Nextflow Modules
Showing module(s) with keyword "samplesheet"
| Module | Keywords | Description |
|---|---|---|
| nf-core/eido/convert | eido convert PEP format samplesheet | Convert any PEP project or Nextflow samplesheet to any format |
| nf-core/parsesdrf/convert | 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/samplesheetparser/diff | illumina samplesheet diff comparison bclconvert bcl2fastq genomics | Compare two Illumina SampleSheet.csv files (any combination of V1 and V2) and emit a structured JSON diff covering header changes, added/removed samples, and per-sample field changes. Exits 0 if identical, 1 if differences are detected — useful as a CI pre-run guard. |
| nf-core/samplesheetparser/info | 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. |
| nf-core/samplesheetparser/validate | illumina samplesheet validation demultiplexing bclconvert bcl2fastq genomics | Validate an Illumina SampleSheet.csv (V1 or V2) for index, adapter, and structural issues. Format is auto-detected. Exits 0 if valid, 1 if errors are found — causing the pipeline to fail early with a clear message rather than discovering demultiplexing problems downstream. |
| nf-core/samshee | samplesheet illumina bclconvert bcl2fastq | Module to validate illumina® Sample Sheet v2 files. |