Nextflow Modules
Showing module(s) with keyword "count"
| Module | Keywords | Description |
|---|---|---|
| nf-core/allelecounter | allele count coverage | Generates a count of coverage of alleles |
| nf-core/cellrangerarc/count | align count reference | Module to use Cell Ranger's ARC pipelines analyze sequencing data produced from Chromium Single Cell ARC. Uses the cellranger-arc count command. |
| nf-core/cellrangeratac/count | align count reference | Module to use Cell Ranger's ATAC pipelines analyze sequencing data produced from Chromium Single Cell ATAC. |
| nf-core/cellranger/count | align count reference | Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression. |
| nf-core/fastk/fastk | k-mer count histogram | A fast K-mer counter for high-fidelity shotgun datasets |
| nf-core/htseq/count | htseq count gtf annotation | count how many reads map to each feature |
| nf-core/kallistobustools/count | scRNA-seq count single-cell kallisto bustools | quantifies scRNA-seq data from fastq files using kb-python. |
| nf-core/kallistobustools/ref | scRNA-seq count single-cell kallisto bustools index | index creation for kb count quantification of single-cell data. |
| nf-core/kat/hist | k-mer histogram count | Creates a histogram of the number of distinct k-mers having a given frequency. |
| nf-core/kmergenie | k-mer count genome assembly | KmerGenie estimates the best k-mer length for genome de novo assembly |
| nf-core/meryl/count | k-mer count reference-free | A genomic k-mer counter (and sequence utility) with nice features. |
| nf-core/spaceranger/count | align count spatial spaceranger imaging | Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data |
| nf-core/star/starsolo | align count genome reference | Create a counts matrix for single-cell data using STARSolo, handling cell barcodes and UMI information. |
| nf-core/universc | demultiplex align single-cell scRNA-Seq count umi | Module to run UniverSC an open-source pipeline to demultiplex and process single-cell RNA-Seq data |
| nf-core/velocyto | count rnaseq rna velocity bam | Velocyto is a library for the analysis of RNA velocity. velocyto.py CLI use `Path(resolve_path=True)` and breaks the nextflow logic of symbolic links. If in the work dir velocyto find a file named EXACTLY `cellsorted_[ORIGINAL_BAM_NAME]` it will skip the samtools sort step. Cellsorted bam file should be cell sorted with: ```bash samtools sort -t CB -O BAM -o cellsorted_input.bam input.bam ``` See module test for an example with the SAMTOOLS_SORT nf-core module. Config example to cellsort input bam using SAMTOOLS_SORT: ```groovy withName: SAMTOOLS_SORT { ext.prefix = { "cellsorted_${bam.baseName}" } ext.args = '-t CB -O BAM' } ``` Optional mask must be passed with `ext.args` and option `--mask` This is why I need to stage in the work dir 2 bam files (cellsorted and original). See also [velocyto tutorial](https://velocyto.org/velocyto.py/tutorial/cli.html#notes-on-first-runtime-and-parallelization) |
| nf-core/yak/count | kmer fastq sequence count assembly | a tool to build k-mer hash table for fasta and fastq files |