mmseqs/createtaxdb": null, "bismark/align": null, "modkit/repair": null } }	modkit/repair	4
mod_amulety_translate_1	tool_selection	"In Nextflow DSL2, which module handles: A module to translate BCR and TCR nucleotide sequences into amino acid sequences using amulety and igblast. (tools: amulety)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "amulety_antiberta2": "A module to create antiberta2 embeddings of antibody (BCR) amino acid sequences using amulety.", "gridss_generateponbedpe": "GRIDSS is a module soft...	amulety_translate	3
resource_binette_2	resource_profiling	{ "process": "BINETTE", "tool": "binette", "description": "A fast and accurate binning refinement tool to construct high quality MAGs from the output of multiple binning tools." }	{ "type": "choice", "instructions": "What resource profile label should be assigned to BINETTE (A fast and accurate binning refinement tool to construct high quality MAGs from ) in conf/base.config?", "criteria": { "process_low": null, "process_high": null, "process_medium": null, "process_single"...	process_single	3
mod_ucsc_bigwigaverageoverbed_0	tool_selection	"In Nextflow DSL2, which module handles: compute average score of bigwig over bed file (tools: ucsc)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "ucsc/bigwigaverageoverbed": "compute average score of bigwig over bed file", "deeptools/bigwigcompare": "Compare two bigWig files based on the number of mapped reads", ...	ucsc/bigwigaverageoverbed	0
mod_gatk4spark_markduplicates_1	tool_selection	"In Nextflow DSL2, which module handles: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. (tools: gatk4)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "gatk4spark_markduplicates": "This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originat", "atlas_splitmerge": "split s...	gatk4spark_markduplicates	0
pipe_all101_dualrnaseq_3	pipeline_routing	"Recommend the most appropriate nf-core workflow for the following project: Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.. Topics: dualrna-seq, host-pathogen, quantification, readmapping, rna-seq. "	{ "type": "choice", "instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.", "criteria": { "magmap": null, "proteinannotator": null, "dualrnaseq": null, "scnanoseq": null, "rnasplice": null, "cageseq": null, "metapep": null, "smrnaseq": null, ...	dualrnaseq	2
subworkflow_pkg_bam_cnv_wisecondorx_3	subworkflow_packaging	{ "subworkflow": "BAM_CNV_WISECONDORX", "modules": [ "wisecondorx/convert", "wisecondorx/predict" ], "description": "A subworkflow for calling CNVs using WisecondorX" }	{ "type": "choice", "instructions": "How should BAM_CNV_WISECONDORX (wisecondorx/convert, wisecondorx/predict) be structured in DSL2?", "criteria": { "Local subworkflow BAM_CNV_WISECONDORX": null, "Keep the modules in the main workflow": null, "Use nf-core subworkflow bam_cnv_wisecondorx": null, "...	Use nf-core subworkflow bam_cnv_wisecondorx	2
mod_localcdsearch_download_0	tool_selection	"In Nextflow DSL2, which module handles: A command-line tool for downloading databases for local protein domain annotation using NCBI's Conserved Domain Database (CDD) (tools: localcdsearch)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "paragraph/vcf2paragraph": "Convert a VCF file to a JSON graph", "localcdsearch/annotate": "A command-line tool for local protein domain annotation using NCBI's Conserved ...	localcdsearch/download	3
samplesheet_scrna_10x_2_25	samplesheet_schema	{ "assay": "Single-cell 10x Genomics 3-prime gene expression", "first_step": "CELLRANGER", "inputs": "Cellular barcode FASTQ pairs" }	{ "type": "choice", "instructions": "What samplesheet CSV header schema is expected when inputs are: Cellular barcode FASTQ pairs?", "criteria": { "sample,fastq_1,fastq_2": null, "sample,barcode,fastq": null, "sample,bam": null, "sample,features": null, "sample,fastq_1": null } }	sample,fastq_1,fastq_2	0
mod_cmaple_0	tool_selection	"In Nextflow DSL2, which module handles: Efficient phylogenetic tree reconstruction for sequences using the CMAPLE algorithm (tools: cmaple)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "epang/place": "phylogenetic placement of query sequences in a reference tree", "cafe": "Analysis of gene family evolution", "cmaple": "Efficient phylogenetic tree rec...	cmaple	2
mod_hmmer_hmmalign_0	tool_selection	"In Nextflow DSL2, which module handles: hmmalign from the HMMER suite aligns a number of sequences to an HMM profile (tools: hmmer)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "hmmer/hmmalign": null, "gappa/examineheattree": null, "alignoth": null, "busco/phylogenomics": null, "coverm/contig": null } }	hmmer/hmmalign	0
samplesheet_atacseq_pe_1_59	samplesheet_schema	{ "assay": "Paired-end ATAC-seq chromatin accessibility", "first_step": "FASTQC", "inputs": "Paired-end Tn5 transposed FASTQs" }	{ "type": "choice", "instructions": "Define the required samplesheet columns for Paired-end ATAC-seq chromatin accessibility with entry step FASTQC.", "criteria": { "sample,fastq_1,fastq_2": null, "sample,bed": null, "sample,bam": null, "sample,fastq_1": null, "sample,vcf": null } }	sample,fastq_1,fastq_2	0
resource_agat_convertbed2gff_4	resource_profiling	{ "process": "AGAT_CONVERTBED2GFF", "tool": "agat/convertbed2gff", "description": "Takes a bed12 file and converts to a GFF3 file" }	{ "type": "choice", "instructions": "What resource profile label should be assigned to AGAT_CONVERTBED2GFF (Takes a bed12 file and converts to a GFF3 file) in conf/base.config?", "criteria": { "process_high": null, "process_low": null, "process_single": null, "process_medium": null } }	process_single	2
mod_shigatyper_0	tool_selection	"In Nextflow DSL2, which module handles: Determine Shigella serotype from Illumina or Oxford Nanopore reads (tools: shigatyper)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "shigatyper": "Determine Shigella serotype from Illumina or Oxford Nanopore reads", "fastq_align_chromap": "Align high throughput chromatin profiles using Chromap, updatin...	shigatyper	0
mod_odgi_draw_0	tool_selection	"In Nextflow DSL2, which module handles: Draw previously-determined 2D layouts of the graph with diverse annotations. (tools: odgi)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "odgi/draw": null, "odgi/layout": null, "odgi/unchop": null, "tiff_segmentation_vpt": null, "lofreq/viterbi": null } }	odgi/draw	0
mod_rnaquast_0	tool_selection	"In Nextflow DSL2, which module handles: Assess the quality of an RNAseq assembly with or without a reference genome (tools: rnaquast)?"	{ "type": "choice", "instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.", "criteria": { "gem2/gem2bedmappability": "Convert a mappability file to bedgraph format", "bam_ngscheckmate": "Take a set of bam files and run NGSCheckMate to determine whether samples ...	rnaquast	3
samplesheet_ont_single_1_1	samplesheet_schema	{ "assay": "Single-end Oxford Nanopore direct RNA", "first_step": "NANOPLOT", "inputs": "Single fastq per sample" }	{ "type": "choice", "instructions": "Define the required samplesheet columns for Single-end Oxford Nanopore direct RNA with entry step NANOPLOT.", "criteria": { "sample,fastq_1": null, "sample,fasta": null, "sample,fastq_1,fastq_2": null, "sample,bam": null, "sample,vcf": null } }	sample,fastq_1	0

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nf-core & Nextflow Laya Decision Dataset (`nfcore-laya-decisions-v3`)

A standardized, multi-task decision-layer dataset for training Laya (System-1 Decision Engines) and fast autonomous agents across Nextflow DSL2 and the complete nf-core bioinformatics ecosystem.

📊 Dataset Summary

Total Decision Records: 11,654 records across 8 core architectural pillars:
1. QC Read Adaptation (1,500 records): Illumina NovaSeq/NextSeq, PacBio HiFi CCS, Oxford Nanopore Direct RNA/DNA quality control adaptation and tool swapping.
2. Resource Profiling & Directives (1,500 records): Process memory, CPU, time, and dynamic retry/error-strategy directive rules across genome-scale tools.
3. Subworkflow Packaging (622 records): Determining when to bundle multi-process tasks into local subworkflows or reuse official nf-core subworkflows.
4. Samplesheet Schema & Header Inference (1,950 records): JSON Schema draft-07 type, format, pattern, and enum constraints for bioinformatics samplesheets.
5. Tool & Module Selection (4,426 records): Spans 2,153 nf-core modules and subworkflows with mined hard-negative distractors.
6. DSL2 Syntax & Rules Check (800 records): Balanced binary noul decisions evaluating idiomatic DSL2 patterns vs anti-patterns.
7. nf-core Pipeline Routing (656 records): Matching biological assay requirements to official nf-core workflows.
8. Intent Routing (200 records): Disambiguating compilation, remediation, parameter tuning, and execution commands.

🗂️ 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%

📋 Data Schema

Each line in data/*.jsonl is formatted for direct consumption by Laya agents and Hugging Face datasets:

{
  "id": "qc_adapt_ont_nanoplot_1_34",
  "category": "qc_read_adaptation",
  "state": {
    "assay": "Direct RNA sequencing on Oxford Nanopore PromethION",
    "tool": "FastQC",
    "read_type": "long_reads_direct_rna"
  },
  "question": {
    "type": "choice",
    "instructions": "How should QC step FastQC be configured given sequencing characteristics: long_reads_direct_rna?",
    "criteria": {
      "Keep FastQC": null,
      "Drop FastQC": null,
      "Swap for NanoPlot": null
    }
  },
  "target": "Swap for NanoPlot",
  "target_idx": 2
}

🚀 Quickstart

Load via Hugging Face `datasets`

from datasets import load_dataset

dataset = load_dataset("Primeomicx/nfcore-laya-decisions")
print(dataset)

🤖 Trained Model

The fine-tuned model checkpoint trained on this dataset is available at: 👉 Primeomicx/laya-nextflow-nfcore

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nf-core & Nextflow Laya Decision Dataset (nfcore-laya-decisions-v3)