Nextflow Modules
Showing module(s) with keyword "bed"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/agat/convertbed2gff | Process | genome bed gff conversion | Takes a bed12 file and converts to a GFF3 file |
| nf-core/agat/convertgff2bed | Process | genome bed gff conversion | Takes a GFF3 file and converts to a bed12 file |
| nf-core/annotsv/annotsv | Process | annotation structural variants vcf bed tsv | Annotation and Ranking of Structural Variation |
| nf-core/bam_cnv_wisecondorx | Workflow | cnv bam bed cram plots genomics | A subworkflow for calling CNVs using WisecondorX |
| nf-core/bamtools/convert | Process | bamtools bamtools/convert bam convert bed fasta fastq json pileup sam yaml | BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. |
| nf-core/bedgovcf | Process | bed vcf conversion variants | Convert a BED file to a VCF file according to a YAML config |
| nf-core/bedops/convert2bed | Process | convert bed genomics | Convert BAM/GFF/GTF/GVF/PSL files to bed |
| nf-core/bedops/gtf2bed | Process | gtf bed conversion | Convert gtf format to bed format |
| 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/getfasta | Process | bed fasta getfasta | extract sequences in a FASTA file based on intervals defined in a feature file. |
| 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/intersect | Process | bed intersect overlap | Allows one to screen for overlaps between two sets of genomic features. |
| nf-core/bedtools/jaccard | Process |