id stringlengths 9 67 | category stringclasses 8
values | state unknown | question unknown | target stringlengths 3 92 | target_idx int64 0 9 |
|---|---|---|---|---|---|
resource_bamstats_generalstats_0 | resource_profiling | {
"process": "BAMSTATS_GENERALSTATS",
"tool": "bamstats/generalstats",
"description": "write your description here"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BAMSTATS_GENERALSTATS (write your description here) in conf/base.config?",
"criteria": {
"process_single": null,
"process_low": null,
"process_high": null,
"process_long": null
}
} | process_single | 0 |
subworkflow_pkg_fastq_align_bowtie2_3 | subworkflow_packaging | {
"subworkflow": "FASTQ_ALIGN_BOWTIE2",
"modules": [
"bowtie2/align",
"samtools/sort",
"samtools/index",
"samtools/stats",
"samtools/idxstats",
"samtools/flagstat",
"bam_sort_stats_samtools"
],
"description": "Align reads to a reference genome using bowtie2 then sort with samtools"
} | {
"type": "choice",
"instructions": "How should FASTQ_ALIGN_BOWTIE2 (bowtie2/align, samtools/sort, samtools/index, samtools/stats, samtools/idxstats, samtools/flagstat, bam_sort_stats_samtools) be structured in DSL2?",
"criteria": {
"Local subworkflow FASTQ_ALIGN_BOWTIE2": null,
"Use nf-core subworkflow f... | Use nf-core subworkflow fastq_align_bowtie2 | 1 |
mod_pasty_0 | tool_selection | "In Nextflow DSL2, which module handles: Serogroup Pseudomonas aeruginosa assemblies (tools: pasty)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"amrfinderplus/run": "Identify antimicrobial resistance in gene or protein sequences",
"fastqutils/info": "Performs quality control of FASTQ files",
"abricate/run": "S... | pasty | 4 |
qc_adapt_singlecell_multiqc_2_12 | qc_read_adaptation | {
"assay": "Multi-sample single-cell RNA-seq cohort",
"tool": "MultiQC",
"read_type": "summary_reporting"
} | {
"type": "choice",
"instructions": "Evaluate the quality control tool choice for: Multi-sample single-cell RNA-seq cohort (summary_reporting).",
"criteria": {
"Keep MultiQC": null,
"Keep FastQC": null,
"Drop MultiQC": null
}
} | Keep MultiQC | 0 |
mod_dshbio_exportsegments_0 | tool_selection | "In Nextflow DSL2, which module handles: Export assembly segment sequences in GFA 1.0 format to FASTA format (tools: dshbio)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"catpack/bins": "Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).",
"kmergenie": "KmerGenie estimates the best k-mer len... | dshbio/exportsegments | 2 |
samplesheet_arch_spatial_visium_3_3 | samplesheet_schema | {
"pipeline": "nf-core/spatialaxe",
"assay_type": "10x Visium spatial transcriptomics with histology image",
"data_format": "Spatial cDNA FASTQs paired with high-resolution brightfield tissue image and slide coordinates"
} | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for 10x Visium spatial transcriptomics with histology image with entry step FASTQC.",
"criteria": {
"sample,bam": null,
"sample,fastq_1,fastq_2,image,slide,area": null,
"sample,image": null,
"sample,fastq_1,imag... | sample,fastq_1,fastq_2,image,slide,area | 1 |
samplesheet_arch_dual_rnaseq_host_pathogen_3_0 | samplesheet_schema | {
"assay": "Dual RNA-seq simultaneous host and pathogen transcriptomics",
"first_step": "FASTQC"
} | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for Dual RNA-seq simultaneous host and pathogen transcriptomics with entry step FASTQC.",
"criteria": {
"sample,bam": null,
"sample,host_fasta": null,
"sample,fastq_1,fastq_2,host,pathogen": null,
"sample,fastq_... | sample,fastq_1,fastq_2,host,pathogen | 2 |
mod_methylsieve_0 | tool_selection | "In Nextflow DSL2, which module handles: Filter/tag unconverted reads in methylation sequencing with methylsieve; for maximum throughput it can also run inline in the alignment pipe (aligner | methylsieve | sort) rather than as a standalone step (tools: methylsieve)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"methylsieve": "Filter/tag unconverted reads in methylation sequencing with methylsieve; for maximum throughput it can also ru",
"stainwarpy/transformsegmask": "Transform ... | methylsieve | 0 |
resource_autocycler_resolve_5 | resource_profiling | {
"process": "AUTOCYCLER_RESOLVE",
"tool": "autocycler/resolve",
"description": "Resolve trimmed assembly graphs into final contigs within Autocycler."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to AUTOCYCLER_RESOLVE (Resolve trimmed assembly graphs into final contigs within Autocycler.) in conf/base.config?",
"criteria": {
"process_low": null,
"process_single": null,
"process_high": null,
"process_long": ... | process_single | 1 |
resource_blast_blastdbcmd_4 | resource_profiling | {
"process": "BLAST_BLASTDBCMD",
"tool": "blast/blastdbcmd",
"description": "Retrieve entries from a BLAST database"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BLAST_BLASTDBCMD (Retrieve entries from a BLAST database) in conf/base.config?",
"criteria": {
"process_single": null,
"process_high": null,
"process_low": null,
"process_long": null
}
} | process_single | 0 |
resource_blobtk_create_3 | resource_profiling | {
"process": "BLOBTK_CREATE",
"tool": "blobtk/create",
"description": "Creates a minimal blobdir."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BLOBTK_CREATE (Creates a minimal blobdir.) in conf/base.config?",
"criteria": {
"process_high": null,
"process_single": null,
"process_low": null,
"process_long": null
}
} | process_single | 1 |
qc_adapt_ont_nanoplot_1_4 | qc_read_adaptation | {
"assay": "Direct RNA sequencing on Oxford Nanopore PromethION",
"tool": "FastQC",
"read_type": "long_reads_direct_rna"
} | {
"type": "choice",
"instructions": "How should QC step FastQC be configured given sequencing characteristics: long_reads_direct_rna?",
"criteria": {
"Keep FastQC": null,
"Swap for NanoPlot": null,
"Drop FastQC": null
}
} | Swap for NanoPlot | 1 |
mod_checkm_lineagewf_1 | tool_selection | "In Nextflow DSL2, which module handles: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. (tools: checkm)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"checkv_endtoend": null,
"checkm_lineagewf": null,
"blobtk_depth": null,
"checkv_downloaddatabase": null,
"sentieon_dnascope": null
}
} | checkm_lineagewf | 1 |
mod_sentieon_applyvarcal_1 | tool_selection | "In Nextflow DSL2, which module handles: Apply a score cutoff to filter variants based on a recalibration table.\nSentieon's Aplyvarcal performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR).\nSpecifically, it applies filtering to the input variants based on the recalibration ... | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"sentieon_collectvcmetrics": "Accelerated implementation of the Picard CollectVariantCallingMetrics tool.",
"checkv_downloaddatabase": "Construct the database necessary fo... | sentieon_applyvarcal | 4 |
mod_unzip_1 | tool_selection | "In Nextflow DSL2, which module handles: Unzip ZIP archive files (tools: unzip)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"spring_decompress": null,
"fusionreport_download": null,
"controlfreec_assesssignificance": null,
"gunzip": null,
"unzip": null
}
} | unzip | 4 |
resource_amrfinderplus_run_4 | resource_profiling | {
"process": "AMRFINDERPLUS_RUN",
"tool": "amrfinderplus/run",
"description": "Identify antimicrobial resistance in gene or protein sequences"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to AMRFINDERPLUS_RUN (Identify antimicrobial resistance in gene or protein sequences) in conf/base.config?",
"criteria": {
"process_low": null,
"process_high": null,
"process_single": null,
"process_medium": null
... | process_single | 2 |
mod_octopusv_merge_0 | tool_selection | "In Nextflow DSL2, which module handles: Merge and harmonize structural variant calls from multiple samples. (tools: octopusv)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"vcflib/vcffixup": "Generates a VCF stream where AC and NS have been generated for each record using sample genotypes.",
"motus/downloaddb": "Download the mOTUs database",... | octopusv/merge | 4 |
mod_sentieon_tnfilter_1 | tool_selection | "In Nextflow DSL2, which module handles: Filters the raw output of sentieon/tnhaplotyper2. (tools: sentieon)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"agat_spfilterbyorfsize": "The script reads a gff annotation file, and create two output files, one contains the gene models with ORF pas",
"bam_sort_stats_samtools": "Sor... | sentieon_tnfilter | 4 |
samplesheet_arch_cancer_somatic_bam_1_1 | samplesheet_schema | "nextflow run nf-core/sarek --input samplesheet.csv (Assay: Somatic tumor-normal calling from pre-aligned BAM files)" | {
"type": "choice",
"instructions": "Which columns should the samplesheet have for Somatic tumor-normal calling from pre-aligned BAM files?",
"criteria": {
"patient,sample,status,fastq_1,fastq_2": null,
"patient,sample,status,bam,bai": null,
"patient,sample,bam": null,
"sample,bam,bai": null
}
} | patient,sample,status,bam,bai | 1 |
schema_std_demultiplex_1_0 | samplesheet_schema | {
"pipeline": "nf-core/demultiplex",
"assay": "demultiplex pipeline processing",
"inputs": "Input files per samplesheet"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected for Nextflow pipeline nf-core/demultiplex (Demultiplexing pipeline for sequencing data)?",
"criteria": {
"id,samplesheet,lane,flowcell,per_flowcell_manifest": null,
"id,fasta,query": null,
"ID,R1,R2,LongFastQ,Fast5": null,
... | id,samplesheet,lane,flowcell,per_flowcell_manifest | 0 |
mod_pydamage_filter_0 | tool_selection | "In Nextflow DSL2, which module handles: Damage parameter estimation for ancient DNA (tools: pydamage)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"atlas/pmd": null,
"amps": null,
"pydamage/filter": null,
"dshbio/splitgff3": null,
"msisensor/msi": null
}
} | pydamage/filter | 2 |
mod_bam_impute_quilt_1 | tool_selection | "In Nextflow DSL2, which module handles: Subworkflow to impute BAM files using QUILT software.\nVariants location to impute are obtain through the tsv file given.\n\"regionout\", \"regionoutPadded\", \"regionSize\" keys will be added to the meta map to distinguish\nthe different files before ligation and therefore shou... | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"bam_impute_quilt": "Subworkflow to impute BAM files using QUILT software.\nVariants location to impute are obtain through the tsv f",
"sam2lca_analyze": "Calling lowest c... | bam_impute_quilt | 0 |
subworkflow_pkg_bam_dedup_stats_samtools_umicollapse_3 | subworkflow_packaging | {
"subworkflow": "BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE",
"modules": [
"umicollapse",
"samtools/index",
"samtools/stats",
"samtools/idxstats",
"samtools/flagstat",
"bam_stats_samtools"
],
"description": "umicollapse, index BAM file and run samtools stats, flagstat and idxstats"
} | {
"type": "choice",
"instructions": "How should BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE (umicollapse, samtools/index, samtools/stats, samtools/idxstats, samtools/flagstat, bam_stats_samtools) be structured in DSL2?",
"criteria": {
"Leave them out": null,
"Local subworkflow BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPS... | Use nf-core subworkflow bam_dedup_stats_samtools_umicollapse | 3 |
resource_bamreadcount_5 | resource_profiling | {
"process": "BAMREADCOUNT",
"tool": "bamreadcount",
"description": "bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strande... | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BAMREADCOUNT (bam-readcount is a utility that runs on a BAM or CRAM file and generates low-lev) in conf/base.config?",
"criteria": {
"process_medium": null,
"process_high": null,
"process_single": null,
"process... | process_single | 2 |
mod_lsa_cosine_0 | tool_selection | "In Nextflow DSL2, which module handles: Calculates the cosine similarity matrix between samples based on a gene expression matrix. (tools: lsa)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"ngsbits/bedannotategc": null,
"custom/clustermetrics": null,
"vardictjava": null,
"comebin/runcomebin": null,
"lsa/cosine": null
}
} | lsa/cosine | 4 |
samplesheet_arch_bulk_rnaseq_pe_standard_5_3 | samplesheet_schema | {
"assay": "Paired-end Illumina RNA-seq",
"first_step": "FASTQC",
"inputs": "FastQ reads per sample"
} | {
"type": "choice",
"instructions": "In Nextflow pipeline nf-core/rnaseq, determine the input samplesheet column structure for: Paired-end Illumina RNA-seq.",
"criteria": {
"sample,fastq_1,fastq_2,group": null,
"sample,fastq_1,fastq_2,strandedness": null,
"sample,bam": null,
"sample,fastq_1,fastq_... | sample,fastq_1,fastq_2 | 3 |
mod_agat_spkeeplongestisoform_1 | tool_selection | "In Nextflow DSL2, which module handles: Filters GFF records to keep only the longest isoform per gene (tools: agat)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"agat_spaddintrons": "Add intron features to gtf/gff file without intron features.",
"agat_spkeeplongestisoform": "Filters GFF records to keep only the longest isoform per... | agat_spkeeplongestisoform | 1 |
mod_fastx_collapser_0 | tool_selection | "In Nextflow DSL2, which module handles: Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts) (tools: fastx)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"gunzip": "Compresses and decompresses files.",
"agat/spfilterfeaturefromkilllist": "The script aims to remove features based on a kill list. The default behaviour is to l... | fastx/collapser | 2 |
samplesheet_arch_ont_demux_barcodes_5_0 | samplesheet_schema | "Building an autonomous Nextflow workflow (nf-core/nanoseq) for Multiplexed Oxford Nanopore run with barcode demultiplexing. Input files: Nanopore sequencing run with sample to barcode assignment and flowcell type." | {
"type": "choice",
"instructions": "In Nextflow pipeline nf-core/nanoseq, determine the input samplesheet column structure for: Multiplexed Oxford Nanopore run with barcode demultiplexing.",
"criteria": {
"sample,bam": null,
"sample,fastq_1": null,
"sample,barcode": null,
"sample,barcode,flowcell... | sample,barcode,flowcell,kit,fastq | 3 |
samplesheet_arch_singlecell_parse_splitseq_4_2 | samplesheet_schema | {
"assay": "Parse Biosciences Split-seq combinatorial barcoding",
"first_step": "FASTQC"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected when inputs are: Combinatorial split-pool barcoded FASTQs with subpool annotations?",
"criteria": {
"sample,bam": null,
"sample,subpool,fastq_1,fastq_2": null,
"sample,fastq_1,fastq_2": null,
"sample,fastq_1": null
}
} | sample,subpool,fastq_1,fastq_2 | 1 |
samplesheet_arch_cageseq_transcription_1_5 | samplesheet_schema | {
"assay": "CAGE-seq 5-prime capped transcript end sequencing",
"first_step": "FASTQC",
"template": "nf-core/cageseq"
} | {
"type": "choice",
"instructions": "Which columns should the samplesheet have for CAGE-seq 5-prime capped transcript end sequencing?",
"criteria": {
"sample,fastq_1": null,
"sample,vcf": null,
"sample,bam": null,
"sample,fastq_1,fastq_2": null
}
} | sample,fastq_1 | 0 |
intent_prepare_data_19 | intent_routing | "Classify this user request: \"I have 50 fastq.gz files in /data/raw. Can you construct a samplesheet.csv with sample, fastq_1, fastq_2, and strandedness columns?\"" | {
"type": "choice",
"instructions": "Classify the user intent into one category.",
"criteria": {
"ask_question": null,
"build_pipeline": null,
"prepare_data": null,
"debug_error": null
}
} | prepare_data | 2 |
mod_paraphrase_0 | tool_selection | "In Nextflow DSL2, which module handles: Parse and annotate paraphrase JSONs (tools: paraphrase)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"paraphrase": "Parse and annotate paraphrase JSONs",
"anndata/barcodes": "Module to subset AnnData object to cells with matching barcodes from the csv file",
"autocycl... | paraphrase | 0 |
mod_perbase_0 | tool_selection | "In Nextflow DSL2, which module handles: Per-base metrics on BAM/CRAM files. (tools: perbase)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"sratools/prefetch": "Download sequencing data from the NCBI Sequence Read Archive (SRA).",
"perbase": "Per-base metrics on BAM/CRAM files.",
"atlas/pmd": "Estimate th... | perbase | 1 |
mod_rasusa_0 | tool_selection | "In Nextflow DSL2, which module handles: Randomly subsample sequencing reads to a specified coverage (tools: rasusa)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"samtools/view": "filter/convert SAM/BAM/CRAM file",
"ucsc/bedtobigbed": "Convert file from bed to bigBed format",
"cmseq/polymut": "Calculates polymorphic site rates ... | rasusa | 3 |
qc_adapt_ffpe_wes_1_39 | qc_read_adaptation | {
"assay": "Degraded FFPE exome capture sequencing on Illumina",
"tool": "FastQC",
"read_type": "short_reads_100bp"
} | {
"type": "choice",
"instructions": "How should QC step FastQC be configured given sequencing characteristics: short_reads_100bp?",
"criteria": {
"Drop FastQC": null,
"Swap for NanoPlot": null,
"Keep FastQC": null
}
} | Keep FastQC | 2 |
samplesheet_arch_spatial_xenium_3_1 | samplesheet_schema | {
"assay": "10x Xenium in situ subcellular spatial RNA transcriptomics",
"first_step": "INPUT_CHECK",
"template": "nf-core/spatialaxe"
} | {
"type": "choice",
"instructions": "Define the required samplesheet CSV header schema for 10x Xenium in situ subcellular spatial RNA transcriptomics with entry step INPUT_CHECK.",
"criteria": {
"sample,vcf": null,
"sample,fastq_1,fastq_2": null,
"sample,bam": null,
"sample,transcripts_csv,morphol... | sample,transcripts_csv,morphology_focus_tif,cells_parquet | 3 |
resource_bbmap_bbduk_0 | resource_profiling | {
"process": "BBMAP_BBDUK",
"tool": "bbmap/bbduk",
"description": "Adapter and quality trimming of sequencing reads"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BBMAP_BBDUK (Adapter and quality trimming of sequencing reads) in conf/base.config?",
"criteria": {
"process_low": null,
"process_single": null,
"process_medium": null,
"process_long": null
}
} | process_single | 1 |
resource_adapterremovalfixprefix_1 | resource_profiling | {
"process": "ADAPTERREMOVALFIXPREFIX",
"tool": "adapterremovalfixprefix",
"description": "Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to ADAPTERREMOVALFIXPREFIX (Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names a) in conf/base.config?",
"criteria": {
"process_low": null,
"process_high": null,
"process_single": null,
... | process_single | 2 |
local_subworkflow_checkirma_2_1 | subworkflow_packaging | {
"subworkflow": "CHECKIRMA",
"modules": [
"custom/checkirma"
],
"description": "Custom validation of assembly output"
} | {
"type": "choice",
"instructions": "Determine the DSL2 structure for CHECKIRMA (custom/checkirma).",
"criteria": {
"Leave them out": null,
"Local subworkflow CHECKIRMA": null,
"Use nf-core subworkflow checkirma": null,
"Keep the modules in the main workflow": null
}
} | Local subworkflow CHECKIRMA | 1 |
noul_concurrent_writes_to_identical_work_dir_paths_17 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"Multiple processes in the same workflow can write simultaneously to the exact same file in the work directory without conflict.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards."
} | false | 0 |
mod_vizgenpostprocessing_compiletilesegmentation_0 | tool_selection | "In Nextflow DSL2, which module handles: The module compiles segmentation tiles using Vizgen's post-processing tool. (tools: vizgenpostprocessing)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"centrifuge/centrifuge": null,
"rgi/bwt": null,
"vizgenpostprocessing/compiletilesegmentation": null,
"vizgenpostprocessing/runsegmentationontile": null,
"cell... | vizgenpostprocessing/compiletilesegmentation | 2 |
noul_exit_code_137_cause_1 | 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."
} | false | 0 |
samplesheet_arch_ont_demux_barcodes_5_5 | samplesheet_schema | {
"assay": "Multiplexed Oxford Nanopore run with barcode demultiplexing",
"first_step": "NANOPLOT",
"template": "nf-core/nanoseq"
} | {
"type": "choice",
"instructions": "In Nextflow pipeline nf-core/nanoseq, determine the input samplesheet column structure for: Multiplexed Oxford Nanopore run with barcode demultiplexing.",
"criteria": {
"sample,barcode,flowcell,kit,fastq": null,
"sample,bam": null,
"sample,fastq_1,fastq_2": null,
... | sample,barcode,flowcell,kit,fastq | 0 |
samplesheet_arch_dual_rnaseq_host_pathogen_6_4 | 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",
"pipeline": "nf-core/dualrnaseq"
} | {
"type": "choice",
"instructions": "Which columns are standard for Dual RNA-seq simultaneous host and pathogen transcriptomics input samplesheet?",
"criteria": {
"sample,fastq_1,fastq_2": null,
"sample,bam": null,
"sample,fastq_1": null,
"sample,fastq_1,fastq_2,host,pathogen": null
}
} | sample,fastq_1,fastq_2,host,pathogen | 3 |
noul_channel_collect_operator_0 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"The `.collect()` operator gathers all channel items into a single list item before passing to downstream processes.\"" | {
"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_pbccs_1 | tool_selection | "In Nextflow DSL2, which module handles: Pacbio ccs - Generate Highly Accurate Single-Molecule Consensus Reads (tools: pbccs)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"emmtyper": "EMM typing of Streptococcus pyogenes assemblies",
"isoseq_refine": "Remove polyA tail and artificial concatemers",
"pbccs": "Pacbio ccs - Generate Highly ... | pbccs | 2 |
mod_foldseek_easysearch_1 | tool_selection | "In Nextflow DSL2, which module handles: Search for protein structural hits against a foldseek database of protein structures (tools: foldseek)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"scvitools_solo": null,
"gstama_merge": null,
"caalm_caalm": null,
"foldseek_easysearch": null,
"deeptmhmm": null
}
} | foldseek_easysearch | 3 |
mod_picard_extractfingerprint_0 | tool_selection | "In Nextflow DSL2, which module handles: Computes/Extracts the fingerprint genotype likelihoods from the supplied file. It is given as a list of PLs at the fingerprinting sites. (tools: picard)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"bam_stringtie_merge": "Assemble transcripts from sorted BAM alignments using StringTie, then merge per-sample transcript GTFs into a ",
"picard/createsequencedictionary":... | picard/extractfingerprint | 2 |
qc_adapt_ont_nanoplot_1_11 | 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": {
"Keep FastQC": null,
"Drop FastQC": null,
"Swap for NanoPlot": null
}
} | Swap for NanoPlot | 2 |
qc_adapt_qc_aggregate_2_42 | qc_read_adaptation | {
"assay": "Multi-sample QC aggregation and reporting",
"tool": "MultiQC",
"read_type": "multiqc_report"
} | {
"type": "choice",
"instructions": "Evaluate the quality control tool choice for: Multi-sample QC aggregation and reporting (multiqc_report).",
"criteria": {
"Drop MultiQC": null,
"Keep MultiQC": null,
"Swap for NanoPlot": null
}
} | Keep MultiQC | 1 |
mod_bamcmp_1 | tool_selection | "In Nextflow DSL2, which module handles: Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX). (tools: bamcmp)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"chopper": "Filter and trim long read data.",
"agat_spfilterbyorfsize": "The script reads a gff annotation file, and create two output files, one contains the gene models ... | bamcmp | 3 |
mod_trnascanse_0 | tool_selection | "In Nextflow DSL2, which module handles: Detection of tRNA sequences using covariance models (tools: trnascanse)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"sentieon/applyvarcal": null,
"mmseqs/linclust": null,
"seqsero2": null,
"repeatmasker/rmouttogff3": null,
"trnascanse": null
}
} | trnascanse | 4 |
samplesheet_arch_ont_direct_rna_se_0_4 | samplesheet_schema | {
"technology": "Long-Read Sequencing",
"workflow_entry": "NANOPLOT",
"library_inputs": "Single fastq per sample"
} | {
"type": "choice",
"instructions": "Which columns should the input samplesheet have for: Single-end Oxford Nanopore direct RNA?",
"criteria": {
"sample,fastq_1,fastq_2": null,
"sample,fastq_1": null,
"sample,bam": null,
"sample,vcf": null
}
} | sample,fastq_1 | 1 |
noul_process_conditional_execution_13 | 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."
} | true | 1 |
mod_fgumi_clip_0 | tool_selection | "In Nextflow DSL2, which module handles: Clip overlapping reads in a BAM file with fgumi (tools: fgumi)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"plink2/indeppairwise": "Produce pruned set of variants in approximatelinkage equilibrium",
"fgumi/clip": "Clip overlapping reads in a BAM file with fgumi",
"peka": "R... | fgumi/clip | 1 |
mod_vcf_annotate_ensemblvep_1 | tool_selection | "In Nextflow DSL2, which module handles: Perform annotation with ensemblvep and bgzip + tabix index the resulting VCF file (tools: vcf_annotate_ensemblvep)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"aardvark_compare": null,
"subread_featurecounts": null,
"vcf_annotate_ensemblvep": null,
"suppa_psiperisoform": null,
"annotsv_annotsv": null
}
} | vcf_annotate_ensemblvep | 2 |
schema_std_rnastructurome_2_1 | samplesheet_schema | "Configuring input samplesheet for nf-core pipeline nf-core/rnastructurome. Description: a bioinformatics pipeline for analysing chemical high-throughput RNA structure-probing data." | {
"type": "choice",
"instructions": "Define the input samplesheet column header for nf-core/rnastructurome.",
"criteria": {
"sample,group,ref_fasta,ref_gff,use_ref": null,
"sample,sample_id,fastq_1,fastq_2,method": null,
"sample,fastq_1,fastq_2,rundir,tags": null,
"family_id,sample,file_path,hpo_t... | sample,sample_id,fastq_1,fastq_2,method | 1 |
mod_deeparg_predict_0 | tool_selection | "In Nextflow DSL2, which module handles: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes (tools: deeparg)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"deeparg/predict": "A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes",
"abricate/run": "Screen assemblies for antimicrobial re... | deeparg/predict | 0 |
qc_adapt_bulk_multiqc_2_46 | qc_read_adaptation | {
"assay": "High-throughput bulk WGS multi-sample run",
"tool": "MultiQC",
"read_type": "summary_reporting"
} | {
"type": "choice",
"instructions": "Evaluate the quality control tool choice for: High-throughput bulk WGS multi-sample run (summary_reporting).",
"criteria": {
"Keep MultiQC": null,
"Keep FastQC": null,
"Swap for NanoPlot": null,
"Drop MultiQC": null
}
} | Keep MultiQC | 0 |
mod_ataqv_ataqv_1 | tool_selection | "In Nextflow DSL2, which module handles: ataqv function of a corresponding ataqv tool (tools: ataqv)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"ataqv_ataqv": "ataqv function of a corresponding ataqv tool",
"umitools_extract": "Extracts UMI barcode from a read and add it to the read name, leaving any sample barcod... | ataqv_ataqv | 0 |
noul_subworkflow_structural_blocks_1 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"Workflows in Nextflow DSL2 define inputs with `take:`, core execution with `main:`, and outputs with `emit:`.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards."
} | true | 1 |
schema_std_drop_1_1 | samplesheet_schema | {
"pipeline": "nf-core/drop",
"assay": "drop pipeline processing",
"inputs": "Input files per samplesheet"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected for Nextflow pipeline nf-core/drop (Pipeline to find aberrant events in RNA-Seq data, useful for)?",
"criteria": {
"RNA_ID,RNA_BAM_FILE,RNA_BAI_FILE,DNA_ID,DNA_VCF_FILE": null,
"sample,fastq_1,fastq_2,batch,condition": null,
"f... | RNA_ID,RNA_BAM_FILE,RNA_BAI_FILE,DNA_ID,DNA_VCF_FILE | 0 |
subworkflow_pkg_fastq_align_bwaaln_0 | subworkflow_packaging | {
"subworkflow": "FASTQ_ALIGN_BWAALN",
"modules": [
"bwa/aln",
"bwa/sampe",
"bwa/samse",
"samtools/index"
],
"description": "Align FASTQ files against reference genome with the bwa aln short-read aligner producing a sorted and indexed BAM files"
} | {
"type": "choice",
"instructions": "How should FASTQ_ALIGN_BWAALN (bwa/aln, bwa/sampe, bwa/samse, samtools/index) be structured in DSL2?",
"criteria": {
"Leave them out": null,
"Keep the modules in the main workflow": null,
"Use nf-core subworkflow fastq_align_bwaaln": null,
"Local subworkflow FA... | Use nf-core subworkflow fastq_align_bwaaln | 2 |
resource_abacas_4 | resource_profiling | {
"process": "ABACAS",
"tool": "abacas",
"description": "Contiguate draft genome assembly"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to ABACAS (Contiguate draft genome assembly) in conf/base.config?",
"criteria": {
"process_medium": null,
"process_long": null,
"process_high": null,
"process_single": null
}
} | process_single | 3 |
qc_adapt_pacbio_hifi_2_42 | qc_read_adaptation | {
"assay": "PacBio HiFi circular consensus sequencing (CCS)",
"tool": "FastQC",
"read_type": "long_reads_hifi_15kb"
} | {
"type": "choice",
"instructions": "Evaluate the quality control tool choice for: PacBio HiFi circular consensus sequencing (CCS) (long_reads_hifi_15kb).",
"criteria": {
"Drop FastQC": null,
"Keep FastQC": null,
"Swap for NanoPlot": null
}
} | Swap for NanoPlot | 2 |
resource_agat_convertspgff2tsv_5 | resource_profiling | {
"process": "AGAT_CONVERTSPGFF2TSV",
"tool": "agat/convertspgff2tsv",
"description": "Converts a GFF/GTF file into a TSV file"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to AGAT_CONVERTSPGFF2TSV (Converts a GFF/GTF file into a TSV file) in conf/base.config?",
"criteria": {
"process_low": null,
"process_long": null,
"process_medium": null,
"process_single": null
}
} | process_single | 3 |
subworkflow_pkg_bam_rseqc_1 | subworkflow_packaging | {
"subworkflow": "BAM_RSEQC",
"modules": [
"rseqc",
"rseqc/tin",
"rseqc/readduplication",
"rseqc/readdistribution",
"rseqc/junctionsaturation",
"rseqc/junctionannotation",
"rseqc/innerdistance",
"rseqc/inferexperiment",
"rseqc/bamstat"
],
"description": "Subworkflow to run mu... | {
"type": "choice",
"instructions": "How should BAM_RSEQC (rseqc, rseqc/tin, rseqc/readduplication, rseqc/readdistribution, rseqc/junctionsaturation, rseqc/junctionannotation, rseqc/innerdistance, rseqc/inferexperiment, rseqc/bamstat) be structured in DSL2?",
"criteria": {
"Local subworkflow BAM_RSEQC": null,... | Use nf-core subworkflow bam_rseqc | 2 |
core_tool_interproscan_bare_1 | tool_selection | "Which bioinformatics tool or module is best suited for this task? Scan protein and nucleotide sequences against multiple member databases to identify structural domains, functional sites, and protein families." | {
"type": "choice",
"instructions": "Select the appropriate bioinformatics tool or module for the specified task.",
"criteria": {
"blastp": null,
"eggnog": null,
"hmmer": null,
"interproscan": null,
"diamond": null
}
} | interproscan | 3 |
mod_graphmap2_index_1 | tool_selection | "In Nextflow DSL2, which module handles: A versatile pairwise aligner for genomic and spliced nucleotide sequences (tools: graphmap2)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"fusioncatcher_fusioncatcher": "FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data",
"bcftools_index": "Index VCF to... | graphmap2_index | 2 |
noul_exit_code_137_cause_8 | 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 |
schema_std_airrflow_2_0 | samplesheet_schema | "Configuring input samplesheet for nf-core pipeline nf-core/airrflow. Description: B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework." | {
"type": "choice",
"instructions": "Define the input samplesheet column header for nf-core/airrflow.",
"criteria": {
"sample_id,subject_id,species,pcr_target_locus,tissue": null,
"sample,fasta,existing_hmms_to_update,existing_msas_to_update": null,
"sample,fastq,cell_count": null,
"sample,fasta,p... | sample_id,subject_id,species,pcr_target_locus,tissue | 0 |
mod_picard_fastqtosam_1 | tool_selection | "In Nextflow DSL2, which module handles: Converts a FASTQ file to an unaligned BAM or SAM file. (tools: picard)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"samplesheetparser_diff": null,
"adapterremoval": null,
"ariba_run": null,
"picard_fastqtosam": null,
"localcdsearch_download": null
}
} | picard_fastqtosam | 3 |
mod_rsem_preparereference_1 | tool_selection | "In Nextflow DSL2, which module handles: Prepare a reference genome for RSEM (tools: rseqc)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"tximeta_tximport": "Import transcript-level abundances and estimated counts for gene-level\nanalysis packages",
"rsem_preparereference": "Prepare a reference genome for R... | rsem_preparereference | 1 |
samplesheet_arch_amplicon_16s_paired_6_3 | samplesheet_schema | "nextflow run nf-core/ampliseq --input samplesheet.csv (Assay: 16S rRNA / ITS microbiome amplicon profiling)" | {
"type": "choice",
"instructions": "Which columns are standard for 16S rRNA / ITS microbiome amplicon profiling input samplesheet?",
"criteria": {
"sample,primer_fwd,primer_rev": null,
"sample,fasta": null,
"sample,fastq_1,fastq_2": null,
"sample,fastq_1": null
}
} | sample,fastq_1,fastq_2 | 2 |
mod_deeptools_bamcompare_1 | tool_selection | "In Nextflow DSL2, which module handles: Compares two BAM files based on the number of mapped reads and generates a bigWig or bedGraph file with the log2 ratio, ratio, difference or other operations. (tools: deeptools)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"mash_screen": "Screens query sequences against large sequence databases",
"ascat": "copy number profiles of tumour cells.",
"deeptools_bamcompare": "Compares two BAM ... | deeptools_bamcompare | 2 |
mod_canu_1 | tool_selection | "In Nextflow DSL2, which module handles: Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. (tools: canu)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"ale": "ALE: assembly likelihood estimator.",
"canu": "Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.",
"... | canu | 1 |
noul_channel_factory_inside_process_body_10 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"Calling `Channel.fromPath()` inside the body of a process is valid Nextflow DSL2.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards.",
"criteria": {
"false": "The statement describes an invalid Nextflow DSL2 syntax, anti-pattern, or deprecated behavior.",
"true": "The statement describes a valid, standard, and re... | false | 0 |
resource_bbmap_filterbyname_5 | resource_profiling | {
"process": "BBMAP_FILTERBYNAME",
"tool": "bbmap/filterbyname",
"description": "Filter out sequences by sequence header name(s)"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BBMAP_FILTERBYNAME (Filter out sequences by sequence header name(s)) in conf/base.config?",
"criteria": {
"process_single": null,
"process_medium": null,
"process_high": null,
"process_low": null
}
} | process_single | 0 |
pipe_all101_bamtofastq_4 | pipeline_routing | "Which pipeline implements best-practice processing for: Converts bam or cram files to fastq format and does quality control.. Topics: bamtofastq, conversion, cramtofastq. ?" | {
"type": "choice",
"instructions": "Select the optimal nf-core pipeline for this bioinformatic analysis task.",
"criteria": {
"lsmquant": "A pipeline for processing and analysis of light-sheet microscopy images. [3dunet, image-analysis, image-processing]",
"crisprseq": "A pipeline for the analysis of CRI... | bamtofastq | 8 |
samplesheet_arch_prealigned_bam_indexed_5_4 | samplesheet_schema | {
"assay": "Pre-aligned BAM variant calling pipeline",
"first_step": "GATK_HAPLOTYPECALLER"
} | {
"type": "choice",
"instructions": "In Nextflow pipeline nf-core/sarek, determine the input samplesheet column structure for: Pre-aligned BAM variant calling pipeline.",
"criteria": {
"sample,bam,bai": null,
"sample,fastq_1,fastq_2": null,
"sample,fastq_1": null,
"sample,bam": null
}
} | sample,bam,bai | 0 |
local_subworkflow_prepontreads_0_4 | subworkflow_packaging | {
"subworkflow": "PREPONTREADS",
"modules": [
"porechop",
"nanoplot"
],
"description": "Nanopore adapter trimming and read quality visualization"
} | {
"type": "choice",
"instructions": "How should PREPONTREADS (porechop, nanoplot) be built?",
"criteria": {
"Keep the modules in the main workflow": null,
"Use nf-core subworkflow prepontreads": null,
"Local subworkflow PREPONTREADS": null,
"Leave them out": null
}
} | Local subworkflow PREPONTREADS | 2 |
resource_angsd_realsfs_4 | resource_profiling | {
"process": "ANGSD_REALSFS",
"tool": "angsd/realsfs",
"description": "Estimate site frequency spectrum from site allele frequencies"
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to ANGSD_REALSFS (Estimate site frequency spectrum from site allele frequencies) in conf/base.config?",
"criteria": {
"process_medium": null,
"process_high": null,
"process_single": null,
"process_long": null
}
} | process_single | 2 |
mod_pdb2pqr_1 | tool_selection | "In Nextflow DSL2, which module handles: Convert PDB files to PQR format by\nassigning charge and radius parameters for\nelectrostatics calculations (e.g. APBS input preparation). (tools: pdb2pqr)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"bam_dedup_stats_samtools_umicollapse": "umicollapse, index BAM file and run samtools stats, flagstat and idxstats",
"pdb2pqr": "Convert PDB files to PQR format by\nassign... | pdb2pqr | 1 |
resource_bismark_summary_5 | resource_profiling | {
"process": "BISMARK_SUMMARY",
"tool": "bismark/summary",
"description": "Uses Bismark report files of several samples in a run folder to generate a graphical summary HTML report."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BISMARK_SUMMARY (Uses Bismark report files of several samples in a run folder to generate a graph) in conf/base.config?",
"criteria": {
"process_long": null,
"process_medium": null,
"process_low": null,
"process... | process_single | 3 |
noul_dynamic_resource_allocation_12 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"Process directive `cpus { check_max( 4 * task.attempt, 'cpus' ) }` allows dynamic resource scaling on task retry.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards.",
"criteria": {
"false": "The statement describes an invalid Nextflow DSL2 syntax, anti-pattern, or deprecated behavior.",
"true": "The statement describes a valid, standard, and re... | true | 1 |
noul_channel_collect_operator_8 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"The `.collect()` operator gathers all channel items into a single list item before passing to downstream processes.\"" | {
"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_bulk_multiqc_0_16 | qc_read_adaptation | {
"assay": "High-throughput bulk WGS multi-sample run",
"tool": "MultiQC",
"read_type": "summary_reporting"
} | {
"type": "choice",
"instructions": "For High-throughput bulk WGS multi-sample run, what is the recommended QC default for MultiQC?",
"criteria": {
"Drop MultiQC": null,
"Keep FastQC": null,
"Swap for NanoPlot": null,
"Keep MultiQC": null
}
} | Keep MultiQC | 3 |
qc_adapt_qc_aggregate_0_14 | 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,
"Drop MultiQC": null,
"Swap for NanoPlot": null
}
} | Keep MultiQC | 0 |
resource_bcftools_annotate_1 | resource_profiling | {
"process": "BCFTOOLS_ANNOTATE",
"tool": "bcftools/annotate",
"description": "Add or remove annotations."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BCFTOOLS_ANNOTATE (Add or remove annotations.) in conf/base.config?",
"criteria": {
"process_high": null,
"process_long": null,
"process_single": null,
"process_low": null
}
} | process_single | 2 |
field_constraint_status_1_11 | samplesheet_schema | {
"column": "status",
"purpose": "Tissue status for somatic cancer workflows"
} | {
"type": "choice",
"instructions": "Determine the schema validation rule for field 'status' (Tissue status for somatic cancer workflows).",
"criteria": {
"pattern: ^[A-Z]+$": null,
"enum: [0, 1] (0=normal, 1=tumor)": null,
"enum: [auto, forward, reverse]": null,
"format: file-path": null
}
} | enum: [0, 1] (0=normal, 1=tumor) | 1 |
qc_adapt_targeted_amplicon_0_45 | 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 |
noul_channel_filter_operator_23 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"Channel `.filter { meta, fastq -> meta.single_end }` filters items based on a boolean closure condition.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards."
} | true | 1 |
schema_std_funcscan_1_1 | samplesheet_schema | {
"pipeline": "nf-core/funcscan",
"assay": "funcscan pipeline processing",
"inputs": "Input files per samplesheet"
} | {
"type": "choice",
"instructions": "What samplesheet columns are expected for Nextflow pipeline nf-core/funcscan ((Meta-)genome screening for functional and natural product g)?",
"criteria": {
"sample,fastq_1,fastq_2,rundir,tags": null,
"id,samplesheet,lane,flowcell,per_flowcell_manifest": null,
"sam... | sample,fasta,protein,gbk,gff | 2 |
mod_checkm2_databasedownload_1 | tool_selection | "In Nextflow DSL2, which module handles: CheckM2 database download (tools: checkm2)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"checkv_endtoend": "Assess the quality of metagenome-assembled viral genomes.",
"checkm2_predict": "CheckM2 bin quality prediction",
"checkm2_databasedownload": "Check... | checkm2_databasedownload | 2 |
field_constraint_bai_2_2 | samplesheet_schema | "Validating samplesheet CSV field 'bai' (Companion BAM index file) in assets/schema_input.json." | {
"type": "choice",
"instructions": "In nf-core samplesheet schema (assets/schema_input.json), how is column 'bai' validated?",
"criteria": {
"pattern: ^\\S+\\.crai$": null,
"pattern: ^\\S+\\.bam\\.bai$ or ^\\S+\\.bai$": null,
"pattern: ^\\S+\\.tbi$": null,
"type: boolean": null
}
} | pattern: ^\S+\.bam\.bai$ or ^\S+\.bai$ | 1 |
resource_bcftools_pluginscatter_3 | resource_profiling | {
"process": "BCFTOOLS_PLUGINSCATTER",
"tool": "bcftools/pluginscatter",
"description": "Split VCF by chunks or regions, creating multiple VCFs."
} | {
"type": "choice",
"instructions": "What resource profile label should be assigned to BCFTOOLS_PLUGINSCATTER (Split VCF by chunks or regions, creating multiple VCFs.) in conf/base.config?",
"criteria": {
"process_high": null,
"process_single": null,
"process_low": null,
"process_long": null
}
} | process_single | 1 |
mod_cnvkit_call_1 | tool_selection | "In Nextflow DSL2, which module handles: Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number (tools: cnvkit)?" | {
"type": "choice",
"instructions": "Select the appropriate nf-core module for the specified bioinformatics operation.",
"criteria": {
"segemehl_align": "A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection",
"cnvkit_call": "Given segmented log2 ratio estimates (... | cnvkit_call | 1 |
noul_channel_filter_operator_1 | dsl2_rules | "Is this statement accurate according to standard Nextflow DSL2 behavior? \"Channel `.filter { meta, fastq -> meta.single_end }` filters items based on a boolean closure condition.\"" | {
"type": "noul",
"instructions": "Determine whether the Nextflow DSL2 statement or idiom is valid and adheres to standards."
} | true | 1 |
qc_adapt_targeted_amplicon_0_15 | 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,
"Drop FastQC": null,
"Swap for NanoPlot": null
}
} | Keep FastQC | 0 |
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