id stringlengths 9 67 | category stringclasses 8
values | state unknown | question unknown | target stringlengths 3 92 | target_idx int64 0 9 |
|---|---|---|---|---|---|
resource_bowtie2_build_5 | resource_profiling | {
"process": "BOWTIE2_BUILD",
"tool": "bowtie2/build",
"description": "Builds bowtie index for reference genome"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BOWTIE2_BUILD (Builds bowtie index for reference genome) in conf/base.config?",
"criteria": {
"process_long": null,
"process_high": null,
"process_low": null,
"process_single": null
}
} | process_single | 3 |
mod_abyss_abysspe_0 | tool_selection | "In Nextflow DSL2, which module handles: ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes. (tools: abyss)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"abyss/abysspe": "ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.",
"agat/convertspgxf2gxf": "Fixes and standardizes GF... | abyss/abysspe | 0 |
samplesheet_arch_cancer_longitudinal_5_5 | samplesheet_schema | {
"assay": "Longitudinal cancer monitoring across multiple timepoints",
"first_step": "FASTQC",
"template": "nf-core/oncoanalyser"
} | {
"type": "choice",
"instructions": "In Nextflow pipeline nf-core/oncoanalyser, determine the input samplesheet column structure for: Longitudinal cancer monitoring across multiple timepoints.",
"criteria": {
"patient,sample,bam": null,
"patient,sample,status,fastq_1,fastq_2": null,
"sample,fastq_1,fa... | patient,sample,timepoint,status,fastq_1,fastq_2 | 3 |
resource_bedtools_intersect_4 | resource_profiling | {
"process": "BEDTOOLS_INTERSECT",
"tool": "bedtools/intersect",
"description": "Allows one to screen for overlaps between two sets of genomic features."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BEDTOOLS_INTERSECT (Allows one to screen for overlaps between two sets of genomic features.) in conf/base.config?",
"criteria": {
"process_high": null,
"process_single": null,
"process_low": null,
"process_mediu... | process_single | 1 |
samplesheet_arch_rnafusion_pe_3_3 | samplesheet_schema | {
"pipeline": "nf-core/rnafusion",
"assay_type": "RNA gene fusion detection (Arriba, STAR-Fusion)",
"data_format": "Paired-end oncology RNA-seq reads for chimeric transcript discovery"
} | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for RNA gene fusion detection (Arriba, STAR-Fusion) with entry step FASTQC.",
"criteria": {
"sample,bam": null,
"sample,fusion_bed": null,
"sample,fastq_1": null,
"sample,fastq_1,fastq_2,strandedness": null
}
... | sample,fastq_1,fastq_2,strandedness | 3 |
noul_multiple_script_sections_invalid_7 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"A process definition in Nextflow can declare multiple `script:` sections within the same process block.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards."
} | false | 0 |
mod_happy_sompy_1 | tool_selection | "In Nextflow DSL2, which module handles: Hap.py is a tool to compare diploid genotypes at haplotype level. som.py is a part of hap.py compares somatic variations. (tools: sompy)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"custom_getchromsizes": "Generates a FASTA file of chromosome sizes and a fasta index file",
"happy_sompy": "Hap.py is a tool to compare diploid genotypes at haplotype lev... | happy_sompy | 1 |
qc_adapt_ont_nanoplot_1_15 | 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": {
"Drop FastQC": null,
"Swap for NanoPlot": null,
"Keep FastQC": null
}
} | Swap for NanoPlot | 1 |
schema_std_methylong_0_1 | samplesheet_schema | {
"pipeline": "nf-core/methylong",
"description": "Extract methylation calls from long reads (ONT/ PacBio) ",
"mode": "standard_execution"
} | {
"type": "choice",
"instructions": "Which standard samplesheet columns are configured in assets/schema_input.json for nf-core/methylong?",
"criteria": {
"sample,fastq_1,fastq_2,replicate,control": null,
"patient,sample,vcf,status,cna": null,
"sample,group,path,ref,method": null,
"sample,fastq_1,f... | sample,group,path,ref,method | 2 |
resource_adapterremoval_2 | resource_profiling | {
"process": "ADAPTERREMOVAL",
"tool": "adapterremoval",
"description": "Trim sequencing adapters and collapse overlapping reads"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to ADAPTERREMOVAL (Trim sequencing adapters and collapse overlapping reads) in conf/base.config?",
"criteria": {
"process_single": null,
"process_high": null,
"process_medium": null,
"process_long": null
}
} | process_single | 0 |
mod_bcftools_pluginfilltags_0 | tool_selection | "In Nextflow DSL2, which module handles: Compute and fill various INFO tags (tools: bcftools)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"bcftools/csq": "bcftools Haplotype-aware consequence caller",
"autocycler/combine": "Merge resolved cluster assemblies into final consensus outputs with Autocycler.",
... | bcftools/pluginfilltags | 3 |
mod_pbtk_pbindex_0 | tool_selection | "In Nextflow DSL2, which module handles: Minimalistic tool which creates an index file that enables random access into PacBio BAM files (tools: pbtk)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"agat/spfilterfeaturefromkilllist": "The script aims to remove features based on a kill list. The default behaviour is to look at the features's ID",
"pbtk/pbindex": "Mini... | pbtk/pbindex | 1 |
resource_bedtools_jaccard_1 | resource_profiling | {
"process": "BEDTOOLS_JACCARD",
"tool": "bedtools/jaccard",
"description": "Calculate Jaccard statistic b/w two feature files."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BEDTOOLS_JACCARD (Calculate Jaccard statistic b/w two feature files.) in conf/base.config?",
"criteria": {
"process_high": null,
"process_low": null,
"process_single": null,
"process_long": null
}
} | process_single | 2 |
samplesheet_arch_bacterial_hybrid_assembly_2_0 | samplesheet_schema | {
"technology": "Microbial Assembly",
"workflow_entry": "FASTQC",
"library_inputs": "Illumina paired-end reads paired with Oxford Nanopore long reads per isolate"
} | {
"type": "choice",
"instructions": "Which columns should the input samplesheet have?",
"criteria": {
"sample,fastq_1": null,
"sample,fasta": null,
"sample,fastq_1,fastq_2,long_fastq": null,
"sample,fastq_1,fastq_2": null
}
} | sample,fastq_1,fastq_2,long_fastq | 2 |
schema_std_pixelator_2_0 | samplesheet_schema | "Configuring input samplesheet for nf-core pipeline nf-core/pixelator. Description: Pipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB)." | {
"type": "choice",
"instructions": "Define the input samplesheet column header for nf-core/pixelator.",
"criteria": {
"sample,fastq_1,fastq_2,pool,hash_index": null,
"sample,short_reads_fastq_1,short_reads_fastq_2,long_reads_fastq_1": null,
"sample_id,idat_red,idat_green,group": null,
"sample,fas... | sample,fastq_1,fastq_2,pool,hash_index | 0 |
qc_adapt_pacbio_hifi_1_8 | qc_read_adaptation | {
"assay": "PacBio HiFi circular consensus sequencing (CCS)",
"tool": "FastQC",
"read_type": "long_reads_hifi_15kb"
} | {
"type": "choice",
"instructions": "How should QC step FastQC be configured given sequencing characteristics: long_reads_hifi_15kb?",
"criteria": {
"Keep FastQC": null,
"Swap for NanoPlot": null,
"Drop FastQC": null
}
} | Swap for NanoPlot | 1 |
samplesheet_arch_singlecell_parse_splitseq_2_5 | samplesheet_schema | {
"assay": "Parse Biosciences Split-seq combinatorial barcoding",
"first_step": "FASTQC",
"inputs": "Combinatorial split-pool barcoded FASTQs with subpool annotations"
} | {
"type": "choice",
"instructions": "Which columns should the input samplesheet have?",
"criteria": {
"sample,well,plate": null,
"sample,fastq_1": null,
"sample,bam": null,
"sample,subpool,fastq_1,fastq_2": null
}
} | sample,subpool,fastq_1,fastq_2 | 3 |
noul_invalid_process_communication_via_globals_21 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"In Nextflow DSL2, processes communicate by directly declaring global variables inside the script block.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards."
} | false | 0 |
mod_mapdamage2_0 | tool_selection | "In Nextflow DSL2, which module handles: Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms. (tools: mapdamage2)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"dedup": null,
"atlas/pmd": null,
"mapdamage2": null,
"oatk": null,
"repeatmodeler/repeatmodeler": null
}
} | mapdamage2 | 2 |
mod_seqtk_sample_0 | tool_selection | "In Nextflow DSL2, which module handles: Subsample reads from FASTQ files (tools: seqtk)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"seqtk/sample": "Subsample reads from FASTQ files",
"spaceranger/count": "Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data",
"ha... | seqtk/sample | 0 |
qc_adapt_illumina_novaseq_1_49 | qc_read_adaptation | {
"assay": "Illumina NovaSeq X paired-end 150bp WGS",
"tool": "FastQC",
"read_type": "short_reads_150bp"
} | {
"type": "choice",
"instructions": "How should QC step FastQC be configured given sequencing characteristics: short_reads_150bp?",
"criteria": {
"Swap for NanoPlot": null,
"Keep FastQC": null,
"Drop FastQC": null
}
} | Keep FastQC | 1 |
noul_default_empty_channel_behavior_6 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"In Nextflow DSL2, `Channel.fromPath('data/*.fq')` emits an error if no files match the wildcard pattern by default.\"" | {
"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 |
field_constraint_fastq_1_0_0 | samplesheet_schema | {
"field_name": "fastq_1",
"datatype": "file_pattern",
"description": "Path to read 1 FASTQ file (gzipped or uncompressed)"
} | {
"type": "choice",
"instructions": "What is the JSON Schema validation constraint for samplesheet column 'fastq_1'?",
"criteria": {
"enum: [auto, forward, reverse, unstranded]": null,
"pattern: ^\\S+\\.f(ast)?q(\\.gz)?$": null,
"pattern: ^\\S+\\.bam$": null,
"type: integer": null
}
} | pattern: ^\S+\.f(ast)?q(\.gz)?$ | 1 |
mod_autocycler_compress_0 | tool_selection | "In Nextflow DSL2, which module handles: Package candidate assemblies for clustering by Autocycler. (tools: autocycler)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"autocycler/resolve": "Resolve trimmed assembly graphs into final contigs within Autocycler.",
"evigene/tr2aacds": "Uses evigene/scripts/prot/tr2aacds.pl to filter a trans... | autocycler/compress | 4 |
schema_std_funcscan_0_1 | samplesheet_schema | {
"pipeline": "nf-core/funcscan",
"description": "(Meta-)genome screening for functional and natural product gene sequences",
"mode": "standard_execution"
} | {
"type": "choice",
"instructions": "Which standard samplesheet columns are configured in assets/schema_input.json for nf-core/funcscan?",
"criteria": {
"sample,fastq_1,fastq_2,barcode": null,
"sample_id,bam,vcf,library_id,lane": null,
"sample,fastq_1,fastq_2,strandedness,condition": null,
"sample... | sample,fasta,protein,gbk,gff | 3 |
mod_isoseq_cluster_0 | tool_selection | "In Nextflow DSL2, which module handles: IsoSeq - Cluster - Cluster trimmed consensus sequences (tools: isoseq)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"isoseq/cluster": "IsoSeq - Cluster - Cluster trimmed consensus sequences",
"cdhit/cdhitest": "Cluster nucleotide sequences using sequence similarity",
"paraclu": "Par... | isoseq/cluster | 0 |
mod_genmod_compound_0 | tool_selection | "In Nextflow DSL2, which module handles: Score compounds (tools: genmod)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"trycycler/cluster": "Cluster contigs from multiple assemblies by similarity",
"genmod/score": "Score the variants of a vcf based on their annotation",
"rhocall/viz": ... | genmod/compound | 4 |
noul_channel_mix_operator_6 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"Channel `.mix()` combines two or more channels of identical emission structure into a single unified stream.\"" | {
"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_binette_0 | tool_selection | "In Nextflow DSL2, which module handles: A fast and accurate binning refinement tool to construct high quality MAGs from the output of multiple binning tools. (tools: binette)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"bbmap/clumpify": "Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates",
"medaka": "A tool to create consensus sequences and variant calls from nanopore ... | binette | 4 |
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 |
subworkflow_pkg_fastq_remove_rrna_2 | subworkflow_packaging | {
"subworkflow": "FASTQ_REMOVE_RRNA",
"modules": [
"bowtie2/align",
"bowtie2/build",
"ribodetector",
"samtools/fastq",
"samtools/view",
"seqkit/replace",
"seqkit/stats",
"sortmerna"
],
"description": "Remove ribosomal RNA reads from FASTQ files using SortMeRNA, RiboDetector, or B... | {
"type": "choice",
"instructions": "How should FASTQ_REMOVE_RRNA (bowtie2/align, bowtie2/build, ribodetector, samtools/fastq, samtools/view, seqkit/replace, seqkit/stats, sortmerna) be structured in DSL2?",
"criteria": {
"Keep the modules in the main workflow": null,
"Use nf-core subworkflow fastq_remove... | Use nf-core subworkflow fastq_remove_rrna | 1 |
mod_xengsort_index_0 | tool_selection | "In Nextflow DSL2, which module handles: Fast lightweight accurate xenograft sorting (tools: xengsort)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"bismark/genomepreparation": "Converts a specified reference genome into two different bisulfite\nconverted versions and indexes them for ali",
"juicertools/pre": "Create ... | xengsort/index | 2 |
mod_seqkit_sliding_0 | tool_selection | "In Nextflow DSL2, which module handles: Use seqkit to generate sliding windows of input fasta (tools: seqkit)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"seqkit/replace": "Use seqkit to find/replace strings within sequences and sequence headers",
"seqkit/grep": "Select sequences from a large file based on name/ID",
"se... | seqkit/sliding | 2 |
pipe_all101_sopa_1 | pipeline_routing | "User query: What is the official nf-core pipeline for segmentation analysis? Specific context: Nextflow version of Sopa - spatial omics pipeline and analysis. Topics: segmentation, spatial-omics, spatial-proteomics, spatial-transcriptomics, spatialdata. " | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"smrnaseq": "A small-RNA sequencing analysis pipeline [small-rna, smrna-seq]",
"marsseq": "MARS-seq v2 pre-processing pipeline with velocity [facs-sorting, mars-seq, single-cell]"... | sopa | 7 |
subworkflow_pkg_bam_markduplicates_picard_1 | subworkflow_packaging | {
"subworkflow": "BAM_MARKDUPLICATES_PICARD",
"modules": [
"picard/markduplicates",
"samtools/index",
"samtools/stats",
"samtools/idxstats",
"samtools/flagstat",
"bam_stats_samtools"
],
"description": "Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats"
} | {
"type": "choice",
"instructions": "How should BAM_MARKDUPLICATES_PICARD (picard/markduplicates, samtools/index, samtools/stats, samtools/idxstats, samtools/flagstat, bam_stats_samtools) be structured in DSL2?",
"criteria": {
"Use nf-core subworkflow bam_markduplicates_picard": null,
"Keep the modules in... | Use nf-core subworkflow bam_markduplicates_picard | 0 |
mod_longstitch_1 | tool_selection | "In Nextflow DSL2, which module handles: \"A genome assembly correction and scaffolding pipeline using long reads, consisting of up to three steps:\n - Tigmint cuts the draft assembly at potentially misassembled regions\n - ntLink is then used to scaffold the corrected assembly\n - followed by ARKS for further scaff... | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"picard_setnmmdanduqtags": null,
"pairix": null,
"longstitch": null,
"strdust": null,
"savana_run": null
}
} | longstitch | 2 |
subworkflow_pkg_fastq_fastqc_umitools_trimgalore_1 | subworkflow_packaging | {
"subworkflow": "FASTQ_FASTQC_UMITOOLS_TRIMGALORE",
"modules": [
"fastqc",
"umitools/extract",
"trimgalore"
],
"description": "Read QC, UMI extraction and trimming"
} | {
"type": "choice",
"instructions": "How should FASTQ_FASTQC_UMITOOLS_TRIMGALORE (fastqc, umitools/extract, trimgalore) be structured in DSL2?",
"criteria": {
"Leave them out": null,
"Use nf-core subworkflow fastq_fastqc_umitools_trimgalore": null,
"Keep the modules in the main workflow": null,
"L... | Use nf-core subworkflow fastq_fastqc_umitools_trimgalore | 1 |
intent_build_pipeline_8 | intent_routing | "Classify this user request: \"Can you generate a Nextflow DSL2 pipeline for paired-end Illumina RNA-seq with FastQC, STAR, and featureCounts?\"" | {
"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",
"debug_error": "User is reporting a runtime error, exit code (137, 127), task failure, or pi... | build_pipeline | 2 |
resource_bowtie2_align_5 | resource_profiling | {
"process": "BOWTIE2_ALIGN",
"tool": "bowtie2/align",
"description": "Align reads to a reference genome using bowtie2"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BOWTIE2_ALIGN (Align reads to a reference genome using bowtie2) in conf/base.config?",
"criteria": {
"process_low": null,
"process_long": null,
"process_high": null,
"process_single": null
}
} | process_single | 3 |
samplesheet_arch_taxprofiler_shotgun_1_4 | samplesheet_schema | {
"assay": "Multi-taxonomic profiling of complex metagenomic shotgun reads",
"first_step": "FASTQC"
} | {
"type": "choice",
"instructions": "Which columns should the samplesheet have for Multi-taxonomic profiling of complex metagenomic shotgun reads?",
"criteria": {
"sample,run_accession,instrument_platform,fastq_1,fastq_2": null,
"sample,kraken_db": null,
"sample,fastq_1,fastq_2": null,
"sample,bam... | sample,run_accession,instrument_platform,fastq_1,fastq_2 | 0 |
resource_ataqv_mkarv_4 | resource_profiling | {
"process": "ATAQV_MKARV",
"tool": "ataqv/mkarv",
"description": "mkarv function of a corresponding ataqv tool"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to ATAQV_MKARV (mkarv function of a corresponding ataqv tool) in conf/base.config?",
"criteria": {
"process_low": null,
"process_medium": null,
"process_single": null,
"process_long": null
}
} | process_single | 2 |
samplesheet_arch_bacterial_hybrid_assembly_5_2 | samplesheet_schema | {
"assay": "Hybrid bacterial assembly combining short Illumina and long Nanopore reads",
"first_step": "FASTQC",
"inputs": "Illumina paired-end reads paired with Oxford Nanopore long reads per isolate",
"pipeline": "nf-core/bacass"
} | {
"type": "choice",
"instructions": "In Nextflow pipeline nf-core/bacass, determine the input samplesheet column structure for: Hybrid bacterial assembly combining short Illumina and long Nanopore reads.",
"criteria": {
"sample,fastq_1,fastq_2": null,
"sample,fasta": null,
"sample,fastq_1,fastq_2,long... | sample,fastq_1,fastq_2,long_fastq | 2 |
mod_vizgenpostprocessing_runsegmentationontile_0 | tool_selection | "In Nextflow DSL2, which module handles: The module runs the segmentation algorithm on a specific tile using Vizgen's\npost-processing tool. (tools: vizgenpostprocessing)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"tiff_segmentation_vpt": "Perform segmentation of MERSCOPE TIFF images using the vizgen-postprocessing tool",
"cellpose": "cellpose segments cells in images using GPU-acce... | vizgenpostprocessing/runsegmentationontile | 3 |
mod_scds_1 | tool_selection | "In Nextflow DSL2, which module handles: Module to use scds for doublet scoring (tools: scds)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"cellbender_removebackground": null,
"bff": null,
"dupblaster": null,
"sourcepredict": null,
"scds": null
}
} | scds | 4 |
field_constraint_expected_cells_3_2 | samplesheet_schema | {
"schema_target": "assets/schema_input.json",
"field": "expected_cells",
"validation_type": "numeric_integer"
} | {
"type": "choice",
"instructions": "Select the appropriate draft-07 JSON Schema property specification for 'expected_cells'.",
"criteria": {
"format: file-path": null,
"pattern: ^\\S+\\.csv$": null,
"enum: [auto, single, paired]": null,
"type: integer, minimum: 100, maximum: 50000": null
}
} | type: integer, minimum: 100, maximum: 50000 | 3 |
mod_blast_updateblastdb_0 | tool_selection | "In Nextflow DSL2, which module handles: Downloads a BLAST database from NCBI (tools: blast)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"rpbp/getperiodiclengthsoffsets": "Filter the per-read-length P-site offset table down to the\n(length, offset) pairs that will actually drive ORF",
"blast/updateblastdb":... | blast/updateblastdb | 1 |
resource_agat_convertspgff2gtf_5 | resource_profiling | {
"process": "AGAT_CONVERTSPGFF2GTF",
"tool": "agat/convertspgff2gtf",
"description": "Converts a GFF/GTF file into a proper GTF file"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to AGAT_CONVERTSPGFF2GTF (Converts a GFF/GTF file into a proper GTF file) in conf/base.config?",
"criteria": {
"process_single": null,
"process_low": null,
"process_high": null,
"process_medium": null
}
} | process_single | 0 |
pipe_all101_bacass_2 | pipeline_routing | "We have raw sequencing data and want to run standard QC, alignment, and quantification for assembly. Best pipeline:" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"viralintegration": "Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach. [chimeri",
"bacass": "Simple bacterial assembl... | bacass | 1 |
qc_adapt_ont_nanoplot_2_36 | qc_read_adaptation | {
"assay": "Direct RNA sequencing on Oxford Nanopore PromethION",
"tool": "FastQC",
"read_type": "long_reads_direct_rna"
} | {
"type": "choice",
"instructions": "Evaluate the quality control tool choice for: Direct RNA sequencing on Oxford Nanopore PromethION (long_reads_direct_rna).",
"criteria": {
"Keep FastQC": null,
"Drop FastQC": null,
"Swap for NanoPlot": null
}
} | Swap for NanoPlot | 2 |
resource_bedtools_shuffle_1 | resource_profiling | {
"process": "BEDTOOLS_SHUFFLE",
"tool": "bedtools/shuffle",
"description": "bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BEDTOOLS_SHUFFLE (bedtools shuffle will randomly permute the genomic locations of a feature file a) in conf/base.config?",
"criteria": {
"process_medium": null,
"process_high": null,
"process_low": null,
"proces... | process_single | 3 |
subworkflow_pkg_fasta_index_methylseq_0 | subworkflow_packaging | {
"subworkflow": "FASTA_INDEX_METHYLSEQ",
"modules": [
"untar",
"gunzip",
"bismark/genomepreparation",
"bwameth/index",
"bwa/index",
"samtools/faidx"
],
"description": "Generate index files from reference fasta for bismark, bwameth and bwamem aligners"
} | {
"type": "choice",
"instructions": "How should FASTA_INDEX_METHYLSEQ (untar, gunzip, bismark/genomepreparation, bwameth/index, bwa/index, samtools/faidx) be structured in DSL2?",
"criteria": {
"Use nf-core subworkflow fasta_index_methylseq": null,
"Keep the modules in the main workflow": null,
"Leave... | Use nf-core subworkflow fasta_index_methylseq | 0 |
resource_bigslice_downloaddb_1 | resource_profiling | {
"process": "BIGSLICE_DOWNLOADDB",
"tool": "bigslice/downloaddb",
"description": "Downloads and extracts the BiG-SLiCE HMM database (biosynthetic and sub Pfams)\nusing the bundled `download_bigslice_hmmdb` script shipped with BiG-SLiCE.\nThe resulting directory can be passed directly as the `hmmdb` input to the\... | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BIGSLICE_DOWNLOADDB (Downloads and extracts the BiG-SLiCE HMM database (biosynthetic and sub Pfams)\nu) in conf/base.config?",
"criteria": {
"process_medium": null,
"process_high": null,
"process_single": null,
... | process_single | 2 |
pipe_all101_viralrecon_1 | pipeline_routing | "User query: What is the official nf-core pipeline for amplicon analysis? Specific context: Assembly and intrahost/low-frequency variant calling for viral samples. Topics: amplicon, artic, assembly, covid-19, covid19, illumina. " | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"scnanoseq": "Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics [10xgenomics, long-read-sequencing, n",
"rnastructurome": "a bioinformatics pipeli... | viralrecon | 3 |
noul_exit_code_137_cause_20 | 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 |
samplesheet_arch_scrna_10x_v3_3_4 | samplesheet_schema | "Building an autonomous Nextflow workflow (nf-core/scrnaseq) for Single-cell 10x Genomics 3-prime Gene Expression (v3 chemistry). Input files: Cellular barcode+UMI R1 (28bp) and transcript cDNA R2 (91bp) FASTQs." | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for Single-cell 10x Genomics 3-prime Gene Expression (v3 chemistry) with entry step FASTQC.",
"criteria": {
"sample,bam": null,
"sample,fastq_1,fastq_2": null,
"sample,fastq_1,fastq_2,expected_cells": null,
"sam... | sample,fastq_1,fastq_2,expected_cells | 2 |
mod_bam_methyldackel_1 | tool_selection | "In Nextflow DSL2, which module handles: Performs methylation quantification based on negative readout of C to T conversion of 3-letter genome alignments using Methyldackel. (tools: bam_methyldackel)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"propr_grea": "Perform Gene Ratio Enrichment Analysis",
"bismark_align": "Performs alignment of BS-Seq reads using bismark",
"bismark_deduplicate": "Removes alignments... | bam_methyldackel | 4 |
samplesheet_arch_atacseq_replicates_6_1 | samplesheet_schema | {
"pipeline": "nf-core/atacseq",
"assay_type": "ATAC-seq chromatin accessibility with biological replicates",
"data_format": "Paired-end Tn5 transposed FASTQs across conditions and replicates"
} | {
"type": "choice",
"instructions": "Which columns are standard for ATAC-seq chromatin accessibility with biological replicates input samplesheet?",
"criteria": {
"sample,bam": null,
"sample,bed": null,
"sample,fastq_1": null,
"sample,fastq_1,fastq_2,replicate": null
}
} | sample,fastq_1,fastq_2,replicate | 3 |
samplesheet_arch_rare_disease_trio_3_1 | samplesheet_schema | {
"assay": "Trio exome/genome sequencing (Proband, Mother, Father)",
"first_step": "FASTQC",
"template": "nf-core/raredisease"
} | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for Trio exome/genome sequencing (Proband, Mother, Father) with entry step FASTQC.",
"criteria": {
"family_id,sample,fastq_1,fastq_2": null,
"family_id,sample,paternal_id,maternal_id,sex,phenotype,fastq_1,fastq_2": null... | family_id,sample,paternal_id,maternal_id,sex,phenotype,fastq_1,fastq_2 | 1 |
mod_plink_vcf_1 | tool_selection | "In Nextflow DSL2, which module handles: Analyses variant calling files using plink (tools: plink)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"plink_bcf": "Analyses binary variant call format (BCF) files using plink",
"plink_vcf": "Analyses variant calling files using plink",
"gem3_gem3indexer": "Create a GE... | plink_vcf | 1 |
field_constraint_sex_1_0 | samplesheet_schema | {
"column": "sex",
"purpose": "Biological sex in pedigree/trio clinical analysis"
} | {
"type": "choice",
"instructions": "Determine the schema validation rule for field 'sex' (Biological sex in pedigree/trio clinical analysis).",
"criteria": {
"enum: [1, 2, other, unknown] (1=male, 2=female)": null,
"pattern: ^\\S+\\.gz$": null,
"format: file-path": null,
"type: boolean": null
}... | enum: [1, 2, other, unknown] (1=male, 2=female) | 0 |
noul_named_process_output_emits_1 | 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 |
local_subworkflow_irma_1_3 | subworkflow_packaging | {
"subworkflow": "IRMA",
"modules": [
"irma"
],
"description": "Iterative assembly step for influenza and coronavirus"
} | {
"type": "choice",
"instructions": "How should this step (irma) be packaged: Iterative assembly step for influenza and coronavirus?",
"criteria": {
"Local subworkflow IRMA": null,
"Keep the modules in the main workflow": null,
"Use nf-core subworkflow irma": null,
"Leave them out": null
}
} | Local subworkflow IRMA | 0 |
mod_deacon_indexintersect_0 | tool_selection | "In Nextflow DSL2, which module handles: Intersect multiple deacon indexes (A ∩ B ...) (tools: deacon)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"deacon/indexintersect": null,
"bowtie/build": null,
"pharmcat/phenotyper": null,
"octopusv/plot": null,
"biscuit/qc": null
}
} | deacon/indexintersect | 0 |
mod_t1k_build_1 | tool_selection | "In Nextflow DSL2, which module handles: A module to create a reference database and coordinate files for T1K. (tools: t1k)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"t1k_build": "A module to create a reference database and coordinate files for T1K.",
"gatk4_cleansam": "Cleans the provided BAM, soft-clipping beyond-end-of-reference ali... | t1k_build | 0 |
mod_fastawindows_0 | tool_selection | "In Nextflow DSL2, which module handles: Quickly compute statistics over a fasta file in windows. (tools: fastawindows)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"fastawindows": null,
"blobtk/snail": null,
"quantify_rsem": null,
"agat/convertspgff2gtf": null,
"agat/convertbed2gff": null
}
} | fastawindows | 0 |
mod_shapeit5_phaserare_1 | tool_selection | "In Nextflow DSL2, which module handles: Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate).\nRequire feature AVX2. (tools: shapeit5)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"shapeit5_phaserare": "Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate).\nRequire feat",
"glimpse2_splitreference": "Tool t... | shapeit5_phaserare | 0 |
schema_std_marsseq_0_1 | samplesheet_schema | {
"pipeline": "nf-core/marsseq",
"description": "MARS-seq v2 pre-processing pipeline with velocity",
"mode": "standard_execution"
} | {
"type": "choice",
"instructions": "Which standard samplesheet columns are configured in assets/schema_input.json for nf-core/marsseq?",
"criteria": {
"sample_id,bam,vcf,library_id,lane": null,
"fastq_1,fastq_2,batch,amp_batches,seq_batches": null,
"sample,fastq_1,strandedness": null,
"sample,seq... | fastq_1,fastq_2,batch,amp_batches,seq_batches | 1 |
mod_entrezdirect_xtract_1 | tool_selection | "In Nextflow DSL2, which module handles: Queries an NCBI database using an UID (tools: entrezdirect)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"entrezdirect_esummary": "Queries an NCBI database using Unique Identifier(s)",
"entrezdirect_xtract": "Queries an NCBI database using an UID",
"utils_nfvalidation_plu... | entrezdirect_xtract | 1 |
pipe_all101_denovotranscript_4 | pipeline_routing | "Which pipeline implements best-practice processing for: A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq. Topics: denovo-assembly, rna-seq, transcriptome. ?" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"drop": "Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders",
"denovotranscript": "A pipeline for de novo transcriptome assembly of paired-en... | denovotranscript | 1 |
mod_echtvar_anno_0 | tool_selection | "In Nextflow DSL2, which module handles: Annotate a decomposed (and normalized) VCF with an echtvar file (tools: echtvar)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"ivar/variants": "Call variants from a BAM file using iVar",
"echtvar/encode": "Make (encode) a new echtvar file from decomposed vcf",
"atlas/call": "generate VCF file... | echtvar/anno | 4 |
schema_std_chipseq_1_1 | samplesheet_schema | {
"pipeline": "nf-core/chipseq",
"assay": "chipseq pipeline processing",
"inputs": "Input files per samplesheet"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected for Nextflow pipeline nf-core/chipseq (ChIP-seq peak-calling, QC and differential analysis pipeline)?",
"criteria": {
"sample,input,output_path,checksum_md5,checksum_sha": null,
"fastq_1,fastq_2,group,replicate,md5_1": null,
"s... | sample,fastq_1,fastq_2,replicate,antibody | 3 |
pipe_all101_rnavar_4 | pipeline_routing | "Which pipeline implements best-practice processing for: gatk4 RNA variant calling pipeline. Topics: gatk4, rna, rnaseq, variant-calling, worflow. ?" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"methylong": "Extract methylation calls from long reads (ONT/ PacBio) [dna-methylation, fiber-seq, long-read]",
"mcmicro": "An end-to-end processing pipeline that transforms mult... | rnavar | 3 |
samplesheet_arch_dual_rnaseq_host_pathogen_0_1 | samplesheet_schema | {
"assay": "Dual RNA-seq simultaneous host and pathogen transcriptomics",
"first_step": "FASTQC",
"inputs": "Paired-end FASTQs from infected tissue undergoing dual mapping to human and pathogen"
} | {
"type": "choice",
"instructions": "Which columns should the input samplesheet have for: Dual RNA-seq simultaneous host and pathogen transcriptomics?",
"criteria": {
"sample,bam": null,
"sample,fastq_1": null,
"sample,host_fasta": null,
"sample,fastq_1,fastq_2,host,pathogen": null
}
} | sample,fastq_1,fastq_2,host,pathogen | 3 |
qc_adapt_pe_illumina_fastqc_2_19 | 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,
"Keep FastQC": null,
"Drop FastQC": null
}
} | Keep FastQC | 1 |
mod_haplogrep2_classify_1 | tool_selection | "In Nextflow DSL2, which module handles: classification into haplogroups (tools: haplogrep2)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"pasty": "Serogroup Pseudomonas aeruginosa assemblies",
"kaiju_kaiju": "Taxonomic classification of metagenomic sequence data using a protein reference database",
"hap... | haplogrep2_classify | 3 |
qc_adapt_ffpe_wes_2_12 | qc_read_adaptation | {
"assay": "Degraded FFPE exome capture sequencing on Illumina",
"tool": "FastQC",
"read_type": "short_reads_100bp"
} | {
"type": "choice",
"instructions": "Evaluate the quality control tool choice for: Degraded FFPE exome capture sequencing on Illumina (short_reads_100bp).",
"criteria": {
"Swap for NanoPlot": null,
"Drop FastQC": null,
"Keep FastQC": null
}
} | Keep FastQC | 2 |
mod_sylphtax_merge_0 | tool_selection | "In Nextflow DSL2, which module handles: Merge multiple taxonomic profiles from sylphtaxt/taxprof into a tsv table (tools: sylphtax)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"clippy": "Runs the Clippy CLIP peak caller",
"sylph/sketchgenomes": "Sylph profile command for taxonoming profiling of genomes",
"sylphtax/merge": "Merge multiple tax... | sylphtax/merge | 2 |
samplesheet_arch_viral_amplicon_artic_3_2 | samplesheet_schema | {
"technology": "Viral Surveillance",
"workflow_entry": "FASTQC",
"library_inputs": "Paired-end tiled viral amplicon FASTQs per clinical swab sample"
} | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for Viral amplicon sequencing with primers with entry step FASTQC.",
"criteria": {
"sample,fasta": null,
"sample,fastq_1,fastq_2": null,
"sample,bam": null,
"sample,vcf": null
}
} | sample,fastq_1,fastq_2 | 1 |
mod_custom_gtffilter_1 | tool_selection | "In Nextflow DSL2, which module handles: Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file (tools: gtffilter)?" | {
"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",
"agat_spkeeplongestisoform": "Filters GFF records to keep only the longest isoform per gene",
... | custom_gtffilter | 2 |
local_subworkflow_variantsofint_0_1 | subworkflow_packaging | {
"subworkflow": "VARIANTSOFINT",
"modules": [
"custom/variantsofint"
],
"description": "Variant filtering and clinical annotation aggregation"
} | {
"type": "choice",
"instructions": "How should VARIANTSOFINT (custom/variantsofint) be built?",
"criteria": {
"Leave them out": null,
"Use nf-core subworkflow variantsofint": null,
"Keep the modules in the main workflow": null,
"Local subworkflow VARIANTSOFINT": null
}
} | Local subworkflow VARIANTSOFINT | 3 |
pipe_all101_nanoseq_0 | pipeline_routing | "I need to run an end-to-end bioinformatics workflow to analyze Nanopore demultiplexing, QC and alignment pipeline. Topics: alignment, demultiplexing, nanopore, qc. . Which nf-core pipeline should I execute?" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"detaxizer": null,
"funcscan": null,
"fetchngs": null,
"rnafusion": null,
"eager": null,
"magmap": null,
"nanoseq": null,
"epitopeprediction": null
}
} | nanoseq | 6 |
mod_leehom_1 | tool_selection | "In Nextflow DSL2, which module handles: Bayesian reconstruction of ancient DNA fragments (tools: leehom)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"biobambam_bamsormadup": "Parallel sorting and duplicate marking",
"segemehl_align": "A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion... | leehom | 3 |
mod_cleanifier_index_1 | tool_selection | "In Nextflow DSL2, which module handles: Builds a Cuckoo filter or Cuckoo hash table index from reference sequences (FASTA/FASTQ) for fast contamination removal. (tools: cleanifier)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"bbmap_index": "Creates an index from a fasta file, ready to be used by bbmap.sh in mapping mode.",
"bcftools_index": "Index VCF tools",
"immunedeconv": "Perform immun... | cleanifier_index | 3 |
noul_mix_operator_async_emission_2 | 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.",
"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 |
schema_std_longraredisease_1_1 | samplesheet_schema | {
"pipeline": "nf-core/longraredisease",
"assay": "longraredisease pipeline processing",
"inputs": "Input files per samplesheet"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected for Nextflow pipeline nf-core/longraredisease (Long read sequencing pipeline to identify variants in patien)?",
"criteria": {
"sample_id,bam,vcf,library_id,lane": null,
"RNA_ID,RNA_BAM_FILE,RNA_BAI_FILE,DNA_ID,DNA_VCF_FILE": null,
... | family_id,sample,file_path,hpo_terms,sex | 3 |
pipe_all101_reportho_3 | pipeline_routing | "Recommend the most appropriate nf-core workflow for the following project: nf-core pipeline for comparative analysis of ortholog predictions. Topics: ortholog. " | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"molkart": null,
"rnadnavar": null,
"seqinspector": null,
"createpanelrefs": null,
"magmap": null,
"reportho": null,
"bamtofastq": null,
"rnavar": null,
... | reportho | 5 |
subworkflow_pkg_fastq_align_dedup_bwamem_1 | subworkflow_packaging | {
"subworkflow": "FASTQ_ALIGN_DEDUP_BWAMEM",
"modules": [
"parabricks/fq2bam",
"samtools/index",
"picard/addorreplacereadgroups",
"picard/markduplicates",
"bam_sort_stats_samtools",
"fastq_align_bwa"
],
"description": "Performs alignment of DNA or TAPS-treated reads using bwamem or parab... | {
"type": "choice",
"instructions": "How should FASTQ_ALIGN_DEDUP_BWAMEM (parabricks/fq2bam, samtools/index, picard/addorreplacereadgroups, picard/markduplicates, bam_sort_stats_samtools, fastq_align_bwa) be structured in DSL2?",
"criteria": {
"Local subworkflow FASTQ_ALIGN_DEDUP_BWAMEM": null,
"Leave the... | Use nf-core subworkflow fastq_align_dedup_bwamem | 3 |
mod_windowmasker_mkcounts_0 | tool_selection | "In Nextflow DSL2, which module handles: A program to generate frequency counts of repetitive units. (tools: windowmasker)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"windowmasker/mkcounts": null,
"nextclade/datasetget": null,
"agat/spextractsequences": null,
"gfatools/gfa2fa": null,
"agrvate": null
}
} | windowmasker/mkcounts | 0 |
samplesheet_arch_atacseq_replicates_0_0 | samplesheet_schema | {
"assay": "ATAC-seq chromatin accessibility with biological replicates",
"first_step": "FASTQC",
"inputs": "Paired-end Tn5 transposed FASTQs across conditions and replicates",
"pipeline": "nf-core/atacseq"
} | {
"type": "choice",
"instructions": "Which columns should the input samplesheet have for: ATAC-seq chromatin accessibility with biological replicates?",
"criteria": {
"sample,fastq_1,fastq_2": null,
"sample,fastq_1": null,
"sample,bam": null,
"sample,fastq_1,fastq_2,replicate": null
}
} | sample,fastq_1,fastq_2,replicate | 3 |
mod_metamdbg_asm_0 | tool_selection | "In Nextflow DSL2, which module handles: Metagenome assembler for long-read sequences (HiFi and ONT). (tools: metamdbg)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"abra2": "Assembly Based ReAligner for next-generation sequencing data",
"seqtk/cutn": "Generates a BED file containing genomic locations of lengths of N.",
"ale": "AL... | metamdbg/asm | 4 |
noul_single_hyphen_cli_params_error_8 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"In Nextflow, `params.my_var` values can be overridden from the command line using single hyphen `-my_var value`.\"" | {
"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_vcf_annotation_pipeline_1_4 | samplesheet_schema | {
"assay": "Downstream functional annotation of pre-called VCF files",
"first_step": "ENSEMBLVEP"
} | {
"type": "choice",
"instructions": "Which columns should the samplesheet have for Downstream functional annotation of pre-called VCF files?",
"criteria": {
"sample,vcf": null,
"sample,vcf,tbi": null,
"sample,bed": null,
"sample,fastq_1,fastq_2": null
}
} | sample,vcf,tbi | 1 |
field_constraint_expected_cells_0_2 | samplesheet_schema | {
"field_name": "expected_cells",
"datatype": "numeric_integer",
"description": "Expected cell count in single-cell droplet pipelines"
} | {
"type": "choice",
"instructions": "What is the JSON Schema validation constraint for samplesheet column 'expected_cells'?",
"criteria": {
"type: integer, minimum: 100, maximum: 50000": null,
"enum: [auto, single, paired]": null,
"format: file-path": null,
"pattern: ^\\S+\\.csv$": null
}
} | type: integer, minimum: 100, maximum: 50000 | 0 |
mod_samtools_bgzip_0 | tool_selection | "In Nextflow DSL2, which module handles: DEPRECATED. Use HTSLIB/BGZIPTABIX instead. Converts an arbitrary compressed or uncompressed file to BGZIP (tools: samtools)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"samtools/bgzip": "DEPRECATED. Use HTSLIB/BGZIPTABIX instead. Converts an arbitrary compressed or uncompressed file to BGZIP",
"gunzip": "Compresses and decompresses files... | samtools/bgzip | 0 |
resource_amulety_balmpaired_1 | resource_profiling | {
"process": "AMULETY_BALMPAIRED",
"tool": "amulety/balmpaired",
"description": "A module to create BALM paired embeddings of antibody (BCR) amino acid sequences using amulety."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to AMULETY_BALMPAIRED (A module to create BALM paired embeddings of antibody (BCR) amino acid sequences) in conf/base.config?",
"criteria": {
"process_high": null,
"process_medium": null,
"process_low": null,
"proc... | process_single | 3 |
qc_adapt_bulk_multiqc_2_29 | 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": {
"Drop MultiQC": null,
"Keep MultiQC": null,
"Keep FastQC": null,
"Swap for NanoPlot": null
}
} | Keep MultiQC | 1 |
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,
"pbsv_discover": null,
"checkm2_predict": null,
"octopusv_correct": null
}
} | tiddit_sv | 0 |
mod_pangolin_run_1 | tool_selection | "In Nextflow DSL2, which module handles: Phylogenetic Assignment of Named Global Outbreak LINeages (tools: pangolin)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"minibwa_map": "Align fastq reads to a fasta reference using minibwa",
"pangolin_updatedata": "Phylogenetic Assignment of Named Global Outbreak LINeages",
"pangolin_ru... | pangolin_run | 2 |
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,
"Swap for NanoPlot": null,
"Keep FastQC": null
}
} | Swap for NanoPlot | 1 |
samplesheet_arch_cutandrun_pe_6_4 | samplesheet_schema | {
"assay": "CUT&RUN / CUT&TAG chromatin profiling with IgG control",
"first_step": "FASTQC",
"inputs": "Paired-end low-input fragment FASTQs with target antibody and IgG negative control",
"pipeline": "nf-core/cutandrun"
} | {
"type": "choice",
"instructions": "Which columns are standard for CUT&RUN / CUT&TAG chromatin profiling with IgG control input samplesheet?",
"criteria": {
"sample,fastq_1,fastq_2,target,control": null,
"sample,fastq_1,fastq_2": null,
"sample,target,control": null,
"sample,bam": null
}
} | sample,fastq_1,fastq_2,target,control | 0 |
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