id stringlengths 9 67 | category stringclasses 8
values | state unknown | question unknown | target stringlengths 3 92 | target_idx int64 0 9 |
|---|---|---|---|---|---|
subworkflow_pkg_fastq_qc_trim_filter_setstrandedness_2 | subworkflow_packaging | {
"subworkflow": "FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS",
"modules": [
"bbmap/bbsplit",
"cat/fastq",
"fastqc",
"fq/lint",
"fastq_remove_rrna",
"fastq_subsample_fq_salmon",
"fastq_fastqc_umitools_trimgalore",
"fastq_fastqc_umitools_fastp"
],
"description": "Performs linting, qualit... | {
"type": "choice",
"instructions": "How should FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS (bbmap/bbsplit, cat/fastq, fastqc, fq/lint, fastq_remove_rrna, fastq_subsample_fq_salmon, fastq_fastqc_umitools_trimgalore, fastq_fastqc_umitools_fastp) be structured in DSL2?",
"criteria": {
"Leave them out": null,
"Loca... | Use nf-core subworkflow fastq_qc_trim_filter_setstrandedness | 2 |
samplesheet_arch_rnafusion_pe_4_4 | samplesheet_schema | {
"technology": "Specialized RNA-seq",
"workflow_entry": "FASTQC",
"library_inputs": "Paired-end oncology RNA-seq reads for chimeric transcript discovery"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected when inputs are: Paired-end oncology RNA-seq reads for chimeric transcript discovery?",
"criteria": {
"sample,fastq_1,fastq_2": null,
"sample,fusion_bed": null,
"sample,bam": null,
"sample,fastq_1,fastq_2,strandedness": nul... | sample,fastq_1,fastq_2,strandedness | 3 |
resource_bedtools_coverage_3 | resource_profiling | {
"process": "BEDTOOLS_COVERAGE",
"tool": "bedtools/coverage",
"description": "computes both the depth and breadth of coverage of features in file B on the features in file A"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BEDTOOLS_COVERAGE (computes both the depth and breadth of coverage of features in file B on the fea) in conf/base.config?",
"criteria": {
"process_medium": null,
"process_low": null,
"process_single": null,
"pro... | process_single | 2 |
samplesheet_arch_riboseq_profiling_5_2 | samplesheet_schema | {
"assay": "Ribosome profiling (Ribo-seq) footprint sequencing",
"first_step": "FASTQC",
"inputs": "Single-end ribosome protected RNA fragments (RPFs) with strandedness",
"pipeline": "nf-core/riboseq"
} | {
"type": "choice",
"instructions": "In Nextflow pipeline nf-core/riboseq, determine the input samplesheet column structure for: Ribosome profiling (Ribo-seq) footprint sequencing.",
"criteria": {
"sample,fastq_1,strandedness": null,
"sample,bam": null,
"sample,cdna_fasta": null,
"sample,fastq_1,f... | sample,fastq_1,strandedness | 0 |
mod_isoseq_cluster_1 | 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": null,
"paraclu": null,
"mat2json": null,
"clusty": null,
"trycycler_subsample": null
}
} | isoseq_cluster | 0 |
qc_adapt_qc_aggregate_0_2 | qc_read_adaptation | {
"assay": "Multi-sample QC aggregation and reporting",
"tool": "MultiQC",
"read_type": "multiqc_report"
} | {
"type": "choice",
"instructions": "For Multi-sample QC aggregation and reporting, what is the recommended QC default for MultiQC?",
"criteria": {
"Keep MultiQC": null,
"Swap for NanoPlot": null,
"Drop MultiQC": null
}
} | Keep MultiQC | 0 |
mod_sawfish_jointcall_1 | tool_selection | "In Nextflow DSL2, which module handles: Joint calling of structural variants from multiple samples using Sawfish (tools: sawfish)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"sawfish_jointcall": "Joint calling of structural variants from multiple samples using Sawfish",
"sniffles": "structural-variant calling with sniffles",
"plink2_score"... | sawfish_jointcall | 0 |
subworkflow_pkg_bam_dedup_umi_2 | 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": {
"Local subworkflow BAM_DEDUP_UMI": null,
"Leave them out": null,
... | Use nf-core subworkflow bam_dedup_umi | 3 |
subworkflow_pkg_fasta_build_add_kraken2_bracken_0 | subworkflow_packaging | {
"subworkflow": "FASTA_BUILD_ADD_KRAKEN2_BRACKEN",
"modules": [
"kraken2/add",
"kraken2/build",
"bracken/build"
],
"description": "KRAKEN2 and BRACKEN build custom database subworkflow"
} | {
"type": "choice",
"instructions": "How should FASTA_BUILD_ADD_KRAKEN2_BRACKEN (kraken2/add, kraken2/build, bracken/build) be structured in DSL2?",
"criteria": {
"Leave them out": null,
"Local subworkflow FASTA_BUILD_ADD_KRAKEN2_BRACKEN": null,
"Use nf-core subworkflow fasta_build_add_kraken2_bracken... | Use nf-core subworkflow fasta_build_add_kraken2_bracken | 2 |
mod_shinyngs_staticdifferential_0 | tool_selection | "In Nextflow DSL2, which module handles: Make plots for interpretation of differential abundance statistics (tools: shinyngs)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"anota2seq/anota2seqrun": null,
"shinyngs/staticdifferential": null,
"dotseq/dotseq": null,
"lima": null,
"viennarna/rnafold": null
}
} | shinyngs/staticdifferential | 1 |
schema_std_genomeqc_0_0 | samplesheet_schema | {
"pipeline": "nf-core/genomeqc",
"description": "Compare the quality of multiple genomes, along with their annotations.",
"mode": "standard_execution"
} | {
"type": "choice",
"instructions": "Which standard samplesheet columns are configured in assets/schema_input.json for nf-core/genomeqc?",
"criteria": {
"fasta,assembly,ncbi,gff,fastq": null,
"sample,bundle,image": null,
"sample,fastq_1,fastq_2,rundir,tags": null,
"patient,sample,vcf,status,cna": ... | fasta,assembly,ncbi,gff,fastq | 0 |
qc_adapt_illumina_novaseq_1_24 | 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": {
"Keep FastQC": null,
"Swap for NanoPlot": null,
"Drop FastQC": null
}
} | Keep FastQC | 0 |
mod_abritamr_run_1 | tool_selection | "In Nextflow DSL2, which module handles: A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes (tools: abritamr)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"abritamr_run": "A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes",
"amrfinderplus_run": "Identify antimicrobial re... | abritamr_run | 0 |
resource_bacphlip_5 | resource_profiling | {
"process": "BACPHLIP",
"tool": "bacphlip",
"description": "A bacteriophage lifestyle prediction tool"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BACPHLIP (A bacteriophage lifestyle prediction tool) in conf/base.config?",
"criteria": {
"process_single": null,
"process_low": null,
"process_long": null,
"process_high": null
}
} | process_single | 0 |
mod_trycycler_subsample_1 | tool_selection | "In Nextflow DSL2, which module handles: Subsample a long-read sequencing fastq file for multiple assemblies (tools: trycycler)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"fastq_subsample_fq_salmon": "Subsample fastq",
"bam2fastx_bam2fastq": "Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data",
... | trycycler_subsample | 4 |
mod_ribocode_metaplots_1 | tool_selection | "In Nextflow DSL2, which module handles: Set up RiboCode ORF calling with metaplots (tools: ribocode)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"ribocode_prepare": "Prepare the annotation files for RiboCode ORF calling",
"custom_orfnormalise": "Convert one ORF caller's per-sample output table into a unified BED12 ... | ribocode_metaplots | 3 |
resource_bcftools_split_5 | resource_profiling | {
"process": "BCFTOOLS_SPLIT",
"tool": "bcftools/split",
"description": "Split a vcf file into files per chromosome"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BCFTOOLS_SPLIT (Split a vcf file into files per chromosome) in conf/base.config?",
"criteria": {
"process_high": null,
"process_low": null,
"process_single": null,
"process_medium": null
}
} | process_single | 2 |
mod_sickle_1 | tool_selection | "In Nextflow DSL2, which module handles: A windowed adaptive trimming tool for FASTQ files using quality (tools: sickle)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"adapterremoval": "Trim sequencing adapters and collapse overlapping reads",
"rapidnj": "Produces a Newick format phylogeny from a multiple sequence alignment using a Neig... | sickle | 2 |
mod_ilastik_pixelclassification_1 | tool_selection | "In Nextflow DSL2, which module handles: Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel c... | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"mash_sketch": "Creates vastly reduced representations of sequences using MinHash",
"coreograph": "Great....yet another TMA dearray program. What does this one do? Coreogr... | ilastik_pixelclassification | 4 |
mod_last_mafconvert_0 | tool_selection | "In Nextflow DSL2, which module handles: Converts MAF alignments in another format. (tools: last)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"diamond/blastx": null,
"last/lastal": null,
"last/split": null,
"last/mafconvert": null,
"lissero": null
}
} | last/mafconvert | 3 |
intent_debug_error_21 | intent_routing | "Classify this user request: \"ERROR ~ Error executing process > 'SAMTOOLS_SORT' (command not found, exit status 127)\"" | {
"type": "choice",
"instructions": "Classify the user intent into one category.",
"criteria": {
"prepare_data": null,
"debug_error": null,
"ask_question": null,
"build_pipeline": null
}
} | debug_error | 1 |
qc_adapt_pacbio_hifi_0_43 | qc_read_adaptation | {
"assay": "PacBio HiFi circular consensus sequencing (CCS)",
"tool": "FastQC",
"read_type": "long_reads_hifi_15kb"
} | {
"type": "choice",
"instructions": "For PacBio HiFi circular consensus sequencing (CCS), what is the recommended QC default for FastQC?",
"criteria": {
"Drop FastQC": null,
"Keep FastQC": null,
"Swap for NanoPlot": null
}
} | Swap for NanoPlot | 2 |
qc_adapt_illumina_novaseq_0_21 | qc_read_adaptation | {
"assay": "Illumina NovaSeq X paired-end 150bp WGS",
"tool": "FastQC",
"read_type": "short_reads_150bp"
} | {
"type": "choice",
"instructions": "For Illumina NovaSeq X paired-end 150bp WGS, what is the recommended QC default for FastQC?",
"criteria": {
"Keep FastQC": null,
"Drop FastQC": null,
"Swap for NanoPlot": null
}
} | Keep FastQC | 0 |
samplesheet_arch_ont_demux_barcodes_1_1 | samplesheet_schema | "nextflow run nf-core/nanoseq --input samplesheet.csv (Assay: Multiplexed Oxford Nanopore run with barcode demultiplexing)" | {
"type": "choice",
"instructions": "Which columns should the samplesheet have for Multiplexed Oxford Nanopore run with barcode demultiplexing?",
"criteria": {
"sample,barcode,flowcell,kit,fastq": null,
"sample,fastq_1,fastq_2": null,
"sample,fastq_1": null,
"sample,bam": null
}
} | sample,barcode,flowcell,kit,fastq | 0 |
mod_art_illumina_1 | tool_selection | "In Nextflow DSL2, which module handles: Simulation tool to generate synthetic Illumina next-generation sequencing reads (tools: art)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"art_illumina": "Simulation tool to generate synthetic Illumina next-generation sequencing reads",
"meryl_histogram": "A genomic k-mer counter (and sequence utility) with ... | art_illumina | 0 |
mod_mapad_index_1 | tool_selection | "In Nextflow DSL2, which module handles: Create mapAD index for reference genome (tools: mapad)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"mapad_map": "Map short-reads to an indexed reference genome",
"bowtie_build": "Create bowtie index for reference genome",
"bismark_genomepreparation": "Converts a spe... | mapad_index | 4 |
resource_bedtools_shift_4 | resource_profiling | {
"process": "BEDTOOLS_SHIFT",
"tool": "bedtools/shift",
"description": "Shifts each feature by specific number of bases"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BEDTOOLS_SHIFT (Shifts each feature by specific number of bases) in conf/base.config?",
"criteria": {
"process_medium": null,
"process_long": null,
"process_single": null,
"process_low": null
}
} | process_single | 2 |
mod_grimer_0 | tool_selection | "In Nextflow DSL2, which module handles: Generates an interactive HTML dashboard integrating taxonomy,\nannotation, and metadata to detect contamination in metagenomic\nand amplicon sequencing datasets. GRIMER is independent of\nquantification methods and directly analyses contingency tables. (tools: grimer)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"bracken/combinebrackenoutputs": null,
"grimer": null,
"bracken/bracken": null,
"odgi/draw": null,
"khmer/uniquekmers": null
}
} | grimer | 1 |
samplesheet_arch_metatranscriptome_denovo_6_5 | samplesheet_schema | {
"assay": "Environmental community metatranscriptomics de novo assembly",
"first_step": "FASTQC",
"inputs": "Paired-end total RNA reads from complex microbial communities with ribosomal RNA filtering"
} | {
"type": "choice",
"instructions": "Which columns are standard for Environmental community metatranscriptomics de novo assembly input samplesheet?",
"criteria": {
"sample,fastq_1": null,
"sample,fastq_1,fastq_2,environment": null,
"sample,bam": null,
"sample,rrna_fasta": null
}
} | sample,fastq_1,fastq_2,environment | 1 |
samplesheet_arch_cutandrun_pe_4_4 | samplesheet_schema | {
"technology": "Epigenomics",
"workflow_entry": "FASTQC",
"library_inputs": "Paired-end low-input fragment FASTQs with target antibody and IgG negative control"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected when inputs are: Paired-end low-input fragment FASTQs with target antibody and IgG negative control?",
"criteria": {
"sample,bam": null,
"sample,target,control": null,
"sample,fastq_1,fastq_2": null,
"sample,fastq_1,fastq_2... | sample,fastq_1,fastq_2,target,control | 3 |
mod_homer_groseq_1 | tool_selection | "In Nextflow DSL2, which module handles: Basic process of trying to analyze GRO-Seq data with HOMER. From the [GRO-Seq Analysis Tutorial](http://homer.ucsd.edu/homer/ngs/groseq/groseq.html). (tools: homer_groseq)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"checkqc": "A simple program to parse Illumina NGS data and check it for quality criteria",
"bbmap_clumpify": "Create 30% Smaller, Faster Gzipped Fastq Files. And remove d... | homer_groseq | 3 |
qc_adapt_targeted_amplicon_0_48 | qc_read_adaptation | {
"assay": "Targeted Illumina amplicon panel",
"tool": "FastQC",
"read_type": "short_reads_pe250"
} | {
"type": "choice",
"instructions": "For Targeted Illumina amplicon panel, what is the recommended QC default for FastQC?",
"criteria": {
"Keep FastQC": null,
"Swap for NanoPlot": null,
"Drop FastQC": null
}
} | Keep FastQC | 0 |
mod_seqkit_sort_1 | tool_selection | "In Nextflow DSL2, which module handles: Sorts sequences by id/name/sequence/length (tools: seqkit)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"seqkit_sort": null,
"agat_spextractsequences": null,
"ultra_align": null,
"custom_orfnormalise": null,
"alignoth": null
}
} | seqkit_sort | 0 |
schema_std_variantbenchmarking_0_0 | samplesheet_schema | {
"pipeline": "nf-core/variantbenchmarking",
"description": "Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research",
"mode": "standard_execution"
} | {
"type": "choice",
"instructions": "Which standard samplesheet columns are configured in assets/schema_input.json for nf-core/variantbenchmarking?",
"criteria": {
"id,test_vcf,test_regions,caller,subsample": null,
"sample,fastq_1,fastq_2,strandedness,seq_platform": null,
"sample,bam,vcf,rna_matrix,ht... | id,test_vcf,test_regions,caller,subsample | 0 |
field_constraint_phenotype_2_14 | samplesheet_schema | "Validating samplesheet CSV field 'phenotype' (Affection status in clinical trio / family analysis) in assets/schema_input.json." | {
"type": "choice",
"instructions": "In nf-core samplesheet schema (assets/schema_input.json), how is column 'phenotype' validated?",
"criteria": {
"format: file-path": null,
"enum: [0, 1, 2, -9] (1=unaffected, 2=affected)": null,
"type: string free-text": null,
"enum: [normal, tumor]": null
}
} | enum: [0, 1, 2, -9] (1=unaffected, 2=affected) | 1 |
mod_jvarkit_sam2tsv_1 | tool_selection | "In Nextflow DSL2, which module handles: Convert sam files to tsv files (tools: jvarkit)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"seqkit_replace": null,
"deepvariant": null,
"bwa_mem": null,
"bwa_samse": null,
"jvarkit_sam2tsv": null
}
} | jvarkit_sam2tsv | 4 |
mod_cache_download_ensemblvep_snpeff_0 | tool_selection | "In Nextflow DSL2, which module handles: downlad annotation cache for snpeff and ensemblvep (tools: cache_download_ensemblvep_snpeff)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"coptr/index": "Indexes a directory of fasta files for use with CoPTR",
"salsa2": "SALSA, A tool to scaffold long read assemblies with HiC",
"vcf_annotate_snpeff": "Pe... | cache_download_ensemblvep_snpeff | 4 |
mod_souporcell_0 | tool_selection | "In Nextflow DSL2, which module handles: souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual. (tools: souporcell)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"ensemblvep/vep": "Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`.",
"autocycler/cluster": "Cluster replicons in comp... | souporcell | 4 |
qc_adapt_pe_illumina_fastqc_2_38 | 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": {
"Drop FastQC": null,
"Keep FastQC": null,
"Swap for NanoPlot": null
}
} | Keep FastQC | 1 |
schema_std_bamtofastq_0_0 | samplesheet_schema | {
"pipeline": "nf-core/bamtofastq",
"description": "Converts bam or cram files to fastq format and does quality control.",
"mode": "standard_execution"
} | {
"type": "choice",
"instructions": "Which standard samplesheet columns are configured in assets/schema_input.json for nf-core/bamtofastq?",
"criteria": {
"id,fasta,sequence": null,
"sample,sample_id,fastq_1,fastq_2,method": null,
"sample_id,mapped,index,file_type": null,
"sample,fastq_1,fastq_2,s... | sample_id,mapped,index,file_type | 2 |
field_constraint_sample_3_8 | samplesheet_schema | {
"schema_target": "assets/schema_input.json",
"field": "sample",
"validation_type": "unique_identifier"
} | {
"type": "choice",
"instructions": "Select the appropriate draft-07 JSON Schema property specification for 'sample'.",
"criteria": {
"pattern: ^\\S+$ (no whitespace, unique)": null,
"enum: [0, 1]": null,
"format: file-path": null,
"type: integer": null
}
} | pattern: ^\S+$ (no whitespace, unique) | 0 |
mod_bismark_methylationextractor_0 | tool_selection | "In Nextflow DSL2, which module handles: Extracts methylation information for individual cytosines from alignments. (tools: bismark)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"pindel/pindel": "Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and",
"bismark/summary": "Uses Bismark report ... | bismark/methylationextractor | 4 |
mod_splitubam_0 | tool_selection | "In Nextflow DSL2, which module handles: split one ubam into multiple, per line, fast (tools: splitubam)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"autocycler/trim": "Trim cluster assembly graphs to remove unsupported segments prior to resolution.",
"shapeit5/phaserare": "Tool to phase rare variants onto a scaffold o... | splitubam | 2 |
resource_autocycler_trim_0 | resource_profiling | {
"process": "AUTOCYCLER_TRIM",
"tool": "autocycler/trim",
"description": "Trim cluster assembly graphs to remove unsupported segments prior to resolution."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to AUTOCYCLER_TRIM (Trim cluster assembly graphs to remove unsupported segments prior to resolution.) in conf/base.config?",
"criteria": {
"process_single": null,
"process_high": null,
"process_low": null,
"process... | process_single | 0 |
noul_retry_errorstrategy_21 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"The `errorStrategy = 'retry'` directive allows Nextflow to re-execute a failed task up to `maxRetries` times.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards."
} | true | 1 |
qc_adapt_ont_nanoplot_1_17 | 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 |
samplesheet_arch_mira_influenza_sc2_3_2 | samplesheet_schema | {
"technology": "Viral Surveillance",
"workflow_entry": "INPUT_CHECK",
"library_inputs": "Paired-end surveillance FASTQs from respiratory pathogen panels"
} | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for Custom MIRA-NF Influenza / SC2 pipeline with entry step INPUT_CHECK.",
"criteria": {
"sample,fastq_1": null,
"sample,fastq_1,fastq_2,group": null,
"sample,bam": null,
"sample,fastq_1,fastq_2": null
}
} | sample,fastq_1,fastq_2 | 3 |
mod_custom_tabulartogseagct_0 | tool_selection | "In Nextflow DSL2, which module handles: Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA (tools: tabulartogseagct)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"tcoffee/alncompare": null,
"seqkit/fx2tab": null,
"custom/tabulartogseagct": null,
"custom/tabulartogseachip": null,
"coptr/index": null
}
} | custom/tabulartogseagct | 2 |
resource_bamutil_trimbam_0 | resource_profiling | {
"process": "BAMUTIL_TRIMBAM",
"tool": "bamutil/trimbam",
"description": "trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BAMUTIL_TRIMBAM (trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality ) in conf/base.config?",
"criteria": {
"process_medium": null,
"process_single": null,
"process_low": null,
"proce... | process_single | 1 |
samplesheet_arch_spatial_xenium_5_4 | samplesheet_schema | {
"assay": "10x Xenium in situ subcellular spatial RNA transcriptomics",
"first_step": "INPUT_CHECK"
} | {
"type": "choice",
"instructions": "In Nextflow pipeline nf-core/spatialaxe, determine the input samplesheet column structure for: 10x Xenium in situ subcellular spatial RNA transcriptomics.",
"criteria": {
"sample,vcf": null,
"sample,fastq_1,fastq_2": null,
"sample,transcripts_csv,morphology_focus_t... | sample,transcripts_csv,morphology_focus_tif,cells_parquet | 2 |
qc_adapt_ont_ultra_long_2_16 | 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_germline_lane_split_1_4 | samplesheet_schema | {
"assay": "Multi-lane Illumina sequencing run of clinical samples",
"first_step": "FASTQC"
} | {
"type": "choice",
"instructions": "Which columns should the samplesheet have for Multi-lane Illumina sequencing run of clinical samples?",
"criteria": {
"lane,fastq_1,fastq_2": null,
"sample,fastq_1,fastq_2": null,
"patient,sample,lane,fastq_1,fastq_2": null,
"sample,bam": null
}
} | patient,sample,lane,fastq_1,fastq_2 | 2 |
resource_basicpy_5 | 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_medium": null,
"process_long": null,
"process_high": null,
"process_single... | process_single | 3 |
field_constraint_status_2_7 | samplesheet_schema | "Validating samplesheet CSV field 'status' (Tissue status for somatic cancer workflows) in assets/schema_input.json." | {
"type": "choice",
"instructions": "In nf-core samplesheet schema (assets/schema_input.json), how is column 'status' validated?",
"criteria": {
"enum: [auto, forward, reverse]": null,
"pattern: ^[A-Z]+$": null,
"enum: [0, 1] (0=normal, 1=tumor)": null,
"format: file-path": null
}
} | enum: [0, 1] (0=normal, 1=tumor) | 2 |
samplesheet_arch_prealigned_bam_indexed_0_4 | samplesheet_schema | {
"technology": "Pre-aligned Assets",
"workflow_entry": "GATK_HAPLOTYPECALLER",
"library_inputs": "Aligned BAM files"
} | {
"type": "choice",
"instructions": "Which columns should the input samplesheet have for: Pre-aligned BAM variant calling pipeline?",
"criteria": {
"sample,vcf": null,
"sample,fastq_1": null,
"sample,fastq_1,fastq_2": null,
"sample,bam,bai": null
}
} | sample,bam,bai | 3 |
mod_svtk_countsvtypes_1 | tool_selection | "In Nextflow DSL2, which module handles: Count the instances of each SVTYPE observed in each sample in a VCF. (tools: svtk)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"svtk_vcf2bed": "Converts VCFs containing structural variants to BED format",
"svtk_countsvtypes": "Count the instances of each SVTYPE observed in each sample in a VCF.",
... | svtk_countsvtypes | 1 |
mod_deeptools_multibigwigsummary_0 | tool_selection | "In Nextflow DSL2, which module handles: Computes the average scores for each of the files in every genomic region (tools: deeptools)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"deeptools/multibigwigsummary": "Computes the average scores for each of the files in every genomic region",
"ultra/pipeline": "uLTRA aligner - A wrapper around minimap2 t... | deeptools/multibigwigsummary | 0 |
noul_multiple_script_sections_invalid_16 | 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.",
"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 |
noul_confusing_combine_with_mix_semantics_15 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"The operator `.combine()` performs the same operation as `.mix()` without cartesian product semantics.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards."
} | false | 0 |
mod_tabix_bgzip_1 | tool_selection | "In Nextflow DSL2, which module handles: DEPRECATED. Use HTSLIB/BGZIPTABIX instead. Compresses/decompresses files (tools: bgzip)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"cat_fastq": "Concatenates fastq files. Supports both compressed (.gz) and uncompressed inputs; uncompressed files are autom",
"bismark_align": "Performs alignment of BS-S... | tabix_bgzip | 2 |
samplesheet_arch_ont_direct_rna_se_1_0 | samplesheet_schema | "Building an autonomous Nextflow workflow (nf-core/nanoseq) for Single-end Oxford Nanopore direct RNA. Input files: Single fastq per sample." | {
"type": "choice",
"instructions": "Which columns should the samplesheet have for Single-end Oxford Nanopore direct RNA?",
"criteria": {
"sample,fastq_1,fastq_2": null,
"sample,vcf": null,
"sample,fast5": null,
"sample,fastq_1": null
}
} | sample,fastq_1 | 3 |
mod_bowtie2_build_1 | tool_selection | "In Nextflow DSL2, which module handles: Builds bowtie index for reference genome (tools: bowtie2)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"fastqscreen_buildfromindex": "Build fastq screen config file from bowtie index files",
"sequencetools_pileupcaller": "PileupCaller is a tool to create genotype calls from... | bowtie2_build | 4 |
noul_named_process_output_emits_6 | 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.",
"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 |
intent_ask_question_20 | 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",
"build_pipeline": "User wants to generate, assemble, compose, or write a Nextflow pipeline, ... | ask_question | 0 |
noul_retry_errorstrategy_8 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"The `errorStrategy = 'retry'` directive allows Nextflow to re-execute a failed task up to `maxRetries` times.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards.",
"criteria": {
"false": "The statement describes an invalid Nextflow DSL2 syntax, anti-pattern, or deprecated behavior.",
"true": "The statement describes a valid, standard, and re... | true | 1 |
pipe_all101_smrnaseq_5 | pipeline_routing | "I need to run an end-to-end bioinformatics workflow to analyze A small-RNA sequencing analysis pipeline. Topics: small-rna, smrna-seq. . Which nf-core pipeline should I execute?" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"coproid": "Coprolite host Identification pipeline [adna, ancient-dna, coprolite]",
"rnavar": "gatk4 RNA variant calling pipeline [gatk4, rna, rnaseq]",
"kmermaid": " k-mer si... | smrnaseq | 3 |
mod_gangstr_1 | tool_selection | "In Nextflow DSL2, which module handles: GangSTR is a tool for genome-wide profiling tandem repeats from short reads. (tools: gangstr)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"sentieon_applyvarcal": "Apply a score cutoff to filter variants based on a recalibration table.\nSentieon's Aplyvarcal performs the sec",
"expansionhunter": "Estimate rep... | gangstr | 4 |
mod_krakenuniq_preloadedkrakenuniq_0 | tool_selection | "In Nextflow DSL2, which module handles: Classifies metagenomic sequence data using unique k-mer counts (tools: krakenuniq)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"snpeff/download": "Genetic variant annotation and functional effect prediction toolbox",
"haplogrep2/classify": "classification into haplogroups",
"centrifuge/kreport... | krakenuniq/preloadedkrakenuniq | 3 |
mod_xz_decompress_1 | tool_selection | "In Nextflow DSL2, which module handles: Decompresses files with xz. (tools: xz)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"spring_decompress": "Fast, efficient, lossless decompression of FASTQ files.",
"unzipfiles": "Unzip ZIP archive files",
"xz_decompress": "Decompresses files with xz."... | xz_decompress | 2 |
mod_ngmaster_0 | tool_selection | "In Nextflow DSL2, which module handles: Serotyping Neisseria gonorrhoeae assemblies (tools: ngmaster)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"any2fasta": "Convert various sequence formats (GenBank, GFF, FASTQ, FASTA, CLUSTAL, Stockholm, GFA) to FASTA format. Input ",
"ichorcna/run": "ichorCNA is an R package fo... | ngmaster | 2 |
mod_manta_tumoronly_1 | tool_selection | "In Nextflow DSL2, which module handles: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. (tools: manta)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"controlfreec_freec": "Copy number and genotype annotation from whole genome and whole exome sequencing data",
"manta_tumoronly": "Manta calls structural variants (SVs) an... | manta_tumoronly | 1 |
qc_adapt_ont_ultra_long_2_17 | 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": {
"Keep FastQC": null,
"Drop FastQC": null,
"Swap for NanoPlot": null
}
} | Swap for NanoPlot | 2 |
mod_oarfish_alignmentmode_0 | tool_selection | "In Nextflow DSL2, which module handles: oarfish is a program for quantifying transcript-level expression from long-read sequencing technologies. Quantify pre-computed alignments of reads to the transcriptome (a name-sorted BAM, e.g. from minimap2/pbmm2). (tools: oarfish)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"kaiju/mkfmi": "Make Kaiju FMI-index file from a protein FASTA file",
"gatk4/gatherbqsrreports": "Gathers scattered BQSR recalibration reports into a single file",
"oa... | oarfish/alignmentmode | 2 |
resource_amulety_antiberta2_3 | resource_profiling | {
"process": "AMULETY_ANTIBERTA2",
"tool": "amulety/antiberta2",
"description": "A module to create antiberta2 embeddings of antibody (BCR) amino acid sequences using amulety."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to AMULETY_ANTIBERTA2 (A module to create antiberta2 embeddings of antibody (BCR) amino acid sequences ) in conf/base.config?",
"criteria": {
"process_medium": null,
"process_long": null,
"process_single": null,
"p... | process_single | 2 |
samplesheet_arch_atacseq_replicates_1_0 | samplesheet_schema | "Building an autonomous Nextflow workflow (nf-core/atacseq) for ATAC-seq chromatin accessibility with biological replicates. Input files: Paired-end Tn5 transposed FASTQs across conditions and replicates." | {
"type": "choice",
"instructions": "Which columns should the samplesheet have for ATAC-seq chromatin accessibility with biological replicates?",
"criteria": {
"sample,fastq_1,fastq_2": null,
"sample,bed": null,
"sample,bam": null,
"sample,fastq_1,fastq_2,replicate": null
}
} | sample,fastq_1,fastq_2,replicate | 3 |
pipe_all101_rnavar_5 | pipeline_routing | "I need to run an end-to-end bioinformatics workflow to analyze gatk4 RNA variant calling pipeline. Topics: gatk4, rna, rnaseq, variant-calling, worflow. . Which nf-core pipeline should I execute?" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"rnavar": "gatk4 RNA variant calling pipeline [gatk4, rna, rnaseq]",
"fastquorum": "Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs) [consensus, ... | rnavar | 0 |
resource_bcftools_isec_3 | resource_profiling | {
"process": "BCFTOOLS_ISEC",
"tool": "bcftools/isec",
"description": "Apply set operations to VCF files"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BCFTOOLS_ISEC (Apply set operations to VCF files) in conf/base.config?",
"criteria": {
"process_medium": null,
"process_long": null,
"process_low": null,
"process_single": null
}
} | process_single | 3 |
noul_channel_join_operator_0 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"The `.join()` operator combines two channels sharing a matching key (like `meta.id`).\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards.",
"criteria": {
"false": "The statement describes an invalid Nextflow DSL2 syntax, anti-pattern, or deprecated behavior.",
"true": "The statement describes a valid, standard, and re... | true | 1 |
samplesheet_arch_atacseq_replicates_3_4 | samplesheet_schema | "Building an autonomous Nextflow workflow (nf-core/atacseq) for ATAC-seq chromatin accessibility with biological replicates. Input files: Paired-end Tn5 transposed FASTQs across conditions and replicates." | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for ATAC-seq chromatin accessibility with biological replicates with entry step FASTQC.",
"criteria": {
"sample,bam": null,
"sample,bed": null,
"sample,fastq_1,fastq_2": null,
"sample,fastq_1,fastq_2,replicate":... | sample,fastq_1,fastq_2,replicate | 3 |
mod_caddsv_get_0 | tool_selection | "In Nextflow DSL2, which module handles: Download CADD-SV annotation resources or SegmentNT model files. (tools: caddsv)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"pypgx/preparedepthofcoverage": null,
"caddsv/get": null,
"genometester4/glistmaker": null,
"caddsv/run": null,
"annotsv/annotsv": null
}
} | caddsv/get | 1 |
noul_single_hyphen_cli_params_error_10 | 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 |
subworkflow_pkg_vcf_phase_shapeit5_3 | subworkflow_packaging | {
"subworkflow": "VCF_PHASE_SHAPEIT5",
"modules": [
"glimpse2/chunk",
"shapeit5/phasecommon",
"shapeit5/ligate",
"bcftools/index"
],
"description": "Subworkflow to phase a reference panel VCF file using SHAPEIT5."
} | {
"type": "choice",
"instructions": "How should VCF_PHASE_SHAPEIT5 (glimpse2/chunk, shapeit5/phasecommon, shapeit5/ligate, bcftools/index) be structured in DSL2?",
"criteria": {
"Leave them out": null,
"Keep the modules in the main workflow": null,
"Use nf-core subworkflow vcf_phase_shapeit5": null,
... | Use nf-core subworkflow vcf_phase_shapeit5 | 2 |
samplesheet_arch_spatial_visium_2_3 | samplesheet_schema | "nextflow run nf-core/spatialaxe --input samplesheet.csv (Assay: 10x Visium spatial transcriptomics with histology image)" | {
"type": "choice",
"instructions": "Which columns should the input samplesheet have?",
"criteria": {
"sample,fastq_1,fastq_2,image,slide,area": null,
"sample,bam": null,
"sample,image": null,
"sample,fastq_1,fastq_2": null
}
} | sample,fastq_1,fastq_2,image,slide,area | 0 |
samplesheet_arch_bulk_wes_pe_6_2 | samplesheet_schema | "Building an autonomous Nextflow workflow (nf-core/sarek) for Paired-end Whole Exome Sequencing (WES) target capture. Input files: Paired-end FASTQs from Agilent/Twist exome target capture." | {
"type": "choice",
"instructions": "Which columns are standard for Paired-end Whole Exome Sequencing (WES) target capture input samplesheet?",
"criteria": {
"sample,fastq_1": null,
"sample,vcf": null,
"sample,fastq_1,fastq_2": null,
"sample,bed": null
}
} | sample,fastq_1,fastq_2 | 2 |
mod_viralconsensus_1 | 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": {
"checkv_updatedatabase": "Construct the database necessary for checkv's quality assessment",
"plink2_score": "Apply a scoring system to each sample in a plink 2 fileset",
... | viralconsensus | 4 |
mod_gatk4_getpileupsummaries_1 | tool_selection | "In Nextflow DSL2, which module handles: Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD. (tools: gatk4)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"sentieon_staralign": null,
"gatk4_getpileupsummaries": null,
"rgi_main": null,
"gatk4_analyzecovariates": null,
"gatk4_annotateintervals": null
}
} | gatk4_getpileupsummaries | 1 |
mod_ucsc_bigwigaverageoverbed_1 | 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": {
"deeptools_multibigwigsummary": "Computes the average scores for each of the files in every genomic region",
"irescue": "Quantification of transposable elements expression... | ucsc_bigwigaverageoverbed | 3 |
samplesheet_arch_cageseq_transcription_3_2 | samplesheet_schema | {
"technology": "Specialized RNA-seq",
"workflow_entry": "FASTQC",
"library_inputs": "Single-end capped 5-prime cDNA tags for transcription start site (TSS) mapping"
} | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for CAGE-seq 5-prime capped transcript end sequencing with entry step FASTQC.",
"criteria": {
"sample,fastq_1,fastq_2": null,
"sample,tss_bed": null,
"sample,bam": null,
"sample,fastq_1": null
}
} | sample,fastq_1 | 3 |
schema_std_sarek_1_1 | samplesheet_schema | {
"pipeline": "nf-core/sarek",
"assay": "sarek pipeline processing",
"inputs": "Input files per samplesheet"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected for Nextflow pipeline nf-core/sarek (Analysis pipeline to detect germline or somatic variants (pr)?",
"criteria": {
"sample,fastq_1,fastq_2,replicate,control": null,
"patient,sample,fastq_1,fastq_2,bam": null,
"sample,fastq_1,f... | patient,sample,fastq_1,fastq_2,bam | 1 |
mod_disambiguate_0 | tool_selection | "In Nextflow DSL2, which module handles: Disambiguates reads aligned to two different organisms (e.g. human and mouse)\nfrom the same source of FASTQ files. Useful in explant RNA/DNA-Seq workflows\nwhere reads from two species are present. For reads aligned to both organisms,\nthe algorithm compares alignment quality s... | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"bcftools/concat": "Concatenate VCF files",
"arcashla/extract": "Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates.",
"disambiguate":... | disambiguate | 2 |
samplesheet_arch_spatial_visium_7_0 | samplesheet_schema | {
"assay": "10x Visium spatial transcriptomics with histology image",
"first_step": "FASTQC"
} | {
"type": "choice",
"instructions": "Which columns should the samplesheet have for grouped metagenomics?",
"criteria": {
"sample,fastq_1,fastq_2": null,
"sample,fastq_1,fastq_2,image,slide,area": null,
"sample,bam": null,
"sample,fastq_1,image": null
}
} | sample,fastq_1,fastq_2,image,slide,area | 1 |
noul_process_conditional_execution_10 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"The `when:` directive in a process controls conditional execution based on workflow parameters.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards.",
"criteria": {
"false": "The statement describes an invalid Nextflow DSL2 syntax, anti-pattern, or deprecated behavior.",
"true": "The statement describes a valid, standard, and re... | true | 1 |
qc_adapt_qc_aggregate_1_13 | qc_read_adaptation | {
"assay": "Multi-sample QC aggregation and reporting",
"tool": "MultiQC",
"read_type": "multiqc_report"
} | {
"type": "choice",
"instructions": "How should QC step MultiQC be configured given sequencing characteristics: multiqc_report?",
"criteria": {
"Swap for NanoPlot": null,
"Drop MultiQC": null,
"Keep MultiQC": null
}
} | Keep MultiQC | 2 |
mod_kaiju_mergeoutputs_0 | tool_selection | "In Nextflow DSL2, which module handles: Merge two tab-separated output files of Kaiju and Kraken in the column format (tools: kaiju)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"centrifuge/centrifuge": "Classifies metagenomic sequence data",
"kaiju/mergeoutputs": "Merge two tab-separated output files of Kaiju and Kraken in the column format",
... | kaiju/mergeoutputs | 1 |
mod_islandpath_0 | tool_selection | "In Nextflow DSL2, which module handles: Genomic island prediction in bacterial and archaeal genomes (tools: islandpath)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"dshbio/exportsegments": "Export assembly segment sequences in GFA 1.0 format to FASTA format",
"deepbgc/pipeline": "DeepBGC detects BGCs in bacterial and fungal genomes u... | islandpath | 2 |
samplesheet_arch_ancient_dna_eager_4_2 | samplesheet_schema | {
"assay": "Ancient DNA (aDNA) sequencing with UDG treatment and damage assessment",
"first_step": "FASTQC"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected when inputs are: Ancient degraded DNA FASTQs with library preparation chemistry and uracil-DNA-glycosylase status?",
"criteria": {
"sample,bam": null,
"patient,sample,status,fastq_1,fastq_2": null,
"sample,fastq_1,fastq_2": nul... | sample,library_id,lane,colour_chemistry,seq_type,paired_end,udg,strandedness,fastq_1,fastq_2 | 3 |
samplesheet_arch_smartseq_plate_based_4_4 | samplesheet_schema | {
"technology": "Single-Cell Genomics",
"workflow_entry": "FASTQC",
"library_inputs": "Full-length transcript cDNA FASTQs sorted across 96-well or 384-well plates"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected when inputs are: Full-length transcript cDNA FASTQs sorted across 96-well or 384-well plates?",
"criteria": {
"plate,sample,bam": null,
"sample,well,fastq": null,
"sample,fastq_1,fastq_2": null,
"plate,well,sample,fastq_1,f... | plate,well,sample,fastq_1,fastq_2 | 3 |
field_constraint_strandedness_3_7 | samplesheet_schema | {
"schema_target": "assets/schema_input.json",
"field": "strandedness",
"validation_type": "categorical_enum"
} | {
"type": "choice",
"instructions": "Select the appropriate draft-07 JSON Schema property specification for 'strandedness'.",
"criteria": {
"type: boolean": null,
"format: file-path": null,
"pattern: ^[0-9]+$": null,
"enum: [auto, forward, reverse, unstranded]": null
}
} | enum: [auto, forward, reverse, unstranded] | 3 |
qc_adapt_bulk_multiqc_1_45 | qc_read_adaptation | {
"assay": "High-throughput bulk WGS multi-sample run",
"tool": "MultiQC",
"read_type": "summary_reporting"
} | {
"type": "choice",
"instructions": "How should QC step MultiQC be configured given sequencing characteristics: summary_reporting?",
"criteria": {
"Keep FastQC": null,
"Drop MultiQC": null,
"Keep MultiQC": null,
"Swap for NanoPlot": null
}
} | Keep MultiQC | 2 |
qc_adapt_ont_ultra_long_1_36 | qc_read_adaptation | {
"assay": "Ultra-long Oxford Nanopore genomic DNA reads",
"tool": "FastQC",
"read_type": "long_reads_20kb_plus"
} | {
"type": "choice",
"instructions": "How should QC step FastQC be configured given sequencing characteristics: long_reads_20kb_plus?",
"criteria": {
"Drop FastQC": null,
"Swap for NanoPlot": null,
"Keep FastQC": null
}
} | Swap for NanoPlot | 1 |
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