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nictrunictru
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Add parameter page
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4 files changed

+158
-10
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‎preprocess.ipynb‎

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"cells": [
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{
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"cell_type": "code",
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"execution_count": 23,
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"execution_count": 50,
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"metadata": {},
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"outputs": [],
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"source": [
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"import json\n",
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"from collections import defaultdict\n",
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"from itertools import product\n",
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"import numpy as np"
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"import numpy as np\n",
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"import yaml"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 24,
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"execution_count": 51,
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"metadata": {},
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"outputs": [],
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"source": [
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"indir = Path(\"/home/nico/Software/nf-core/tfactivity/testing/work/61/1c5dc465e6b56743422f90800e0b13/\")\n",
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"indir = Path(\"/home/nico/Software/nf-core/tfactivity/testing/work/82/d26ec8c82550eedc7e354a5b166ed1\")\n",
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"assets_dir = Path(\"src/assets\")\n",
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"public_dir = Path(\"public\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 25,
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"execution_count": 52,
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"metadata": {},
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"outputs": [],
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"source": [
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"counts_design_path = indir / \"counts_design/samplesheet_rnaseq.csv\"\n",
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"counts_design_path = indir / \"samplesheet_rnaseq.csv\"\n",
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"assert counts_design_path.exists()\n",
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"\n",
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"params_path = indir / \"params.yaml\"\n",
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"assert params_path.exists()\n",
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"\n",
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"affinity_ratio_dir = indir / \"affinity_ratio\"\n",
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"assert affinity_ratio_dir.exists()\n",
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"\n",
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},
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{
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"cell_type": "code",
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"execution_count": 26,
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"execution_count": 53,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/tmp/ipykernel_26974/1389659800.py:3: DeprecationWarning: DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.\n",
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"/tmp/ipykernel_26974/1292875757.py:3: DeprecationWarning: DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.\n",
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" \"conditions\": df_design.groupby(\"condition\").apply(lambda x: x[\"sample\"].tolist()).to_dict()\n"
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]
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}
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],
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"source": [
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"df_design = pd.read_csv(indir / \"counts_design/samplesheet_rnaseq.csv\")\n",
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"df_design = pd.read_csv(counts_design_path)\n",
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"metadata = {\n",
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" \"conditions\": df_design.groupby(\"condition\").apply(lambda x: x[\"sample\"].tolist()).to_dict()\n",
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"}"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 29,
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"execution_count": 55,
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"metadata": {},
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"outputs": [],
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"source": [
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"params = yaml.load(open(params_path), yaml.CSafeLoader)\n",
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"json.dump(params, open(assets_dir / \"params.json\", \"w\"), indent=4)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 47,
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"metadata": {},
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"outputs": [],
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"source": [

‎src/assets/params.json‎

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{
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"Core Nextflow options": {
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"configFiles": "/home/nico/Software/nf-core/tfactivity/nextflow.config, /home/nico/Software/nf-core/tfactivity/testing/nextflow.config",
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"containerEngine": "docker",
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"launchDir": "/home/nico/Software/nf-core/tfactivity/testing",
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"profile": "test,docker",
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"projectDir": "/home/nico/Software/nf-core/tfactivity",
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"runName": "silly_franklin",
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"userName": "nico",
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"workDir": "/home/nico/Software/nf-core/tfactivity/testing/work"
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},
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"Generic options": {
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"trace_report_suffix": "2025-06-29_13-46-35"
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},
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"Input/output options": {
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"counts": "https://raw.githubusercontent.com/nf-core/test-datasets/tfactivity/rna-seq/Gene_id.txt",
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"counts_design": "https://raw.githubusercontent.com/nf-core/test-datasets/tfactivity/samplesheet/samplesheet_rnaseq.csv",
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"input": "https://raw.githubusercontent.com/nf-core/test-datasets/tfactivity/samplesheet/samplesheet_peaks.csv",
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"input_bam": "https://raw.githubusercontent.com/nf-core/test-datasets/tfactivity/samplesheet/samplesheet_bam.csv",
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"outdir": "results"
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},
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"Institutional config options": {
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"config_profile_description": "Minimal test dataset to check pipeline function",
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"config_profile_name": "Test profile"
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},
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"Reference genome options": {
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"blacklist": "/home/nico/Software/nf-core/tfactivity/assets/blacklists/mm10-blacklist.bed",
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"fasta": "https://github.com/nf-core/test-datasets/raw/tfactivity/reference/chr1.fa.gz",
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"genome": "mm10",
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"gtf": "https://github.com/nf-core/test-datasets/raw/tfactivity/reference/chr1.gtf.gz",
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"snps": "https://github.com/nf-core/test-datasets/raw/tfactivity/reference/snps_chr1.bed.gz",
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"taxon_id": 10090
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},
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"SNEEP options": {
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"sneep_motif_file": "/home/nico/Software/nf-core/tfactivity/assets/sneep_transfac_mouse_218.txt",
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"sneep_scale_file": "/home/nico/Software/nf-core/tfactivity/assets/sneep_scale_mouse_218.txt"
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}
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}

‎src/pages/index.astro‎

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<img src={logo.src} alt="nf-core/tfactivity Pipeline Logo" class="h-40 w-auto" />
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</div>
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<!-- Navigation -->
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<div class="max-w-4xl mx-auto px-4 mb-8">
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<nav class="flex justify-center space-x-6">
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<a href="/" class="text-gray-800 font-bold">Rankings</a>
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<a href="/parameters" class="text-blue-600 hover:text-blue-800 font-medium">Parameters</a>
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</nav>
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</div>
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<RankingContainer />
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</div>
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</body>

‎src/pages/parameters.astro‎

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---
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import "../styles/global.css";
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import logo from "../assets/images/nf-core-tfactivity_logo_light.png";
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import params from "../assets/params.json";
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// Type the params properly
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const typedParams = params as Record<string, Record<string, string | number>>;
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---
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<html lang="en">
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<head>
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<meta charset="utf-8" />
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<link rel="icon" type="image/svg+xml" href="/favicon.svg" />
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<meta name="viewport" content="width=device-width" />
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<meta name="generator" content={Astro.generator} />
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<title>Pipeline Parameters - nf-core/tfactivity report</title>
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</head>
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<body class="bg-gray-50">
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<div class="max-w-6xl mx-auto py-8 px-4">
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<div class="flex justify-center py-8">
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<img src={logo.src} alt="nf-core/tfactivity Pipeline Logo" class="h-40 w-auto" />
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</div>
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<!-- Navigation -->
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<div class="max-w-4xl mx-auto px-4 mb-8">
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<nav class="flex justify-center space-x-6">
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<a href="/" class="text-blue-600 hover:text-blue-800 font-medium">Rankings</a>
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<a href="/parameters" class="text-gray-800 font-bold">Parameters</a>
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</nav>
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</div>
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<div class="max-w-4xl mx-auto px-4 py-6">
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<h1 class="text-3xl font-bold text-gray-800 mb-6 text-center">Pipeline Parameters</h1>
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<p class="text-gray-600 text-center mb-8">
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Configuration parameters used for this nf-core/tfactivity pipeline run
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</p>
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<div class="space-y-8">
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{Object.entries(typedParams).map(([sectionName, sectionParams]) => (
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<div class="bg-white rounded-lg border border-gray-200 shadow-sm overflow-hidden">
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<div class="px-6 py-4 border-b border-gray-200 bg-gray-50">
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<h2 class="text-xl font-semibold text-gray-800">{sectionName}</h2>
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</div>
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<div class="px-6 py-4">
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<div class="space-y-3">
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{Object.entries(sectionParams).map(([paramKey, paramValue]) => (
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<div class="flex flex-col sm:flex-row sm:justify-between border-b border-gray-100 pb-3 last:border-b-0 last:pb-0">
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<dt class="font-medium text-gray-700 mb-1 sm:mb-0">{paramKey}</dt>
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<dd class="text-gray-900 font-mono text-sm break-all max-w-md">
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{typeof paramValue === 'string' && (paramValue.startsWith('http://') || paramValue.startsWith('https://')) ? (
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<a href={paramValue} target="_blank" rel="noopener noreferrer" class="text-blue-600 hover:text-blue-800 underline">
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{paramValue}
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</a>
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) : (
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String(paramValue)
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)}
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</dd>
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</div>
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))}
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</div>
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</div>
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</div>
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))}
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</div>
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<!-- Back to Rankings Button -->
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<div class="mt-12 text-center">
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<a
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href="/"
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class="inline-flex items-center px-6 py-3 border border-transparent text-base font-medium rounded-md text-white bg-blue-600 hover:bg-blue-700 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-blue-500 transition-colors duration-200"
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>
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<svg class="w-5 h-5 mr-2" fill="none" stroke="currentColor" viewBox="0 0 24 24">
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<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M10 19l-7-7m0 0l7-7m-7 7h18"></path>
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</svg>
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Back to Rankings
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</a>
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</div>
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</div>
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</div>
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</body>
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</html>
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<style>
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html {
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font-family: system-ui, sans-serif;
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}
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</style>

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