Nextflow Modules
Showing module(s) with keyword "gff"
| 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/agat/convertspgff2gtf | Process | genome gff gtf conversion | Converts a GFF/GTF file into a proper GTF file |
| nf-core/agat/convertspgff2tsv | Process | genome gff gtf conversion tsv | Converts a GFF/GTF file into a TSV file |
| nf-core/agat/convertspgxf2gxf | Process | genome gff gtf conversion | Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file |
| nf-core/agat/spaddintrons | Process | gtf gff introns | Add intron features to gtf/gff file without intron features. |
| nf-core/agat/spextractsequences | Process | genomics gff extract fasta sequence feature | This script extracts sequences in fasta format according to features described in a gff file. |
| nf-core/agat/spfilterfeaturefromkilllist | Process | genomics gff remove feature | The script aims to remove features based on a kill list. The default behaviour is to look at the features's ID. If the feature has an ID (case insensitive) listed among the kill list it will be removed. /!\ Removing a level1 or level2 feature will automatically remove all linked subfeatures, and removing all children of a feature will automatically remove this feature too. |
| nf-core/agat/spflagshortintrons | Process | genomics gtf gff intron short annotation | The script flags the short introns with the attribute <pseudo>. Is is usefull to avoid ERROR when submiting the data to EBI. (Typical EBI error message: ********ERROR: Intron usually expected to be at least 10 nt long. Please check the accuracy) |
| nf-core/agat/spkeeplongestisoform | Process | gff gtf filter isoform gene longest agat | Filters GFF records to keep only the longest isoform per gene |
| nf-core/agat/spmergeannotations | Process | genomics gff merge combine | This script merge different gff annotation files in one. It uses the AGAT parser that takes care of duplicated names and fixes other oddities met in those files. |
| nf-core/agat/spstatistics | Process | genome gff gtf statistics | Provides different type of statistics in text format from a GFF/GTF annotation file |
| nf-core/agat/sqstatbasic | Process | genome gff gtf statistics | Provides basic statistics in text format from a GFF/GTF annotation file |
| nf-core/bcftools/csq | Process | annotation gff gff3 protein functional vcf bcf bcftools | bcftools Haplotype-aware consequence caller |
| 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 |