Nextflow Modules
Showing module(s) with keyword "metadata"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| cellgeni/fetch10xmeta | Process | metadata GEO SRA ENA ArrayExpress BioProject 10x single-cell public data | Fetches and parses metadata for public 10x datasets from GEO (GSE*), ArrayExpress (E-MTAB*), or BioProject (PRJ*). Downloads raw metadata from SRA/ENA/BioStudies, resolves sample-to-run mappings, classifies each run by download type, and produces a merged links file. |
| cellgeni/irods/getmetadata | Process | irods metadata csv | Module to get metadata from an iRODS collections and data objects and output as CSV |
| nf-core/bftools/showinf | Process | metadata ome-tif ome-tiff imaging bioinformatics tools | Extract OME xml data from OME-tif |
| nf-core/blobtk/create | Process | blobdir btk blobtoolkit metadata | Creates a minimal blobdir. |
| nf-core/entrezdirect/esummary | Process | public datasets ncbi entrez metadata query database | Queries an NCBI database using Unique Identifier(s) |
| nf-core/ffq | Process | SRA ENA GEO metadata fetch public databases | A command line tool that makes it easier to find sequencing data from the SRA / GEO / ENA. |
| nf-core/parsesdrf/convert | Process | sdrf sdrf-pipelines samplesheet proteomics immunopeptidomics mhcquant openms maxquant msstats normalyzerde diann metadata | Convert an SDRF (Sample and Data Relationship Format) file into a pipeline-specific samplesheet/configuration using the `parse_sdrf convert-<format>` subcommands of the sdrf-pipelines package. The chosen `format` selects the subcommand; the module owns the output filenames and emits one tuple per supported format (mhcquant, openms, maxquant, msstats, normalyzerde, diann). |
| nf-core/pridepy/fetchsdrf | Process | pride sdrf proteomics download metadata | Fetch an SDRF file from the PRIDE Archive for a given project accession. |
| nf-core/samplesheetparser/info | Process | illumina samplesheet metadata bclconvert bcl2fastq genomics | Display a structured JSON summary of an Illumina SampleSheet.csv (V1 or V2) including format version, sample count, lanes, index type, read lengths, adapter sequences, experiment name, and instrument platform. Useful for logging run metadata or conditional branching in pipelines. |