Nextflow Modules
Showing module(s) with keyword "illumina"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/artic/aligntrim | Process | artic primer trimming amplicon genomics sequencing nanopore illumina | Standalone version of fieldbioinformatics aligntrim. Soft clips amplicon scheme primer sites in BAM/SAM files. |
| nf-core/art/illumina | Process | fastq fasta illumina simulate | Simulation tool to generate synthetic Illumina next-generation sequencing reads |
| nf-core/bcl2fastq | Process | demultiplex illumina fastq | Demultiplex Illumina BCL files |
| nf-core/bclconvert | Process | demultiplex illumina fastq | Demultiplex Illumina BCL files |
| nf-core/cellrangerarc/mkfastq | Process | reference mkfastq fastq illumina bcl2fastq | Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkfastq command. |
| nf-core/cellrangeratac/mkfastq | Process | reference mkfastq fastq illumina bcl2fastq | Module to create fastqs needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkfastq command. |
| nf-core/cellranger/mkfastq | Process | reference mkfastq fastq illumina bcl2fastq | Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command. |
| nf-core/fastq_shortreads_preprocess_qc | Workflow | fastq illumina short reads qc stats preprocessing barcoding adapters merge complexity deduplication host decontamination | Quality check and preprocessing subworkflow of Illumina short reads that can do: quality check of input reads and generate statistics, preprocess and validate reads, barcode removal, remove adapters and merge reads, filter by sequence complexity, deduplicate reads, remove host contamination, concatenate reads and generate statistics for post-processing reads. WARNING: requires at least the process configurations from the nextflow.config to be added to the modules.config in the pipeline in order to work as intended. |
| nf-core/getorganelle/fromreads | Process | assembly organelle mitochondria illumina | Assembles organelle genomes from genomic data |
| nf-core/hypo | Process | assembly polishing nanopore illumina | Assembly polisher using short (and long) reads |
| nf-core/samplesheetparser/diff | Process | 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 | 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. |
| nf-core/samplesheetparser/merge | Process | 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 | Process | 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 | Process | illumina samplesheet validation |