Nextflow Modules
Showing module(s) with keyword "filter"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/agat/spfilterbyorfsize | Process | 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/spkeeplongestisoform | Process | gff gtf filter isoform gene longest agat | Filters GFF records to keep only the longest isoform per gene |
| 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/bamcmp | Process | filter xenograft host graft contamination mouse | Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX). |
| nf-core/bbmap/filterbyname | Process | fastq fasta filter | Filter out sequences by sequence header name(s) |
| nf-core/biscuit/bsconv | Process | biscuit DNA methylation WGBS scWGBS bisulfite sequencing aligner bam filter | Summarize and/or filter reads based on bisulfite conversion rate |
| nf-core/chopper | Process | filter trimming fastq nanopore qc chopper pigz multi-tool | Filter and trim long read data. |
| nf-core/cleanifier/filter | Process | contamination removal metagenomics microbiome filter | Fast, lightweight contamination removal from microbiome data (FASTQ) using a probabilistic Cuckoo filter or Cuckoo hash table index |
| nf-core/custom/filterdifferentialtable | Process | filter differential expression logFC significance statistic p-value | Filters a differential expression table based on logFC and adjusted p-value thresholds |
| 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/matrixfilter | Process | matrix filter abundance na | filter a matrix based on a minimum value and numbers of samples that must pass. |
| nf-core/deacon/filter | Process | filter index fasta fastq genome reference minimizer decontamination | Filter DNA sequences using index of reference genome |
| nf-core/deeptools/alignmentsieve | Process | ATACseq filter shift ATACshift | This tool filters alignments in a BAM/CRAM file according the the specified parameters. |
| nf-core/dshbio/filterbed | Process | bed filter feature | Filter features in gzipped BED format |
| nf-core/dshbio/filtergff3 | Process | gff3 filter feature | Filter features in gzipped GFF3 format |
| nf-core/echtvar/anno | Process | echtvar vcf annotate filter genomics | Annotate a decomposed (and normalized) VCF with an echtvar file |
| nf-core/elprep/filter | Process | sort bam sam filter |