nextflow-development
Audited by Runlayer on Feb 23, 2026
Malicious tool definition detected
Tool: LICENSE.txt [1/2] Description: Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1.
Tool: LICENSE.txt [2/2] Description: this License.
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Tool: SKILL.md [1/2] Description: --- name: nextflow-development description: Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data.
Tool: SKILL.md [2/2] Description: nf-core community.
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Tool: references/geo-sra-acquisition.md [1/2] Description: # GEO/SRA Data Acquisition Download raw sequencing data from NCBI GEO/SRA and prepare it for nf-core pipelines. **Use this when:** Reanalyzing published datasets, validating findings, or comparing results against public cohorts.
Tool: references/geo-sra-acquisition.md [2/2] Description: ChIP-seq | nf-core/chipseq | Manual | | Bisulfite-Seq | nf-core/methylseq | Manual | | miRNA-Seq | nf-core/smrnaseq | Manual | | Amplicon | nf-core/ampliseq | Manual | --- ## Supported Organisms Common organisms with auto-suggested genomes: | Organism | Genome | Notes | |----------|--------|-------| | Homo sapiens | GRCh38 | Human reference | | Mus musculus | GRCm39 | Mouse reference | | Saccharomyces cerevisiae | R64-1-1 | Yeast S288C |
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Tool: references/installation.md Description: # Installation ## Contents - [Quick install](#quick-install) - [Docker setup](#docker-setup) - [Singularity setup (HPC)](#singularity-setup-hpc) - [nf-core tools (optional)](#nf-core-tools-optional) - [Verify installation](#verify-installation) - [Common issues](#common-issues) ## Quick install ```bash # Nextflow curl -s https://get.nextflow.io | bash mv nextflow ~/bin/ export PATH="$HOME/bin:$PATH" # Verify nextflow -version java -version # Require
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Tool: references/pipelines/atacseq.md Description: # nf-core/atacseq **Version:** 2.1.2 **Official Documentation:** https://nf-co.re/atacseq/2.1.2/ **GitHub:** https://github.com/nf-core/atacseq > **Note:** When updating to a new version, check the [releases page](https://github.com/nf-core/atacseq/releases) for breaking changes and update the version in commands below.
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Tool: references/pipelines/rnaseq.md Description: # nf-core/rnaseq **Version:** 3.22.2 **Official Documentation:** https://nf-co.re/rnaseq/3.22.2/ **GitHub:** https://github.com/nf-core/rnaseq > **Note:** When updating to a new version, check the [releases page](https://github.com/nf-core/rnaseq/releases) for breaking changes and update the version in commands below.
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Tool: references/pipelines/sarek.md Description: # nf-core/sarek **Version:** 3.7.1 **Official Documentation:** https://nf-co.re/sarek/3.7.1/ **GitHub:** https://github.com/nf-core/sarek > **Note:** When updating to a new version, check the [releases page](https://github.com/nf-core/sarek/releases) for breaking changes and update the version in commands below.
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Tool: references/troubleshooting.md Description: # Troubleshooting Quick fixes for common nf-core pipeline issues.
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Tool: scripts/check_environment.py [1/2] Description: #!/usr/bin/env python3 """ Pre-flight environment validation for nf-core pipelines.
Tool: scripts/check_environment.py [2/2] Description: = "\033[92m[PASS]\033[0m" if check.passed else "\033[91m[FAIL]\033[0m" print(f"{status} {check.name}: {check.message}") if check.details: print(f" {check.details}") if not check.passed and check.fix: print(f" \033[93mFix:\033[0m {check.fix}") elif check.passed and check.fix: # Warning print(f" \033[93mWarning:\033[0m {check.fix}") print() if report.ready: print("\033[92m✓ Environment is READY for nf-core pipelines.\033[0m") else: print("\033[
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Tool: scripts/config/genomes.yaml Description: # Organism to Genome Mapping for nf-core Pipelines # Maps organism names (as they appear in GEO/SRA) to iGenomes keys organisms: # Human "Homo sapiens": genome: "GRCh38" taxid: 9606 aliases: ["human", "hg38", "GRCh38"] notes: "Primary human reference genome" "Homo sapiens (legacy)": genome: "GRCh37" taxid: 9606 aliases: ["hg19", "GRCh37"] notes: "Legacy human reference, still used for some clinical data" # Mouse "Mus musculus": genome: "GRCm39" taxi
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Tool: scripts/config/pipelines/atacseq.yaml Description: name: atacseq version: "2.1.2" description: "Chromatin accessibility analysis and peak calling" # Documentation and source - NOTE: Update version in URLs when upgrading pipeline urls: documentation: "https://nf-co.re/atacseq/{version}/" parameters: "https://nf-co.re/atacseq/{version}/parameters/" output_docs: "https://nf-co.re/atacseq/{version}/docs/output/" github: "https://github.com/nf-core/atacseq" releases: "https://github.com/nf-core
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Tool: scripts/config/pipelines/rnaseq.yaml Description: name: rnaseq version: "3.22.2" description: "Gene expression quantification and differential expression analysis" # Documentation and source - NOTE: Update version in URLs when upgrading pipeline urls: documentation: "https://nf-co.re/rnaseq/{version}/" parameters: "https://nf-co.re/rnaseq/{version}/parameters/" output_docs: "https://nf-co.re/rnaseq/{version}/docs/output/" github: "https://github.com/nf-core/rnaseq" releases: "https://githu
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Tool: scripts/config/pipelines/sarek.yaml Description: name: sarek version: "3.7.1" description: "Variant calling for WGS/WES data (germline and somatic)" # Documentation and source - NOTE: Update version in URLs when upgrading pipeline urls: documentation: "https://nf-co.re/sarek/{version}/" parameters: "https://nf-co.re/sarek/{version}/parameters/" output_docs: "https://nf-co.re/sarek/{version}/docs/output/" github: "https://github.com/nf-core/sarek" releases: "https://github.com/nf-core/sarek
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Tool: scripts/detect_data_type.py Description: #!/usr/bin/env python3 """ Auto-detect appropriate nf-core pipeline from data directory.
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Tool: scripts/generate_samplesheet.py [1/2] Description: #!/usr/bin/env python3 """ Enhanced nf-core samplesheet generator.
Tool: scripts/generate_samplesheet.py [2/2] Description: Dict, output_path: str): """Write samplesheet to CSV file.""" columns = config.get("samplesheet", {}).get("columns", []) column_names = [c['name'] for c in columns] # Filter to columns that have data active_columns = [c for c in column_names if any(c in row and row[c] for row in rows)] # Ensure fastq_1/fastq_2 or bam/bai are included for required in ['fastq_1', 'bam']: if required in column_names and required not in active_columns: if any(
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Tool: scripts/manage_genomes.py [1/2] Description: #!/usr/bin/env python3 """ Genome reference management for nf-core pipelines.
Tool: scripts/manage_genomes.py [2/2]
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Tool: scripts/sra_geo_fetch.py [1/3] Description: #!/usr/bin/env python3 """ GEO/SRA Data Fetcher ==================== Download raw sequencing data from NCBI GEO/SRA and prepare for nf-core pipelines.
Tool: scripts/sra_geo_fetch.py [2/3] Description: # Already exists success = download_file(url, output_path, timeout=timeout, show_progress=False) return filename, success def interactive_select_group(groups: Dict[str, Dict]) -> Optional[str]: """Interactively select a sample group.""" if len(groups) <= 1: return None # No selection needed print(" " + "=" * 60) print(" SELECT SAMPLE GROUP TO DOWNLOAD") print("=" * 60) sorted_groups = sorted(groups.items(), key=lambda x: -x[1]['count']) for i, (k
Tool: scripts/sra_geo_fetch.py [3/3]
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Tool: scripts/utils/__init__.py Description: """ Utility modules for nf-core pipeline deployment.
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Tool: scripts/utils/file_discovery.py Description: """ File discovery utilities for FASTQ, BAM, and CRAM files.
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Tool: scripts/utils/ncbi_utils.py [1/3] Description: #!/usr/bin/env python3 """ NCBI Utilities for GEO/SRA Data Access ====================================== Shared utilities for fetching metadata and downloading data from NCBI services.
Tool: scripts/utils/ncbi_utils.py [2/3] Description: URLs are semicolon-separated, convert to HTTP URLs # ENA supports both FTP and HTTP, HTTP is easier with requests urls = [f"http://{url}" for url in ftp_urls.split(';') if url] fastq_urls[srr] = urls return fastq_urls except Exception as e: logger.error(f"Error fetching ENA URLs for {study_accession}: {e}") return fastq_urls def download_file(url: str, output_path: Path, timeout: int = 300, show_progress: bool = True) -> bool: """ Download a f
Tool: scripts/utils/ncbi_utils.py [3/3] Description: if len(fields) < len(header): continue def get_field(name, default=''): idx = col_map.get(name, -1) return fields[idx] if idx >= 0 and idx < len(fields) else default run = { 'srr': get_field('Run'), 'srx': get_field('Experiment'), 'gsm': get_field('SampleName'), # Often GSM ID 'sample_name': get_field('SampleName'), 'library_name': get_field('LibraryName'), 'layout': get_field('LibraryLayout', 'UNKNOWN').upper(), 'library_strategy': get_field(
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Tool: scripts/utils/sample_inference.py Description: """ Sample name and metadata inference from filenames.
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Tool: scripts/utils/validators.py Description: """ Samplesheet validation utilities.