| { |
| "alzheimer-mouse": { |
| "task_name": "Alzheimer Mouse Models: Comparative Pathway Analysis", |
| "gold_tools": [ |
| "DESeq2", |
| "edgeR", |
| "limma", |
| "clusterProfiler", |
| "KEGGREST" |
| ], |
| "gold_servers": [ |
| "mcp_bioconductor-deseq2", |
| "mcp_bioconductor-edger", |
| "mcp_bioconductor-limma", |
| "mcp_bioconductor-clusterprofiler", |
| "mcp_bioconductor-keggrest" |
| ], |
| "workflow": [ |
| { |
| "name": "load_mouse_count_tables", |
| "tool_patterns": [ |
| "read", |
| "csv", |
| "count", |
| "pandas", |
| "data.table" |
| ] |
| }, |
| { |
| "name": "normalize_and_model_expression", |
| "tool_patterns": [ |
| "deseq", |
| "edger", |
| "limma", |
| "normalize" |
| ] |
| }, |
| { |
| "name": "run_kegg_pathway_enrichment", |
| "tool_patterns": [ |
| "clusterprofiler", |
| "kegg", |
| "enrich", |
| "pathway" |
| ] |
| }, |
| { |
| "name": "compare_shared_pathways", |
| "tool_patterns": [ |
| "merge", |
| "join", |
| "shared", |
| "csv", |
| "pandas" |
| ] |
| } |
| ] |
| }, |
| "comparative-genomics": { |
| "task_name": "Comparative Genomics: Co-evolving Gene Clusters", |
| "gold_tools": [ |
| "OrthoFinder", |
| "BLAST", |
| "DIAMOND", |
| "gffread", |
| "seqkit" |
| ], |
| "gold_servers": [ |
| "mcp_orthofinder", |
| "mcp_blast", |
| "mcp_diamond", |
| "mcp_gffread", |
| "mcp_seqkit" |
| ], |
| "workflow": [ |
| { |
| "name": "extract_or_prepare_proteomes", |
| "tool_patterns": [ |
| "gffread", |
| "seqkit", |
| "fasta", |
| "faa" |
| ] |
| }, |
| { |
| "name": "infer_orthogroups", |
| "tool_patterns": [ |
| "orthofinder", |
| "orthogroup", |
| "blast", |
| "diamond" |
| ] |
| }, |
| { |
| "name": "filter_core_coding_clusters", |
| "tool_patterns": [ |
| "core", |
| "present", |
| "coding", |
| "orthogroup", |
| "pandas" |
| ] |
| }, |
| { |
| "name": "assign_consensus_annotations", |
| "tool_patterns": [ |
| "blast", |
| "diamond", |
| "kegg", |
| "annotation", |
| "consensus" |
| ] |
| } |
| ] |
| }, |
| "cystic-fibrosis": { |
| "task_name": "Cystic Fibrosis Mendelian Variant Identification", |
| "gold_tools": [ |
| "BWA", |
| "samtools", |
| "bcftools", |
| "GATK", |
| "SnpEff", |
| "SnpSift" |
| ], |
| "gold_servers": [ |
| "mcp_bwa", |
| "mcp_samtools", |
| "mcp_bcftools", |
| "mcp_gatk4", |
| "mcp_snpeff", |
| "mcp_snpsift" |
| ], |
| "workflow": [ |
| { |
| "name": "prepare_family_variant_data", |
| "tool_patterns": [ |
| "bwa", |
| "samtools", |
| "bam", |
| "vcf" |
| ] |
| }, |
| { |
| "name": "call_or_filter_variants", |
| "tool_patterns": [ |
| "bcftools", |
| "gatk", |
| "variant", |
| "filter" |
| ] |
| }, |
| { |
| "name": "annotate_with_effect_and_clinvar", |
| "tool_patterns": [ |
| "snpeff", |
| "snpsift", |
| "clinvar", |
| "annotation" |
| ] |
| }, |
| { |
| "name": "apply_recessive_family_filter", |
| "tool_patterns": [ |
| "recessive", |
| "affected", |
| "family", |
| "genotype", |
| "pandas" |
| ] |
| } |
| ] |
| }, |
| "deseq": { |
| "task_name": "RNA-Seq Differential Expression (DESeq2)", |
| "gold_tools": [ |
| "STAR", |
| "HISAT2", |
| "featureCounts", |
| "Subread", |
| "DESeq2", |
| "tximport" |
| ], |
| "gold_servers": [ |
| "mcp_star", |
| "mcp_hisat2", |
| "mcp_subread", |
| "mcp_bioconductor-rsubread", |
| "mcp_bioconductor-deseq2", |
| "mcp_bioconductor-tximport" |
| ], |
| "workflow": [ |
| { |
| "name": "align_rnaseq_reads", |
| "tool_patterns": [ |
| "star", |
| "hisat2", |
| "align", |
| "bam" |
| ] |
| }, |
| { |
| "name": "count_gene_features", |
| "tool_patterns": [ |
| "featurecounts", |
| "subread", |
| "count" |
| ] |
| }, |
| { |
| "name": "differential_expression", |
| "tool_patterns": [ |
| "deseq", |
| "edger", |
| "limma", |
| "log2foldchange" |
| ] |
| }, |
| { |
| "name": "write_de_results_csv", |
| "tool_patterns": [ |
| "csv", |
| "gene_id", |
| "padj", |
| "pvalue" |
| ] |
| } |
| ] |
| }, |
| "evolution": { |
| "task_name": "Experimental Evolution Variant Calling (E. coli)", |
| "gold_tools": [ |
| "BWA", |
| "samtools", |
| "bcftools", |
| "FreeBayes", |
| "SnpEff", |
| "SnpSift" |
| ], |
| "gold_servers": [ |
| "mcp_bwa", |
| "mcp_samtools", |
| "mcp_bcftools", |
| "mcp_freebayes", |
| "mcp_snpeff", |
| "mcp_snpsift" |
| ], |
| "workflow": [ |
| { |
| "name": "align_evolved_and_ancestor_reads", |
| "tool_patterns": [ |
| "bwa", |
| "samtools", |
| "align", |
| "bam" |
| ] |
| }, |
| { |
| "name": "call_variants_per_line", |
| "tool_patterns": [ |
| "bcftools", |
| "freebayes", |
| "variant", |
| "vcf" |
| ] |
| }, |
| { |
| "name": "annotate_variant_effects", |
| "tool_patterns": [ |
| "snpeff", |
| "effect", |
| "impact", |
| "moderate" |
| ] |
| }, |
| { |
| "name": "intersect_shared_variants", |
| "tool_patterns": [ |
| "shared", |
| "intersect", |
| "evolved", |
| "pandas" |
| ] |
| } |
| ] |
| }, |
| "giab": { |
| "task_name": "GIAB Variant Calling", |
| "gold_tools": [ |
| "BWA", |
| "samtools", |
| "bcftools", |
| "GATK", |
| "FreeBayes", |
| "VariantAnnotation" |
| ], |
| "gold_servers": [ |
| "mcp_bwa", |
| "mcp_samtools", |
| "mcp_bcftools", |
| "mcp_gatk4", |
| "mcp_freebayes", |
| "mcp_bioconductor-variantannotation" |
| ], |
| "workflow": [ |
| { |
| "name": "align_exome_reads", |
| "tool_patterns": [ |
| "bwa", |
| "samtools", |
| "align", |
| "bam" |
| ] |
| }, |
| { |
| "name": "sort_index_and_qc_bam", |
| "tool_patterns": [ |
| "samtools", |
| "sort", |
| "index", |
| "flagstat" |
| ] |
| }, |
| { |
| "name": "call_germline_variants", |
| "tool_patterns": [ |
| "gatk", |
| "bcftools", |
| "freebayes", |
| "haplotypecaller" |
| ] |
| }, |
| { |
| "name": "compress_and_index_vcf", |
| "tool_patterns": [ |
| "vcf", |
| "bgzip", |
| "tabix", |
| "index" |
| ] |
| } |
| ] |
| }, |
| "metagenomics": { |
| "task_name": "Metagenomics: Community Comparison (Cuatro Cienegas)", |
| "gold_tools": [ |
| "Kraken2", |
| "csvtk", |
| "pandas" |
| ], |
| "gold_servers": [ |
| "mcp_kraken2", |
| "mcp_csvtk" |
| ], |
| "workflow": [ |
| { |
| "name": "classify_paired_reads", |
| "tool_patterns": [ |
| "kraken2", |
| "classify", |
| "paired", |
| "fastq" |
| ] |
| }, |
| { |
| "name": "parse_kraken_reports", |
| "tool_patterns": [ |
| "report", |
| "taxonomy", |
| "taxid", |
| "phylum" |
| ] |
| }, |
| { |
| "name": "compute_bacterial_phylum_relative_abundance", |
| "tool_patterns": [ |
| "bacteria", |
| "phylum", |
| "relative", |
| "abundance" |
| ] |
| }, |
| { |
| "name": "write_phylum_abundance_csv", |
| "tool_patterns": [ |
| "csv", |
| "OTU", |
| "Kingdom", |
| "Phylum", |
| "JP4D", |
| "JC1A" |
| ] |
| } |
| ] |
| }, |
| "single-cell": { |
| "task_name": "Single-cell RNA-seq: Skeletal Muscle Exercise Response", |
| "gold_tools": [ |
| "Scanpy", |
| "Seurat", |
| "CellTypist" |
| ], |
| "gold_servers": [ |
| "mcp_scanpy", |
| "mcp_scanpy-cli", |
| "mcp_scanpy-scripts", |
| "mcp_seurat-scripts", |
| "mcp_celltypist" |
| ], |
| "workflow": [ |
| { |
| "name": "load_single_cell_matrix", |
| "tool_patterns": [ |
| "scanpy", |
| "read_h5ad", |
| "h5ad", |
| "matrix" |
| ] |
| }, |
| { |
| "name": "normalize_cluster_and_embed", |
| "tool_patterns": [ |
| "normalize", |
| "neighbors", |
| "leiden", |
| "umap", |
| "scanpy" |
| ] |
| }, |
| { |
| "name": "annotate_cell_types", |
| "tool_patterns": [ |
| "celltypist", |
| "marker", |
| "annotation", |
| "cell_type" |
| ] |
| }, |
| { |
| "name": "differential_expression_by_condition", |
| "tool_patterns": [ |
| "rank_genes", |
| "differential", |
| "exercise", |
| "wilcoxon" |
| ] |
| } |
| ] |
| }, |
| "transcript-quant": { |
| "task_name": "Transcript Quantification (Simulated RNA-Seq)", |
| "gold_tools": [ |
| "Kallisto", |
| "Salmon" |
| ], |
| "gold_servers": [ |
| "mcp_kallisto", |
| "mcp_salmon" |
| ], |
| "workflow": [ |
| { |
| "name": "build_transcriptome_index", |
| "tool_patterns": [ |
| "kallisto_index", |
| "salmon", |
| "index", |
| "transcriptome" |
| ] |
| }, |
| { |
| "name": "quantify_paired_end_reads", |
| "tool_patterns": [ |
| "kallisto_quant", |
| "salmon", |
| "quant", |
| "paired" |
| ] |
| }, |
| { |
| "name": "extract_transcript_counts", |
| "tool_patterns": [ |
| "abundance", |
| "est_counts", |
| "count", |
| "transcript_id" |
| ] |
| }, |
| { |
| "name": "write_no_header_tsv", |
| "tool_patterns": [ |
| "tsv", |
| "transcript_id", |
| "count" |
| ] |
| } |
| ] |
| }, |
| "viral-metagenomics": { |
| "task_name": "Viral Metagenomics: Species Identification (Dolphin)", |
| "gold_tools": [ |
| "MEGAHIT", |
| "SPAdes", |
| "Kaiju", |
| "fastp", |
| "BLAST" |
| ], |
| "gold_servers": [ |
| "mcp_megahit", |
| "mcp_spades", |
| "mcp_kaiju", |
| "mcp_fastp", |
| "mcp_blast" |
| ], |
| "workflow": [ |
| { |
| "name": "assemble_viral_metagenomic_contigs", |
| "tool_patterns": [ |
| "megahit", |
| "spades", |
| "assembly", |
| "contig" |
| ] |
| }, |
| { |
| "name": "classify_contigs_taxonomically", |
| "tool_patterns": [ |
| "kaiju", |
| "blast", |
| "taxonomy", |
| "virus" |
| ] |
| }, |
| { |
| "name": "resolve_taxon_names", |
| "tool_patterns": [ |
| "names", |
| "nodes", |
| "taxon", |
| "species" |
| ] |
| }, |
| { |
| "name": "summarize_contig_counts_by_species", |
| "tool_patterns": [ |
| "species", |
| "contig_count", |
| "domain", |
| "csv" |
| ] |
| } |
| ] |
| } |
| } |
|
|
