Nextflow Modules
Showing module(s) with keyword "bedtools"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bed_scatter_bedtools | Workflow | bed scatter bedtools | Scatters inputted BED files by the amount specified. The configuration in nextflow.config should be added to your modules.config for the subworkflow to work. |
| nf-core/bedtools/bamtobed | Process | bam bed bedtools bamtobed converter | Converts a bam file to a bed12 file. |
| nf-core/bedtools/closest | Process | bedtools closest bed vcf gff | For each feature in A, finds the closest feature (upstream or downstream) in B. |
| nf-core/bedtools/complement | Process | bed gff vcf complement bedtools intervals | Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file. |
| nf-core/bedtools/coverage | Process | bedtools coverage bam bed gff vcf histogram | computes both the depth and breadth of coverage of features in file B on the features in file A |
| nf-core/bedtools/flank | Process | bed flankBed bedtools | Creates two new flanking intervals for each interval in a BED/GFF/VCF file. |
| nf-core/bedtools/genomecov | Process | bed bam genomecov bedtools histogram | Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. |
| nf-core/bedtools/groupby | Process | bed groupby bedtools | Groups features in a BED file by given column(s) and computes summary statistics for each group to another column. |
| nf-core/bedtools/map | Process | bed vcf gff map bedtools | Allows one to screen for overlaps between two sets of genomic features. |
| nf-core/bedtools/merge | Process | bed merge bedtools overlapped bed | combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features. |
| nf-core/bedtools/multiinter | Process | bedtools multinterval bed vcf gff | Identifies common intervals among multiple (and subsets thereof) sorted BED/GFF/VCF files. |
| nf-core/bedtools/nuc | Process | bed nucBed bedtools GC content AT content nucleotide content intervals | Profiles the nucleotide content of intervals in a fasta file. |
| nf-core/bedtools/slop | Process | bed slopBed bedtools | Adds a specified number of bases in each direction (unique values may be specified for either -l or -r) |
| nf-core/bedtools/sort | Process | bed sort bedtools chromosome | Sorts a feature file by chromosome and other criteria. |
| nf-core/bedtools/split | Process | bedtools split bed | Split BED files into several smaller BED files |