Nextflow Modules
Showing module(s) with keyword "preprocessing"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bbmap/repair | Process | paired reads re-pairing fastq preprocessing | Re-pairs reads that became disordered or had some mates eliminated. |
| nf-core/faa_seqfu_seqkit | Workflow | fasta protein preprocessing statistics quality check | Subworkflow that optionally preprocesses amino acid FASTA sequences (seqkit seq/replace/rmdup), computes sequence statistics before and after preprocessing using seqfu stats, and exports MultiQC-compatible statistics and software versions. |
| nf-core/fastq_preprocess_seqkit | Workflow | fastq seqkit preprocessing | Subworkflow that preprocesses FASTQ files |
| nf-core/fastq_sanitise_seqkit | Workflow | fastq quality control filtering malformed pairing seqkit preprocessing | Filters and reports malformed FASTQ sequences with seqkit/sana, and then pairs any paired-end files using seqkit/pair |
| 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/gens/preparecovandbaf | Process | gens preparecovandbaf preprocessing genomics CNV | Tools for preparing inputs for visualization in Gens |
| nf-core/leehom | Process | ancient DNA adapter removal clipping trimming merging collapsing preprocessing bayesian | Bayesian reconstruction of ancient DNA fragments |
| nf-core/pharmcat/vcfpreprocessor | Process | preprocessing vcf phamrcat | The PharmCAT VCF Preprocessor is a script that can pre-process VCF files for PharmCAT to make sure the VCF file complies with PharmCAT's VCF Requirements |
| nf-core/scanpy/filter | Process | filter quality-control scanpy single-cell preprocessing | Filter cells and genes in single-cell RNA-seq data using Scanpy |
| nf-core/sequali | Process | quality_control qc preprocessing | Sequence quality metrics for FASTQ and uBAM files. |
| nf-core/varlociraptor/preprocess | Process | observations variants preprocessing | Obtains per-sample observations for the actual calling process with varlociraptor calls |