Nextflow Modules
Showing module(s) with keyword "bclconvert"
| Module | Keywords | Description |
|---|---|---|
| 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/merge | illumina samplesheet merge bclconvert bcl2fastq genomics | Merge multiple per-project Illumina SampleSheet.csv files into one combined sheet. Detects index collisions, Hamming distance violations, and read-length mismatches across sheets. Mixed V1/V2 inputs are auto-converted to the target format. Exits 0 on clean merge, 1 if conflicts or warnings were found. |
| nf-core/samplesheetparser/split | illumina samplesheet split bclconvert bcl2fastq genomics | Split a combined Illumina SampleSheet.csv into one file per project or per lane. Header, reads, and settings are copied into every output file; only the sample rows are divided. Output filenames follow the pattern ``{prefix}{group}_SampleSheet.csv``. Exits 0 on success, 1 if warnings were produced. |
| 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. |