Nextflow Modules
Showing module(s) with keyword "filter"
| 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/spkeeplongestisoform | gff gtf filter isoform gene longest agat | Filters GFF records to keep only the longest isoform per gene |
| nf-core/bamcmp | 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 | fastq fasta filter | Filter out sequences by sequence header name(s) |
| nf-core/biscuit/bsconv | biscuit DNA methylation WGBS scWGBS bisulfite sequencing aligner bam filter | Summarize and/or filter reads based on bisulfite conversion rate |
| nf-core/chopper | filter trimming fastq nanopore qc | Filter and trim long read data. |
| nf-core/custom/filterdifferentialtable | 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 | 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 | matrix filter abundance na | filter a matrix based on a minimum value and numbers of samples that must pass. |
| nf-core/deacon/filter | filter index fasta fastq genome reference minimizer decontamination | Filter DNA sequences using index of reference genome |
| nf-core/deeptools/alignmentsieve | ATACseq filter shift ATACshift | This tool filters alignments in a BAM/CRAM file according the the specified parameters. |
| nf-core/dshbio/filterbed | bed filter feature | Filter features in gzipped BED format |
| nf-core/dshbio/filtergff3 | gff3 filter feature | Filter features in gzipped GFF3 format |
| nf-core/elprep/filter | sort bam sam filter variant calling | Filter, sort and markdup sam/bam files, with optional BQSR and variant calling. |
| nf-core/ensemblvep/filtervep | annotation vcf tab filter | Filter variants based on Ensembl Variant Effect Predictor (VEP) annotations. |
| nf-core/evigene/tr2aacds | genomics transcript assembly clean polish filter redundant duplicate | Uses evigene/scripts/prot/tr2aacds.pl to filter a transcript assembly |
| nf-core/fgbio/filterconsensusreads | fgbio filter consensus umi duplexumi | Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads. |
| nf-core/gatk4/filtermutectcalls | filtermutectcalls filter gatk4 mutect2 vcf | Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering. |
| nf-core/gatk4/variantfiltration |