Nextflow Modules
Showing module(s) with keyword "gtf"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| 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/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/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/arcane/filter | Process | single-cell rnaseq filter gtf fasta transcriptomics | Filter GTF annotations and genome sequence for alignment-free single-cell RNA-seq quantification with Arcane |
| nf-core/atlasgeneannotationmanipulation/gtf2featureannotation | Process | gtf gene annotation | Generate tables of feature metadata from GTF files |
| nf-core/bam_stringtie_merge | Workflow | rna-seq transcript-assembly transcript-merge stringtie gtf | Assemble transcripts from sorted BAM alignments using StringTie, then merge per-sample transcript GTFs into a unified annotation. |
| nf-core/bedops/gtf2bed | Process | gtf bed conversion | Convert gtf format to bed format |
| nf-core/braker3 | Process | genome annotation braker gff gtf | Gene prediction in novel genomes using RNA-seq and protein homology information |
| nf-core/custom/catadditionalfasta | Process | fasta gtf genomics | Custom module to Add a new fasta file to an old one and update an associated GTF |
| nf-core/custom/gtffilter | Process | gtf fasta filter | Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file |
| nf-core/custom/tx2gene | Process | gene gtf pseudoalignment rsem transcript | Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications. |
| nf-core/dexseq/prepareannotation | Process | dexseq exon annotation gtf alternative splicing differential exon usage | Flatten a GTF annotation into the exonic counting bins used by DEXSeq |
| nf-core/eautils/gtf2bed | Process | gtf gff bed bed12 annotation conversion | Convert a GTF/GFF annotation file to BED12 format |