Nextflow Modules
Showing module(s) with keyword "sort"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_sort_stats_samtools | Workflow | sort bam sam cram | Sort SAM/BAM/CRAM file |
| nf-core/bam_variant_calling_sort_freebayes_bcftools | Workflow | variant sort index bam cram vcf | Call variants using freebayes, then sort and index |
| nf-core/bedtools/sort | Process | bed sort bedtools chromosome | Sorts a feature file by chromosome and other criteria. |
| nf-core/biobambam/bamsormadup | Process | markduplicates sort bam cram | Parallel sorting and duplicate marking |
| nf-core/clame | Process | sort genomics binning metagenomics | binning of metagenomic sequences |
| nf-core/crisprcleanr/normalize | Process | sort CNV correction CRISPR | remove false positives of functional crispr genomics due to CNVs |
| nf-core/csvtk/sort | Process | sort tsv csv | Sort CSV (or TSV) tables |
| nf-core/duphold | Process | sort duphold structural variation depth information | SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content. |
| nf-core/elprep/filter | Process | sort bam sam filter variant calling | Filter, sort and markdup sam/bam files, with optional BQSR and variant calling. |
| nf-core/fastq_align_dna | Workflow | fastq bam sort bwamem bwamem2 dragmap snapaligner strobealign | Align fastq files to a reference genome |
| nf-core/fastq_align_hisat2 | Workflow | align sort rnaseq genome fastq bam sam cram | Align reads to a reference genome using hisat2 then sort with samtools |
| nf-core/fastq_align_mapad | Workflow | sort fastq bam mapad align map | Align FASTQ files against reference genome with the mapAD aDNA short-read aligner producing a sorted and indexed BAM files |
| nf-core/fgbio/sortbam | Process | sort bam sam | Sorts a SAM or BAM file. Several sort orders are available, including coordinate, queryname, random, and randomquery. |
| nf-core/fgumi/merge | Process | merge bam alignment sort | Merge pre-sorted BAM files into a single sorted BAM |
| nf-core/fgumi/sort | Process | sort bam sam | Sorts a SAM or BAM file. Several sort orders are available, including coordinate, queryname, and template-coordinate. This is a high-performance replacement for fgbio SortBam. |
| nf-core/finaletoolkit/fraglengthbins | Process | sort genomics fragmentomics | Generate a binned fragment profile and a fragment distribution histogram |
| nf-core/flash | Process | sort reads merging merge mate pairs | Perform merging of mate paired-end sequencing reads |
| nf-core/fusionreport/detect | Process | sort RNA-seq fusion report detect | fusionreport_detect |
| nf-core/fusionreport/download | Process | sort RNA-seq fusion_report download | Build DB for fusionreport |
| nf-core/gappa/examinegraft | Process | sort graft phylogeny | Grafts query sequences from phylogenetic placement on the reference tree |