From 02086d9e8f6d08168d9e05e0d6c9094bf47061ce Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 13 May 2026 14:03:18 +0200 Subject: [PATCH 1/5] add parameter table page and --- bin/params.json.js | 192 + package.json | 3 +- public/params.json | 73851 ++++++++++++++++ sites/main-site/public/params.json | 1 + sites/main-site/src/components/BaseHead.astro | 4 + .../src/components/ParameterTable.svelte | 240 + .../main-site/src/pages/pipeline_params.astro | 12 + 7 files changed, 74302 insertions(+), 1 deletion(-) create mode 100644 bin/params.json.js create mode 100644 public/params.json create mode 120000 sites/main-site/public/params.json create mode 100644 sites/main-site/src/components/ParameterTable.svelte create mode 100644 sites/main-site/src/pages/pipeline_params.astro diff --git a/bin/params.json.js b/bin/params.json.js new file mode 100644 index 0000000000..5fe10e1d1b --- /dev/null +++ b/bin/params.json.js @@ -0,0 +1,192 @@ +#! /usr/bin/env node +import { getGitHubFile, getCurrentRateLimitRemaining } from '../sites/main-site/src/components/octokit.js'; +import { readFileSync, writeFileSync, existsSync } from 'fs'; +import path from 'path'; +import ProgressBar from 'progress'; + +const __dirname = path.resolve(); + +const args = process.argv.slice(2); +const singlePipelineName = args[0] || null; +const singleVersion = args[1] || null; + +if (singleVersion && !singlePipelineName) { + console.error('A pipeline name must be provided when specifying a version'); + process.exit(1); +} + +console.log(await getCurrentRateLimitRemaining()); + +// Internal key combining param name + type so same-named params with different types stay separate. +const internalKey = (name, type) => `${name}|${type ?? ''}`; + +// Convert the grouped output format { paramName: [{type, pipelines}] } +// back into the flat internal map { "paramName|type": {name, type, pipelines} }. +function ungroupParams(grouped) { + const flat = {}; + for (const [name, variants] of Object.entries(grouped)) { + for (const { type, pipelines } of variants) { + flat[internalKey(name, type)] = { name, type, pipelines }; + } + } + return flat; +} + +// Convert the flat internal map into the grouped output format. +function groupParams(flat) { + const grouped = {}; + for (const { name, type, pipelines } of Object.values(flat)) { + if (!grouped[name]) grouped[name] = []; + grouped[name].push({ type, pipelines }); + } + // Sort each variant list by type name, then sort params alphabetically by key. + return Object.fromEntries( + Object.keys(grouped) + .sort() + .map((name) => [ + name, + grouped[name] + .sort((a, b) => (a.type ?? '').localeCompare(b.type ?? '')) + .map(({ type, pipelines }) => ({ + type, + pipelines: pipelines.sort( + (a, b) => a.name.localeCompare(b.name) || a.version.localeCompare(b.version), + ), + })), + ]), + ); +} + +export const writeParamsJson = async () => { + const pipelinesJson = readFileSync(path.join(__dirname, '/public/pipelines.json')); + const pipelines = JSON.parse(pipelinesJson); + + const paramsJsonPath = path.join(__dirname, '/public/params.json'); + + // Internal map keyed by "paramName|type" + let params = {}; + + if (singlePipelineName) { + if (existsSync(paramsJsonPath)) { + params = ungroupParams(JSON.parse(readFileSync(paramsJsonPath))); + } + // Remove existing entries for the targeted pipeline+version before re-processing + for (const key of Object.keys(params)) { + params[key].pipelines = params[key].pipelines.filter((p) => { + if (p.name !== singlePipelineName) return true; + return singleVersion ? p.version !== singleVersion : false; + }); + if (params[key].pipelines.length === 0) { + delete params[key]; + } + } + + const pipelineEntry = pipelines.remote_workflows.find((p) => p.name === singlePipelineName); + if (!pipelineEntry) { + console.error(`Pipeline ${singlePipelineName} not found in pipelines.json`); + process.exit(1); + } + if (singleVersion && !pipelineEntry.releases.some((r) => r.tag_name === singleVersion)) { + console.error(`Version ${singleVersion} not found for pipeline ${singlePipelineName} in pipelines.json`); + process.exit(1); + } + console.log(`Processing parameters for: ${singlePipelineName}${singleVersion ? `@${singleVersion}` : ''}`); + } + + const pipelinesToProcess = singlePipelineName + ? pipelines.remote_workflows.filter((p) => p.name === singlePipelineName) + : pipelines.remote_workflows; + + // Build a set of already-processed {pipeline@version} pairs so re-runs skip unchanged releases + const processed = new Set(); + if (!singlePipelineName) { + for (const { pipelines: pipelineList } of Object.values(params)) { + for (const { name, version } of pipelineList) { + processed.add(`${name}@${version}`); + } + } + } + + const CONCURRENCY_LIMIT = 10; + const bar = new ProgressBar(' fetching schemas [:bar] :percent :etas', { total: pipelinesToProcess.length }); + + const processPipeline = async (pipeline) => { + const targetRelease = singleVersion + ? pipeline.releases?.find((r) => r.tag_name === singleVersion && r.has_schema) + : (pipeline.releases?.find((r) => r.tag_name !== 'dev' && r.has_schema) ?? + pipeline.releases?.find((r) => r.tag_name === 'dev' && r.has_schema)); + + if (!targetRelease) { + if (singleVersion) { + console.error(`Version ${singleVersion} not found or has no schema for ${pipeline.name}`); + } + bar.tick(); + return; + } + + // Skip if this exact release was already parsed into params.json + if (processed.has(`${pipeline.name}@${targetRelease.tag_name}`)) { + bar.tick(); + return; + } + + const schemaContent = await getGitHubFile(pipeline.name, 'nextflow_schema.json', targetRelease.tag_name); + + if (!schemaContent) { + bar.tick(); + return; + } + + let schema; + try { + schema = JSON.parse(schemaContent); + } catch { + bar.tick(); + return; + } + + // Collect param names + types from definitions (draft-07) or $defs (draft 2020-12) + const defs = schema.definitions || schema['$defs'] || {}; + const paramMap = new Map(); // paramName -> type + + for (const def of Object.values(defs)) { + if (def.properties) { + for (const [paramName, propValue] of Object.entries(def.properties)) { + const t = propValue.type ?? null; + paramMap.set(paramName, Array.isArray(t) ? t.filter((x) => x !== 'null')[0] ?? t[0] ?? null : t); + } + } + } + + // Top-level properties that aren't $ref pointers to definition groups + if (schema.properties) { + for (const [paramName, propValue] of Object.entries(schema.properties)) { + if (!propValue.$ref) { + const t = propValue.type ?? null; + paramMap.set(paramName, Array.isArray(t) ? t.filter((x) => x !== 'null')[0] ?? t[0] ?? null : t); + } + } + } + + const entry = { name: pipeline.name, version: targetRelease.tag_name }; + for (const [paramName, type] of paramMap) { + const key = internalKey(paramName, type); + if (!params[key]) { + params[key] = { name: paramName, type, pipelines: [] }; + } + params[key].pipelines.push(entry); + } + + bar.tick(); + }; + + for (let i = 0; i < pipelinesToProcess.length; i += CONCURRENCY_LIMIT) { + const batch = pipelinesToProcess.slice(i, i + CONCURRENCY_LIMIT); + await Promise.all(batch.map(processPipeline)); + } + + console.log(' writing params.json'); + writeFileSync(paramsJsonPath, JSON.stringify(groupParams(params), null, 2)); +}; + +writeParamsJson(); diff --git a/package.json b/package.json index bb96fe2647..3b36de742f 100644 --- a/package.json +++ b/package.json @@ -4,9 +4,10 @@ "private": true, "type": "module", "scripts": { - "build-cache": "npm run build-pipeline-json && npm run build-component-json", + "build-cache": "npm run build-pipeline-json && npm run build-component-json && npm run build-params-json", "build-pipeline-json": "node bin/pipelines.json.js", "build-component-json": "node bin/components.json.js", + "build-params-json": "node bin/params.json.js", "update": "npx npm-check-updates --interactive --format group --workspaces", "test-all": "for dir in sites/*; do (cd $dir && npm run test); done" }, diff --git a/public/params.json b/public/params.json new file mode 100644 index 0000000000..714ede018f --- /dev/null +++ b/public/params.json @@ -0,0 +1,73851 @@ +{ + "A": [ + { + "type": "string", + "pipelines": [ + { + "name": "dualrnaseq", + "version": "1.0.0" + } + ] + } + ], + "ACANConfig": [ + { + "type": "string", + "pipelines": [ + { + "name": "rarevariantburden", + "version": "dev" + } + ] + } + ], + "AFMax": [ + { + "type": "number", + "pipelines": [ + { + "name": "rarevariantburden", + "version": "dev" + } + ] + } + ], + "CoCoRVFolder": [ + { + "type": "string", + "pipelines": [ + { + "name": "rarevariantburden", + "version": "dev" + } + ] + } + ], + "CoCoRVOptions": [ + { + "type": "string", + "pipelines": [ + { + "name": "rarevariantburden", + "version": "dev" + } + ] + } + ], + "DNA": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "epigenomesegmentation", + "version": "dev" + } + ] + } + ], + "FDR_level": [ + { + "type": "string", + "pipelines": [ + { + "name": "proteomicslfq", + "version": "1.0.0" + }, + { + "name": "quantms", + "version": "1.2.0" + } + ] + } + ], + "FW_primer": [ + { + "type": "string", + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + } + ] + } + ], + "IL_equivalent": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "quantms", + "version": "1.2.0" + } + ] + }, + { + "type": "string", + "pipelines": [ + { + "name": "proteomicslfq", + "version": "1.0.0" + } + ] + } + ], + "REVELThreshold": [ + { + "type": "number", + "pipelines": [ + { + "name": "rarevariantburden", + "version": "dev" + } + ] + } + ], + "RV_primer": [ + { + "type": "string", + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + } + ] + } + ], + "VCFAnno": [ + { + "type": "string", + "pipelines": [ + { + "name": "rarevariantburden", + "version": "dev" + } + ] + } + ], + "VEPAnnotations": [ + { + "type": "string", + "pipelines": [ + { + "name": "rarevariantburden", + "version": "dev" + } + ] + } + ], + "a": [ + { + "type": "string", + "pipelines": [ + { + "name": "dualrnaseq", + "version": "1.0.0" + } + ] + } + ], + "aa_cngain": [ + { + "type": "string", + "pipelines": [ + { + "name": "circdna", + "version": "1.1.0" + } + ] + } + ], + "aa_data_repo": [ + { + "type": "string", + "pipelines": [ + { + "name": "circdna", + "version": "1.1.0" + } + ] + } + ], + "accel": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } + ] + } + ], + "accession2taxid": [ + { + "type": "string", + "pipelines": [ + { + "name": "createtaxdb", + "version": "3.0.0" + } + ] + } + ], + "accessions": [ + { + "type": "string", + "pipelines": [ + { + "name": "stableexpression", + "version": "dev" + } + ] + } + ], + "accessions_file": [ + { + "type": "string", + "pipelines": [ + { + "name": "stableexpression", + "version": "dev" + } + ] + } + ], + "accessions_only": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "stableexpression", + "version": "dev" + } + ] + } + ], + "acquisition_method": [ + { + "type": "string", + "pipelines": [ + { + "name": "quantms", + "version": "1.2.0" + } + ] + } + ], + "activation_method": [ + { + "type": "string", + "pipelines": [ + { + "name": "mhcquant", + "version": "3.1.0" + } + ] + } + ], + "adapter": [ + { + "type": "string", + "pipelines": [ + { + "name": "clipseq", + "version": "1.0.0" + } + ] + } + ], + "adapter_fasta": [ + { + "type": "string", + "pipelines": [ + { + "name": "airrflow", + "version": "5.0.0" + }, + { + "name": "denovotranscript", + "version": "1.2.1" + }, + { + "name": "rnafusion", + "version": "4.1.0" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } + ] + } + ], + "adapter_file": [ + { + "type": "string", + "pipelines": [ + { + "name": "bactmap", + "version": "1.0.0" + } + ] + } + ], + "adapterremoval_adapter1": [ + { + "type": "string", + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } + ] + } + ], + "adapterremoval_adapter2": [ + { + "type": "string", + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } + ] + } + ], + "adapterremoval_minquality": [ + { + "type": "integer", + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } + ] + } + ], + "adapterremoval_trim_quality_stretch": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "mag", + "version": "5.4.2" + } + ] + } + ], + "adapters": [ + { + "type": "string", + "pipelines": [ + { + "name": "dualrnaseq", + "version": "1.0.0" + } + ] + } + ], + "addSexToCaseGroup": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "rarevariantburden", + "version": "dev" + } + ] + } + ], + "add_decoys": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "proteomicslfq", + "version": "1.0.0" + }, + { + "name": "quantms", + "version": "1.2.0" + } + ] + } + ], + "add_reference": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "proteogenomicsdb", + "version": "1.0.0" + } + ] + } + ], + "add_stop_codons": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "proteogenomicsdb", + "version": "1.0.0" + } + ] + } + ], + "add_triqler_output": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "quantms", + "version": "1.2.0" + } + ] + } + ], + "add_variants": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "diseasemodulediscovery", + "version": "dev" + } + ] + } + ], + "additional_annotation": [ + { + "type": "string", + "pipelines": [ + { + "name": "viralrecon", + "version": "3.0.0" + } + ] + } + ], + "additional_fasta": [ + { + "type": "string", + "pipelines": [ + { + "name": "callingcards", + "version": "1.0.0" + }, + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "panoramaseq", + "version": "dev" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + } + ] + } + ], + "additional_vcf_files": [ + { + "type": "string", + "pipelines": [ + { + "name": "eager", + "version": "2.5.3" + } + ] + } + ], + "addsh": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + } + ] + } + ], + "adducts_neg": [ + { + "type": "string", + "pipelines": [ + { + "name": "metaboigniter", + "version": "2.0.1" + } + ] + } + ], + "adducts_pos": [ + { + "type": "string", + "pipelines": [ + { + "name": "metaboigniter", + "version": "2.0.1" + } + ] + } + ], + "adjust_batch_effect": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "methylarray", + "version": "dev" + } + ] + } + ], + "adjust_cell_composition": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "methylarray", + "version": "dev" + } + ] + } + ], + "adjustment": [ + { + "type": "integer", + "pipelines": [ + { + "name": "epigenomesegmentation", + "version": "dev" + } + ] + } + ], + "ae_fpkm_cutoff": [ + { + "type": "integer", + "pipelines": [ + { + "name": "drop", + "version": "1.0.0" + } + ] + } + ], + "ae_genes_to_test": [ + { + "type": "string", + "pipelines": [ + { + "name": "drop", + "version": "1.0.0" + } + ] + } + ], + "ae_groups": [ + { + "type": "string", + "pipelines": [ + { + "name": "drop", + "version": "1.0.0" + } + ] + } + ], + "ae_implementation": [ + { + "type": "string", + "pipelines": [ + { + "name": "drop", + "version": "1.0.0" + } + ] + } + ], + "ae_max_tested_dimension_proportion": [ + { + "type": "integer", + "pipelines": [ + { + "name": "drop", + "version": "1.0.0" + } + ] + } + ], + "ae_min_ids": [ + { + "type": "integer", + "pipelines": [ + { + "name": "drop", + "version": "1.0.0" + } + ] + } + ], + "ae_padj_cutoff": [ + { + "type": "number", + "pipelines": [ + { + "name": "drop", + "version": "1.0.0" + } + ] + } + ], + "ae_skip": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "drop", + "version": "1.0.0" + } + ] + } + ], + "ae_use_grid_search_to_obtain_q": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "drop", + "version": "1.0.0" + } + ] + } + ], + "ae_yield_size": [ + { + "type": "integer", + "pipelines": [ + { + "name": "drop", + "version": "1.0.0" + } + ] + } + ], + "ae_z_score_cutoff": [ + { + "type": "number", + "pipelines": [ + { + "name": "drop", + "version": "1.0.0" + } + ] + } + ], + "af_field": [ + { + "type": "string", + "pipelines": [ + { + "name": "proteogenomicsdb", + "version": "1.0.0" + } + ] + } + ], + "affinity_aggregation": [ + { + "type": "string", + "pipelines": [ + { + "name": "tfactivity", + "version": "dev" + } + ] + } + ], + "affix_type": [ + { + "type": "string", + "pipelines": [ + { + "name": "proteomicslfq", + "version": "1.0.0" + } + ] + } + ], + "affy_background": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } + ] + } + ], + "affy_bgversion": [ + { + "type": "integer", + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } + ] + } + ], + "affy_build_annotation": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } + ] + } + ], + "affy_cdfname": [ + { + "type": "string", + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } + ] + } + ], + "affy_cel_files_archive": [ + { + "type": "string", + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } + ] + } + ], + "affy_destructive": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } + ] + } + ], + "affy_file_name_col": [ + { + "type": "string", + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } + ] + } + ], + "affy_rm_extra": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } + ] + } + ], + "affy_rm_mask": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } + ] + } + ], + "affy_rm_outliers": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "differentialabundance", + "version": "1.5.0" + } + ] + } + ], + "aggregate_channels": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "sopa", + "version": "dev" + } + ] + } + ], + "aggregate_genes": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "sopa", + "version": "dev" + } + ] + } + ], + "aggregate_isoforms": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "scdownstream", + "version": "dev" + } + ] + } + ], + "aggregation": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "rnasplice", + "version": "1.0.4" + } + ] + } + ], + "aimed_cov": [ + { + "type": "integer", + "pipelines": [ + { + "name": "deepmutscan", + "version": "dev" + } + ] + } + ], + "algorithm_common_chrom_fwhm_featurefindermetabo_openms": [ + { + "type": "number", + "pipelines": [ + { + "name": "metaboigniter", + "version": "2.0.1" + } + ] + } + ], + "algorithm_common_chrom_peak_snr_featurefindermetabo_openms": [ + { + "type": "number", + "pipelines": [ + { + "name": "metaboigniter", + "version": "2.0.1" + } + ] + } + ], + "algorithm_common_noise_threshold_int_featurefindermetabo_openms": [ + { + "type": "number", + "pipelines": [ + { + "name": "metaboigniter", + "version": "2.0.1" + } + ] + } + ], + "algorithm_distance_intensity_exponent_featurelinkerunlabeledkd_openms": [ + { + "type": "number", + "pipelines": [ + { + "name": "metaboigniter", + "version": "2.0.1" + } + ] + } + ], + "algorithm_distance_intensity_log_transform_featurelinkerunlabeledkd_openms": [ + { + "type": "string", + "pipelines": [ + { + "name": "metaboigniter", + "version": "2.0.1" + } + ] + } + ], + "algorithm_distance_intensity_weight_featurelinkerunlabeledkd_openms": [ + { + "type": "number", + "pipelines": [ + { + "name": "metaboigniter", + "version": "2.0.1" + } + ] + } + ], + 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"name": "sopa", + "version": "dev" + }, + { + "name": "spatialvi", + "version": "dev" + }, + { + "name": "spatialxe", + "version": "dev" + }, + { + "name": "spinningjenny", + "version": "dev" + }, + { + "name": "stableexpression", + "version": "dev" + }, + { + "name": "taxprofiler", + "version": "2.0.0" + }, + { + "name": "tbanalyzer", + "version": "dev" + }, + { + "name": "tfactivity", + "version": "dev" + }, + { + "name": "troughgraph", + "version": "dev" + }, + { + "name": "tumourevo", + "version": "dev" + }, + { + "name": "variantbenchmarking", + "version": "1.5.0" + }, + { + "name": "variantcatalogue", + "version": "dev" + }, + { + "name": "variantprioritization", + "version": "1.0.0" + }, + { + "name": "viralintegration", + "version": "0.1.1" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + }, + { + "name": "viralrecon", + "version": "3.0.0" + } + ] + } + ], + "viber_a_0": [ + { + "type": "integer", + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] + } + ], + "viber_alpha_0": [ + { + "type": "number", + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] + } + ], + "viber_b_0": [ + { + "type": "integer", + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] + } + ], + "viber_binomial_cutoff": [ + { + "type": "number", + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] + } + ], + "viber_dimensions_cutoff": [ + { + "type": "integer", + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] + } + ], + "viber_epsilon_conv": [ + { + "type": "number", + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] + } + ], + "viber_k": [ + { + "type": "integer", + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] + } + ], + "viber_max_iter": [ + { + "type": "integer", + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] + } + ], + "viber_pi_cutoff": [ + { + "type": "number", + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] + } + ], + "viber_q_init": [ + { + "type": "string", + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] + } + ], + "viber_re_assign": [ + { + "type": "string", + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] + } + ], + "viber_samples": [ + { + "type": "integer", + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] + } + ], + "viber_trace": [ + { + "type": "string", + "pipelines": [ + { + "name": "tumourevo", + "version": "dev" + } + ] + } + ], + "viral_fasta": [ + { + "type": "string", + "pipelines": [ + { + "name": "viralintegration", + "version": "0.1.1" + } + ] + } + ], + "vireo_ase_mode": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "hadge", + "version": "dev" + } + ] + } + ], + "vireo_cell_ambient_rnas": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "hadge", + "version": "dev" + } + ] + } + ], + "vireo_cell_range": [ + { + "type": "string", + "pipelines": [ + { + "name": "hadge", + "version": "dev" + } + ] + } + ], + "vireo_extra_donor": [ + { + "type": "integer", + "pipelines": [ + { + "name": "hadge", + "version": "dev" + } + ] + } + ], + "vireo_extra_donor_mode": [ + { + "type": "string", + "pipelines": [ + { + "name": "hadge", + "version": "dev" + } + ] + } + ], + "vireo_filtered_variants": [ + { + "type": "string", + "pipelines": [ + { + "name": "hadge", + "version": "dev" + } + ] + } + ], + "vireo_force_learn_gt": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "hadge", + "version": "dev" + } + ] + } + ], + "vireo_genotag": [ + { + "type": "string", + "pipelines": [ + { + "name": "hadge", + "version": "dev" + } + ] + } + ], + "vireo_n_init": [ + { + "type": "integer", + "pipelines": [ + { + "name": "hadge", + "version": "dev" + } + ] + } + ], + "vireo_no_doublet": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "hadge", + "version": "dev" + } + ] + } + ], + "vireo_no_plot": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "hadge", + "version": "dev" + } + ] + } + ], + "vireo_rand_seed": [ + { + "type": "integer", + "pipelines": [ + { + "name": "hadge", + "version": "dev" + } + ] + } + ], + "virtual_4c": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "hicar", + "version": "1.0.0" + } + ] + } + ], + "visium_hd_imread_page": [ + { + "type": "number", + "pipelines": [ + { + "name": "sopa", + "version": "dev" + } + ] + } + ], + "visium_hd_prior_shapes_key": [ + { + "type": "string", + "pipelines": [ + { + "name": "sopa", + "version": "dev" + } + ] + } + ], + "visualization_max_nodes": [ + { + "type": "integer", + "pipelines": [ + { + "name": "diseasemodulediscovery", + "version": "dev" + } + ] + } + ], + "vprimer_start": [ + { + "type": "integer", + "pipelines": [ + { + "name": "airrflow", + "version": "5.0.0" + } + ] + } + ], + "vprimers": [ + { + "type": "string", + "pipelines": [ + { + "name": "airrflow", + "version": "5.0.0" + } + ] + } + ], + "vsearch_cluster": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + } + ] + } + ], + "vsearch_cluster_id": [ + { + "type": "number", + "pipelines": [ + { + "name": "ampliseq", + "version": "2.17.0" + } + ] + } + ], + "vsearch_id": [ + { + "type": "number", + "pipelines": [ + { + "name": "crisprseq", + "version": "2.3.0" + } + ] + } + ], + "vsearch_maxseqlength": [ + { + "type": "integer", + "pipelines": [ + { + "name": "crisprseq", + "version": "2.3.0" + } + ] + } + ], + "vsearch_minseqlength": [ + { + "type": "integer", + "pipelines": [ + { + "name": "crisprseq", + "version": "2.3.0" + } + ] + } + ], + "webin_cli_version": [ + { + "type": "string", + "pipelines": [ + { + "name": "seqsubmit", + "version": "dev" + } + ] + } + ], + "webincli_mode": [ + { + "type": "string", + "pipelines": [ + { + "name": "seqsubmit", + "version": "dev" + } + ] + } + ], + "wes": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.8.1" + } + ] + } + ], + "wfmash_block_length": [ + { + "type": "string", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_chunks": [ + { + "type": "integer", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_exclude_delim": [ + { + "type": "string", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_hg_filter_ani_diff": [ + { + "type": "integer", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_map_pct_id": [ + { + "type": "number", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_mash_kmer": [ + { + "type": "integer", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_mash_kmer_thres": [ + { + "type": "number", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_merge_segments": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_n_mappings": [ + { + "type": "integer", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_no_splits": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_only": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_segment_length": [ + { + "type": "string", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_sparse_map": [ + { + "type": "string", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "wfmash_temp_dir": [ + { + "type": "string", + "pipelines": [ + { + "name": "pangenome", + "version": "1.1.3" + } + ] + } + ], + "whitelist": [ + { + "type": "string", + "pipelines": [ + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "rnafusion", + "version": "4.1.0" + }, + { + "name": "scnanoseq", + "version": "1.2.2" + } + ] + } + ], + "wholegenome": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_error_rate": [ + { + "type": "number", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_indel_extended": [ + { + "type": "number", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_indel_fraction": [ + { + "type": "number", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_mutation_rate": [ + { + "type": "number", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_n_reads": [ + { + "type": "integer", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_outer_dist": [ + { + "type": "integer", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_r1_length": [ + { + "type": "integer", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_r2_length": [ + { + "type": "integer", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wholegenome_standard_dev": [ + { + "type": "integer", + "pipelines": [ + { + "name": "readsimulator", + "version": "1.0.1" + } + ] + } + ], + "wide_format_output": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "epitopeprediction", + "version": "3.1.0" + } + ] + } + ], + "wild_type": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "epitopeprediction", + "version": "3.1.0" + } + ] + } + ], + "winAnchorMultimapNmax": [ + { + "type": "integer", + "pipelines": [ + { + "name": "dualrnaseq", + "version": "1.0.0" + } + ] + } + ], + "window_size": [ + { + "type": "integer", + "pipelines": [ + { + "name": "tfactivity", + "version": "dev" + } + ] + } + ], + "winnowmap_kmers": [ + { + "type": "string", + "pipelines": [ + { + "name": "longraredisease", + "version": "dev" + } + ] + } + ], + "winnowmap_model": [ + { + "type": "string", + "pipelines": [ + { + "name": "longraredisease", + "version": "dev" + } + ] + } + ], + "with_control": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "atacseq", + "version": "2.1.2" + } + ] + } + ], + "with_umi": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "lncpipe", + "version": "dev" + }, + { + "name": "nascent", + "version": "2.3.0" + }, + { + "name": "riboseq", + "version": "1.2.0" + }, + { + "name": "rnaseq", + "version": "3.26.0" + }, + { + "name": "smrnaseq", + "version": "2.4.1" + }, + { + "name": "viralmetagenome", + "version": "1.1.1" + } + ] + } + ], + "workflow": [ + { + "type": "string", + "pipelines": [ + { + "name": "pacsomatic", + "version": "dev" + }, + { + "name": "pacvar", + "version": "1.0.1" + } + ] + } + ], + "writeMappings": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "dualrnaseq", + "version": "1.0.0" + } + ] + } + ], + "writeUnmappedNames": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "dualrnaseq", + "version": "1.0.0" + } + ] + } + ], + "write_allele_frequencies": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "eager", + "version": "2.5.3" + } + ] + } + ], + "write_barcode_meta_csv": [ + { + "type": "string", + "pipelines": [ + { + "name": "kmermaid", + "version": "0.1.0-alpha" + } + ] + } + ], + "wvdb": [ + { + "type": "string", + "pipelines": [ + { + "name": "rangeland", + "version": "1.0.0" + } + ] + } + ], + "xeniumranger_only": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "spatialxe", + "version": "dev" + } + ] + } + ], + "xreactive_chr_targets": [ + { + "type": "string", + "pipelines": [ + { + "name": "methylarray", + "version": "dev" + } + ] + } + ], + "zenodo_link": [ + { + "type": "string", + "pipelines": [ + { + "name": "drugresponseeval", + "version": "1.2.0" + } + ] + } + ], + "zymo": [ + { + "type": "boolean", + "pipelines": [ + { + "name": "methylseq", + "version": "4.2.0" + } + ] + } + ] +} \ No newline at end of file diff --git a/sites/main-site/public/params.json b/sites/main-site/public/params.json new file mode 120000 index 0000000000..5000dd24ae --- /dev/null +++ b/sites/main-site/public/params.json @@ -0,0 +1 @@ +../../../public/params.json \ No newline at end of file diff --git a/sites/main-site/src/components/BaseHead.astro b/sites/main-site/src/components/BaseHead.astro index 2a22866524..de7cda81ba 100644 --- a/sites/main-site/src/components/BaseHead.astro +++ b/sites/main-site/src/components/BaseHead.astro @@ -100,6 +100,10 @@ description = description?.replaceAll(/<[^>]*>?/g, ""); + +{#if loading} +
+ + Loading params data… +
+{:else if error} +
Failed to load params.json: {error}
+{:else} +
+
+ + +
+ +
+ + +
+ +
+ + +
+ +
+ +
+ + + {filteredParams.length} params and {sortedPipelines.length} pipelines + +
+ +
+ + + + + {#each sortedPipelines as pipeline} + {@const usedCount = filteredParams.filter((p) => p.pipelineSet.has(pipeline)).length} + {@const version = pipelineVersions.get(pipeline)} + {@const isDev = version === "dev"} + + {/each} + + + + {#each filteredParams as param} + + + {#each sortedPipelines as pipeline} + + {/each} + + {/each} + +
+
+ {pipeline} + {#if isDev} + + {/if} +
+
{@html param.label}
+
+{/if} + + diff --git a/sites/main-site/src/pages/pipeline_params.astro b/sites/main-site/src/pages/pipeline_params.astro new file mode 100644 index 0000000000..c7dd143da6 --- /dev/null +++ b/sites/main-site/src/pages/pipeline_params.astro @@ -0,0 +1,12 @@ +--- +import PageLayout from "@layouts/PageLayout.astro"; +import ParameterTable from "@components/ParameterTable.svelte"; +--- + + +

+ Each column is a parameter shared by multiple pipelines; each row is a pipeline. A green cell means that + pipeline uses the parameter. Hover any cell for details. +

+ + From 9578930ba6991d0f63b77b92db1de650728ce430 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 13 May 2026 14:11:07 +0200 Subject: [PATCH 2/5] simplify code --- .../src/components/ParameterTable.svelte | 39 +++++++------------ 1 file changed, 15 insertions(+), 24 deletions(-) diff --git a/sites/main-site/src/components/ParameterTable.svelte b/sites/main-site/src/components/ParameterTable.svelte index c704a148f4..cf86def0b3 100644 --- a/sites/main-site/src/components/ParameterTable.svelte +++ b/sites/main-site/src/components/ParameterTable.svelte @@ -3,13 +3,14 @@ type ParamVariant = { type: string | null; pipelines: { name: string; version: string }[] }; type ParamsData = Record; + type SortMode = "count" | "alpha"; let paramsData = $state(null); let loading = $state(true); let error = $state(null); let minOverlap = $state(5); - let sortParams = $state<"count" | "alpha">("count"); - let sortPipelines = $state<"count" | "alpha">("count"); + let sortParams = $state("count"); + let sortPipelines = $state("count"); let searchQuery = $state(""); function bsTooltip(node: HTMLElement) { @@ -38,13 +39,12 @@ if (!res.ok) throw new Error(`HTTP ${res.status}`); paramsData = await res.json(); } catch (e) { - error = String(e); + error = e instanceof Error ? e.message : String(e); } finally { loading = false; } }); - // Map of pipeline name → version string (from any param entry) const pipelineVersions = $derived.by(() => { const map = new Map(); if (!paramsData) return map; @@ -54,27 +54,17 @@ return map; }); - const totalPipelines = $derived.by(() => { - if (!paramsData) return 0; - const s = new Set(); - for (const variants of Object.values(paramsData)) - for (const { pipelines } of variants) for (const { name } of pipelines) s.add(name); - return s.size; - }); - const filteredParams = $derived.by(() => { if (!paramsData) return []; - const maxOv = totalPipelines - 1; const q = searchQuery.toLowerCase(); - // Flatten name × type variants into individual rows const rows = Object.entries(paramsData).flatMap(([name, variants]) => variants.map(({ type, pipelines }) => ({ name, type, pipelines })), ); let filtered = rows.filter(({ name, pipelines }) => { const n = pipelines.length; - return n >= minOverlap && n <= maxOv && (!q || name.toLowerCase().includes(q)); + return n >= minOverlap && n < pipelineVersions.size && (!q || name.toLowerCase().includes(q)); }); filtered.sort((a, b) => @@ -92,15 +82,16 @@ })); }); + const pipelineCounts = $derived( + new Map( + [...pipelineVersions.keys()].map((p) => [p, filteredParams.filter((fp) => fp.pipelineSet.has(p)).length]), + ), + ); + const sortedPipelines = $derived.by(() => { - if (!paramsData) return []; - const all = new Set(); - for (const variants of Object.values(paramsData)) - for (const { pipelines } of variants) for (const { name } of pipelines) all.add(name); - const pipes = [...all]; + const pipes = [...pipelineVersions.keys()]; if (sortPipelines === "count") { - const counts = new Map(pipes.map((p) => [p, filteredParams.filter((fp) => fp.pipelineSet.has(p)).length])); - pipes.sort((a, b) => (counts.get(b) ?? 0) - (counts.get(a) ?? 0)); + pipes.sort((a, b) => (pipelineCounts.get(b) ?? 0) - (pipelineCounts.get(a) ?? 0)); } else { pipes.sort((a, b) => a.localeCompare(b)); } @@ -126,7 +117,7 @@ type="range" class="form-range" min="1" - max="100" + max={pipelineVersions.size} bind:value={minOverlap} style="width:120px" /> @@ -173,7 +164,7 @@ {#each sortedPipelines as pipeline} - {@const usedCount = filteredParams.filter((p) => p.pipelineSet.has(pipeline)).length} + {@const usedCount = pipelineCounts.get(pipeline) ?? 0} {@const version = pipelineVersions.get(pipeline)} {@const isDev = version === "dev"} Date: Wed, 13 May 2026 14:19:39 +0200 Subject: [PATCH 3/5] fix bootstrap handling in svelte components --- .../src/components/CopyButton.svelte | 4 +++- .../main-site/src/components/FilterBar.svelte | 5 +++-- .../src/components/InstallCmd.svelte | 4 +++- .../src/components/ListingTableHeader.svelte | 3 ++- .../src/components/ParameterTable.svelte | 21 +------------------ .../SpecialInterestGroupsListing.svelte | 5 +++-- .../src/components/TagSection.svelte | 4 +++- .../src/components/ThemeSwitch.svelte | 3 ++- sites/main-site/src/components/actions.ts | 16 ++++++++++++++ .../components/pipeline/PipelineCard.svelte | 10 ++++----- .../pipeline/PipelinesListing.svelte | 10 ++++----- 11 files changed, 45 insertions(+), 40 deletions(-) create mode 100644 sites/main-site/src/components/actions.ts diff --git a/sites/main-site/src/components/CopyButton.svelte b/sites/main-site/src/components/CopyButton.svelte index a30a09a171..8cce0da167 100644 --- a/sites/main-site/src/components/CopyButton.svelte +++ b/sites/main-site/src/components/CopyButton.svelte @@ -17,6 +17,8 @@ children, }: Props = $props(); + import { bsTooltip } from "@components/actions"; + let copied = $state(false); let currentClasses = $derived(copied ? copiedClasses : classes); @@ -34,7 +36,7 @@ class={"copy-url " + currentClasses} onclick={() => copyToClipboard(text)} onkeypress={() => copyToClipboard(text)} - data-bs-toggle="tooltip" + use:bsTooltip title="Copy to clipboard" role="button" tabindex="0" diff --git a/sites/main-site/src/components/FilterBar.svelte b/sites/main-site/src/components/FilterBar.svelte index 5c58967184..63e76aedd6 100644 --- a/sites/main-site/src/components/FilterBar.svelte +++ b/sites/main-site/src/components/FilterBar.svelte @@ -1,6 +1,7 @@ -
+