Fetch sequencing metadata and FastQ files from accession lists.
npx skills add https://github.com/danilomonge/nf-claw --skill fetchngs
Please help me install this Agent Skill. Skill: fetchngs Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/fetchngs Command: npx skills add https://github.com/danilomonge/nf-claw --skill fetchngs
fetchngs removes the manual overhead of turning public sequencing accessions into downloadable metadata and raw FastQ files, while keeping runs reproducible and schema-validated.
Ask the fetchngs skill to process your accession list into an output directory using the desired profile, and specify a pipeline version only when you need a non-latest release.
High-intent search queries and answers about installing and using this skill.
You can bulk download FASTQ files from SRA, ENA, DDBJ, and GEO by supplying a validated input accession list and an output directory, which automatically retrieves raw data and associated metadata.
Yes, you can generate a samplesheet for nf-core pipelines from public sequencing data. The skill creates optional samplesheets during the retrieval process to prepare outputs for downstream nf-core analysis workflows.
Yes, fetchngs supports ENA and DDBJ database identifiers for raw data retrieval. It processes SRA, ENA, DDBJ, and GEO accession numbers from your input list to fetch the corresponding FastQ files and metadata.
To pin an nf-core pipeline version for reproducible sequencing downloads, you specify the desired pipeline release version when initiating the run. This applies Nextflow-aware version control and records run provenance with schema-checked parameters.
The best way to retrieve public sequencing metadata with provenance tracking is using a schema-validated pipeline that pins Nextflow versions and records run logs. This approach removes manual overhead while keeping runs fully reproducible.
Yes, you need a validated input file containing the accession numbers to fetch raw FastQ data. The input list is processed alongside a specified output directory to properly retrieve and organize the sequencing files and metadata.
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