Nextflow Modules
Showing module(s) with keyword "illumina"
| Module | Keywords | Description |
|---|---|---|
| nf-core/artic/aligntrim | 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 | fastq fasta illumina simulate | Simulation tool to generate synthetic Illumina next-generation sequencing reads |
| nf-core/bcl2fastq | demultiplex illumina fastq | Demultiplex Illumina BCL files |
| nf-core/bclconvert | demultiplex illumina fastq | Demultiplex Illumina BCL files |
| nf-core/cellrangerarc/mkfastq | 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 | 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 | reference mkfastq fastq illumina bcl2fastq | Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command. |
| nf-core/getorganelle/fromreads | assembly organelle mitochondria illumina | Assembles organelle genomes from genomic data |
| nf-core/hypo | assembly polishing nanopore illumina | Assembly polisher using short (and long) reads |
| 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. |
| nf-core/shovill | bacterial assembly illumina | Assemble bacterial isolate genomes from Illumina paired-end reads |
| nf-core/srst2/srst2 | mlst typing illumina | Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. |