Nextflow Modules
Showing 2,051 module(s)
| Module | Keywords | Description |
|---|---|---|
| nf-core/agat/spfilterbyorfsize | genomics GFF/GTF filter annotation | The script reads a gff annotation file, and create two output files, one contains the gene models with ORF passing the test, the other contains the rest. By default the test is "> 100" that means all gene models that have ORF longer than 100 Amino acids, will pass the test. |
| nf-core/agat/spfilterfeaturefromkilllist | 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 | 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 | gff gtf filter isoform gene longest agat | Filters GFF records to keep only the longest isoform per gene |
| nf-core/agat/spmergeannotations | 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 | genome gff gtf statistics | Provides different type of statistics in text format from a GFF/GTF annotation file |
| nf-core/agat/sqstatbasic | genome gff gtf statistics | Provides basic statistics in text format from a GFF/GTF annotation file |
| nf-core/agrvate | fasta virulence Staphylococcus aureus | Rapid identification of Staphylococcus aureus agr locus type and agr operon variants |
| nf-core/ale | reference-independent assembly evaluation | ALE: assembly likelihood estimator. |
| nf-core/alignoth | genomics alignment visualization pileup plotting | Creating alignment plots from bam files |
| nf-core/allelecounter | allele count coverage | Generates a count of coverage of alleles |
| nf-core/ampcombi | antimicrobial peptides amps parsing reporting align macrel amplify hmmsearch neubi ampir DRAMP | A tool to parse and summarise results from antimicrobial peptides tools and present functional classification. |
| nf-core/ampcombi2/cluster | antimicrobial peptides amps parsing reporting align clustering mmseqs2 | A submodule that clusters the merged AMP hits generated from ampcombi2/parsetables and ampcombi2/complete using MMseqs2 cluster. |
| nf-core/ampcombi2/complete | antimicrobial peptides amps parsing reporting align macrel amplify hmmsearch neubi ampir ampgram amptransformer DRAMP | A submodule that merges all output summary tables from ampcombi/parsetables in one summary file. |
| nf-core/ampcombi2/parsetables | antimicrobial peptides amps parsing reporting align macrel amplify hmmsearch neubi ampir ampgram amptransformer DRAMP MMseqs2 InterProScan | A submodule that parses and standardizes the results from various antimicrobial peptide identification tools. |
| nf-core/ampir | ampir |