Nextflow Modules
Showing module(s) with keyword "decontamination"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/deacon/filter | Process | filter index fasta fastq genome reference minimizer decontamination | Filter DNA sequences using index of reference genome |
| nf-core/deacon/index | Process | index fasta genome reference minimizer decontamination | Create deacon index for reference genome |
| nf-core/deacon/indexdiff | Process | index fasta genome reference minimizer decontamination | Subtract minimizers in deacon index (or fasta file) from another index (A - B) |
| nf-core/deacon/indexintersect | Process | index fasta genome reference minimizer decontamination | Intersect multiple deacon indexes (A ∩ B ...) |
| nf-core/deacon/indexunion | Process | index fasta genome reference minimizer decontamination | Combine multiple deacon indexes (A ∪ B ...) |
| nf-core/fastq_decontaminate_deacon_hostile | Workflow | hostile deacon filter index fasta fastq genome reference minimizer decontamination | Decontaminate FastQ files by filtering reads that match a reference genome using Deacon or Hostile |
| nf-core/fastq_fetch_clean_hostile | Workflow | hostile decontamination human removal download host removal clean | Downloads required reference genomes for hostile and removes host reads from short-read FASTQ sequencing files |
| nf-core/fastq_index_filter_deacon | Workflow | filter index fasta fastq genome reference minimizer decontamination | Decontaminate FastQ files by filtering reads that match a reference genome using Deacon |
| 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/hostile/clean | Process | hostile decontamination human removal host removal clean | Removes host reads from short- and long-read FASTQ sequencing files |
| nf-core/hostile/fetch | Process | hostile decontamination human removal download | Downloads required reference genomes for Hostile |