Available Modules

Modules are the building stones of all DSL2 nf-core blocks. You can find more info from nf-core website, if you would like to write your own module.

  • bam 170
  • fasta 166
  • vcf 120
  • fastq 117
  • genomics 114
  • metagenomics 79
  • genome 71
  • index 70
  • reference 65
  • alignment 62
  • gatk4 61
  • bed 60
  • assembly 59
  • cram 56
  • sam 49
  • sort 48
  • variant calling 38
  • annotation 38
  • structural variants 38
  • align 37
  • database 34
  • merge 32
  • filter 31
  • gff 28
  • bacteria 28
  • map 28
  • statistics 27
  • coverage 26
  • variants 24
  • qc 23
  • quality control 22
  • gtf 21
  • classify 21
  • nanopore 20
  • download 20
  • cnv 20
  • taxonomic profiling 18
  • k-mer 18
  • gfa 18
  • variant 18
  • split 18
  • contamination 18
  • pacbio 17
  • sentieon 17
  • classification 16
  • taxonomy 16
  • MSA 16
  • binning 15
  • somatic 15
  • count 15
  • quality 15
  • convert 15
  • clustering 14
  • ancient DNA 14
  • copy number 14
  • proteomics 14
  • VCF 14
  • contigs 13
  • phylogeny 13
  • single-cell 13
  • imputation 13
  • bedtools 13
  • conversion 13
  • graph 12
  • gvcf 12
  • bisulfite 12
  • sv 12
  • trimming 12
  • reporting 12
  • isoseq 12
  • variation graph 12
  • bcftools 12
  • methylseq 11
  • picard 11
  • cna 11
  • rnaseq 11
  • methylation 11
  • protein 11
  • bisulphite 11
  • databases 11
  • build 11
  • illumina 11
  • QC 11
  • consensus 11
  • bqsr 11
  • compression 11
  • table 11
  • sequences 10
  • phage 10
  • 5mC 10
  • imaging 10
  • metrics 10
  • antimicrobial resistance 10
  • kmer 10
  • long-read 10
  • expression 10
  • stats 10
  • serotype 10
  • visualisation 10
  • indexing 10
  • tsv 10
  • matrix 9
  • searching 9
  • openms 9
  • depth 9
  • cluster 9
  • markduplicates 9
  • plot 9
  • bins 9
  • base quality score recalibration 9
  • amr 9
  • protein sequence 9
  • histogram 9
  • neural network 9
  • DNA methylation 9
  • scWGBS 9
  • WGBS 9
  • wgs 9
  • aDNA 9
  • haplotype 9
  • pairs 9
  • demultiplex 9
  • pangenome graph 9
  • metagenome 8
  • mappability 8
  • completeness 8
  • annotate 8
  • bwa 8
  • virus 8
  • LAST 8
  • checkm 8
  • db 8
  • damage 8
  • aligner 8
  • mmseqs2 8
  • genotype 8
  • samtools 8
  • archaeogenomics 8
  • palaeogenomics 8
  • validation 8
  • cooler 8
  • transcript 8
  • biscuit 8
  • iCLIP 8
  • bcf 8
  • low-coverage 8
  • machine learning 8
  • bisulfite sequencing 8
  • filtering 8
  • repeat 8
  • segmentation 7
  • bismark 7
  • spatial 7
  • transcriptome 7
  • kraken2 7
  • blast 7
  • phasing 7
  • peaks 7
  • glimpse 7
  • decompression 7
  • hmmsearch 7
  • structure 7
  • population genetics 7
  • gff3 7
  • gene 7
  • ucsc 7
  • dedup 7
  • mags 7
  • complexity 7
  • newick 7
  • umi 7
  • long reads 7
  • sequence 7
  • germline 7
  • ncbi 7
  • mkref 7
  • evaluation 7
  • mag 7
  • seqkit 7
  • differential 7
  • example 7
  • duplicates 6
  • prokaryote 6
  • hmmer 6
  • mitochondria 6
  • snp 6
  • json 6
  • single 6
  • NCBI 6
  • demultiplexing 6
  • antimicrobial resistance genes 6
  • bedGraph 6
  • deduplication 6
  • feature 6
  • tumor-only 6
  • cnvkit 6
  • mapping 6
  • vsearch 6
  • gzip 6
  • plasmid 6
  • short-read 6
  • pangenome 6
  • mirna 6
  • antimicrobial peptides 6
  • low frequency variant calling 6
  • genotyping 6
  • prediction 6
  • kmers 6
  • scRNA-seq 6
  • riboseq 5
  • counts 5
  • mutect2 5
  • arg 5
  • enrichment 5
  • de novo 5
  • csv 5
  • adapters 5
  • text 5
  • isolates 5
  • mem 5
  • report 5
  • single cell 5
  • multiple sequence alignment 5
  • fragment 5
  • call 5
  • 3-letter genome 5
  • interval 5
  • antibiotic resistance 5
  • deamination 5
  • splicing 5
  • query 5
  • de novo assembly 5
  • amps 5
  • MAF 5
  • detection 5
  • clipping 5
  • svtk 5
  • summary 5
  • kallisto 5
  • microbiome 5
  • mpileup 5
  • view 5
  • benchmark 5
  • extract 5
  • idXML 5
  • visualization 5
  • diversity 5
  • msa 5
  • sourmash 5
  • family 4
  • DNA sequencing 4
  • quantification 4
  • palaeogenetics 4
  • ampir 4
  • hic 4
  • chunk 4
  • paf 4
  • containment 4
  • interval_list 4
  • bgzip 4
  • fungi 4
  • diamond 4
  • haplotypecaller 4
  • bcl2fastq 4
  • reference-free 4
  • resistance 4
  • ancestry 4
  • umitools 4
  • ngscheckmate 4
  • read depth 4
  • malt 4
  • copy number alteration calling 4
  • merging 4
  • phylogenetic placement 4
  • STR 4
  • public datasets 4
  • ATAC-seq 4
  • ont 4
  • microsatellite 4
  • taxonomic classification 4
  • CLIP 4
  • fgbio 4
  • SV 4
  • circrna 4
  • hybrid capture sequencing 4
  • genome assembler 4
  • cut 4
  • ganon 4
  • indels 4
  • profiling 4
  • targeted sequencing 4
  • retrotransposon 4
  • sequencing 4
  • matching 4
  • logratio 4
  • DNA sequence 4
  • compare 4
  • structural 4
  • BGC 4
  • deep learning 4
  • ccs 4
  • fastx 4
  • archaeogenetics 4
  • tabular 4
  • bin 4
  • propr 4
  • hmmcopy 4
  • HiFi 4
  • xeniumranger 4
  • FASTQ 4
  • happy 4
  • isomir 4
  • miscoding lesions 4
  • redundancy 4
  • biosynthetic gene cluster 4
  • compress 4
  • profile 4
  • genmod 4
  • telomere 4
  • bigwig 4
  • concatenate 4
  • ranking 4
  • bedgraph 4
  • parsing 4
  • microarray 4
  • normalization 4
  • peak-calling 4
  • sample 4
  • add 4
  • insert 3
  • das_tool 3
  • typing 3
  • informative sites 3
  • observations 3
  • lossless 3
  • bacterial 3
  • PCA 3
  • tabix 3
  • pairsam 3
  • deeparg 3
  • structural_variants 3
  • identity 3
  • snps 3
  • scores 3
  • relatedness 3
  • kinship 3
  • fingerprint 3
  • survivor 3
  • plink2 3
  • genomes 3
  • mtDNA 3
  • bim 3
  • fam 3
  • replace 3
  • pan-genome 3
  • spaceranger 3
  • entrez 3
  • mzml 3
  • prokka 3
  • rsem 3
  • preprocessing 3
  • duplication 3
  • score 3
  • mapper 3
  • html 3
  • organelle 3
  • krona 3
  • genome assembly 3
  • transcripts 3
  • pseudoalignment 3
  • krona chart 3
  • reports 3
  • windowmasker 3
  • notebook 3
  • amplicon sequencing 3
  • variant_calling 3
  • dna 3
  • cfDNA 3
  • HMM 3
  • ligate 3
  • PacBio 3
  • gridss 3
  • chimeras 3
  • gatk4spark 3
  • npz 3
  • transposons 3
  • uLTRA 3
  • SNP 3
  • minimap2 3
  • genotype-based deconvoltion 3
  • popscle 3
  • long_read 3
  • fastk 3
  • reads 3
  • untar 3
  • UMI 3
  • uncompress 3
  • mlst 3
  • subsample 3
  • unzip 3
  • wxs 3
  • wastewater 3
  • zip 3
  • archiving 3
  • polishing 3
  • shapeit 3
  • vrhyme 3
  • spark 3
  • benchmarking 3
  • dictionary 3
  • amplicon sequences 3
  • small indels 3
  • panel 3
  • indel 3
  • ambient RNA removal 3
  • das tool 3
  • clean 3
  • adapter trimming 3
  • atac-seq 3
  • chip-seq 3
  • pileup 3
  • bamtools 3
  • wig 3
  • png 3
  • rna 3
  • host 3
  • bakta 3
  • checkv 3
  • highly_multiplexed_imaging 3
  • mcmicro 3
  • image_analysis 3
  • ataqv 3
  • arriba 3
  • fusion 3
  • eukaryotes 3
  • prokaryotes 3
  • genome mining 3
  • cut up 3
  • quality trimming 3
  • remove 3
  • angsd 3
  • chromosome 3
  • bwameth 3
  • aln 3
  • abundance 3
  • bracken 3
  • combine 3
  • comparisons 3
  • cat 3
  • nucleotide 3
  • image 3
  • mkfastq 3
  • microbes 3
  • fai 3
  • cellranger 3
  • intervals 3
  • converter 3
  • gene expression 3
  • C to T 3
  • roh 3
  • pypgx 3
  • complement 3
  • kraken 3
  • cool 3
  • hi-c 3
  • gsea 3
  • rna_structure 3
  • repeat expansion 3
  • neubi 3
  • RNA 3
  • amplify 3
  • fcs-gx 3
  • macrel 3
  • prefetch 3
  • virulence 3
  • DRAMP 3
  • CRISPR 3
  • dump 3
  • polyA_tail 2
  • comparison 2
  • proportionality 2
  • screening 2
  • ichorcna 2
  • junctions 2
  • mitochondrion 2
  • salmonella 2
  • rtgtools 2
  • image_processing 2
  • maximum likelihood 2
  • iphop 2
  • registration 2
  • gwas 2
  • refine 2
  • preseq 2
  • reheader 2
  • krakentools 2
  • concat 2
  • Pharmacogenetics 2
  • interactive 2
  • allele 2
  • rename 2
  • krakenuniq 2
  • tbi 2
  • intersect 2
  • SimpleAF 2
  • scatter 2
  • union 2
  • screen 2
  • khmer 2
  • bustools 2
  • seqtk 2
  • normalize 2
  • guide tree 2
  • norm 2
  • hidden Markov model 2
  • cleaning 2
  • hlala_typing 2
  • cnvnator 2
  • transcriptomic 2
  • collate 2
  • gene set analysis 2
  • ome-tif 2
  • orthology 2
  • parallelized 2
  • awk 2
  • phase 2
  • concordance 2
  • BAM 2
  • bedpe 2
  • blastn 2
  • repeats 2
  • mudskipper 2
  • dict 2
  • fixmate 2
  • proteome 2
  • soft-clipped clusters 2
  • ChIP-seq 2
  • trgt 2
  • gene set 2
  • bam2fq 2
  • nucleotides 2
  • rgfa 2
  • mask 2
  • mapcounter 2
  • hla_typing 2
  • hlala 2
  • hla 2
  • intersection 2
  • windows 2
  • scaffolding 2
  • tnhaplotyper2 2
  • MCMICRO 2
  • smrnaseq 2
  • RNA sequencing 2
  • somatic variants 2
  • varcal 2
  • mirdeep2 2
  • fusions 2
  • trancriptome 2
  • tama 2
  • gstama 2
  • pair 2
  • serogroup 2
  • sketch 2
  • aggregate 2
  • signature 2
  • ped 2
  • small genome 2
  • de novo assembler 2
  • RNA-Seq 2
  • GPU-accelerated 2
  • simulate 2
  • artic 2
  • svdb 2
  • read-group 2
  • demultiplexed reads 2
  • standardization 2
  • ancient dna 2
  • taxonomic profile 2
  • standardise 2
  • standardisation 2
  • otu tables 2
  • taxon tables 2
  • FracMinHash sketch 2
  • antismash 2
  • anndata 2
  • bfiles 2
  • adapter 2
  • import 2
  • edit distance 2
  • library 2
  • HOPS 2
  • variant pruning 2
  • gene labels 2
  • shigella 2
  • secondary metabolites 2
  • MaltExtract 2
  • switch 2
  • effect prediction 2
  • snpeff 2
  • snpsift 2
  • cancer genomics 2
  • join 2
  • NRPS 2
  • RiPP 2
  • antibiotics 2
  • graph layout 2
  • nextclade 2
  • primer 2
  • long-read sequencing 2
  • checksum 2
  • tree 2
  • contig 2
  • trim 2
  • minhash 2
  • mash 2
  • sequence analysis 2
  • scaffold 2
  • megan 2
  • distance 2
  • frame-shift correction 2
  • polish 2
  • runs_of_homozygosity 2
  • lofreq 2
  • authentication 2
  • barcode 2
  • transformation 2
  • vg 2
  • vcflib 2
  • removal 2
  • purge duplications 2
  • doublets 2
  • msisensor-pro 2
  • micro-satellite-scan 2
  • tumor 2
  • msi 2
  • instability 2
  • MSI 2
  • homoploymer 2
  • Streptococcus pneumoniae 2
  • GC content 2
  • Duplication purging 2
  • Read depth 2
  • xenograft 2
  • spatial_transcriptomics 2
  • duplicate 2
  • resolve_bioscience 2
  • genomad 2
  • graft 2
  • sequenzautils 2
  • profiles 2
  • instrain 2
  • interval list 2
  • joint genotyping 2
  • eido 2
  • expansionhunterdenovo 2
  • regression 2
  • interactions 2
  • salmon 2
  • lift 2
  • metamaps 2
  • deconvolution 2
  • bayesian 2
  • gatk 2
  • format 2
  • transcriptomics 2
  • identifier 2
  • calling 2
  • metagenomic 2
  • blastp 2
  • deseq2 2
  • rna-seq 2
  • estimation 2
  • immunoprofiling 2
  • amptransformer 2
  • repeat_expansions 2
  • samplesheet 2
  • long terminal retrotransposon 2
  • cnv calling 2
  • zlib 2
  • filtermutectcalls 2
  • allele-specific 2
  • orf 2
  • tab 2
  • single cells 2
  • genome bins 2
  • emboss 2
  • dereplicate 2
  • realignment 2
  • unaligned 2
  • validate 2
  • CNV 2
  • evidence 2
  • vdj 2
  • metadata 2
  • panelofnormals 2
  • microbial 2
  • eigenstrat 2
  • variation 2
  • cvnkit 2
  • leviosam2 2
  • correction 2
  • ampgram 2
  • bloom filter 2
  • settings 2
  • GEO 2
  • regions 2
  • merge mate pairs 2
  • baf 2
  • parse 2
  • short reads 2
  • spatial_omics 2
  • fetch 2
  • function 2
  • random forest 2
  • xz 2
  • sra-tools 2
  • k-mer index 2
  • COBS 2
  • archive 2
  • metagenomes 2
  • pharokka 2
  • fasterq-dump 2
  • reads merging 2
  • long terminal repeat 2
  • eCLIP 2
  • duplex 2
  • retrotransposons 2
  • UMIs 2
  • gem 2
  • heatmap 2
  • structural-variant calling 2
  • recombination 2
  • taxids 1
  • nuclear segmentation 1
  • sccmec 1
  • emoji 1
  • taxon name 1
  • circular 1
  • variantcalling 1
  • spot 1
  • umicollapse 1
  • tag 1
  • extraction 1
  • ribosomal RNA 1
  • streptococcus 1
  • signatures 1
  • spatype 1
  • realign 1
  • quality_control 1
  • scvi 1
  • scRNA-Seq 1
  • cell_barcodes 1
  • orthogroup 1
  • solo 1
  • fracminhash sketch 1
  • hash sketch 1
  • import segmentation 1
  • quality check 1
  • spa 1
  • go 1
  • coptr 1
  • featuretable 1
  • genepred 1
  • bedtobigbed 1
  • bigbed 1
  • bedgraphtobigwig 1
  • mass spectrometry 1
  • Mycobacterium tuberculosis 1
  • chromosomal rearrangements 1
  • eucaryotes 1
  • fast5 1
  • coding 1
  • logFC 1
  • differential expression 1
  • subsetting 1
  • mygene 1
  • cds 1
  • transcroder 1
  • sage 1
  • polya tail 1
  • detecting svs 1
  • barcodes 1
  • ptr 1
  • short-read sequencing 1
  • sequencing adapters 1
  • doublet_detection 1
  • svtk/baftest 1
  • baftest 1
  • countsvtypes 1
  • rdtest2vcf 1
  • p-value 1
  • rdtest 1
  • pile up 1
  • ucsc/liftover 1
  • gtftogenepred 1
  • refflat 1
  • orthologs 1
  • vcf2bed 1
  • decompress 1
  • homology 1
  • paired reads merging 1
  • rRNA 1
  • pseudodiploid 1
  • guidetree 1
  • interleave 1
  • droplet based single cells 1
  • header 1
  • human removal 1
  • seq 1
  • busco 1
  • selection 1
  • random draw 1
  • pseudohaploid 1
  • bwamem2 1
  • sertotype 1
  • bwameme 1
  • grabix 1
  • freqsum 1
  • ribosomal 1
  • 10x 1
  • bam2seqz 1
  • gc_wiggle 1
  • induce 1
  • retrieval 1
  • sex determination 1
  • Pacbio 1
  • metagenome assembler 1
  • relative coverage 1
  • cut&run 1
  • cellsnp 1
  • scramble 1
  • trimfq 1
  • cluster analysis 1
  • donor deconvolution 1
  • genotype-based demultiplexing 1
  • clusteridentifier 1
  • vcflib/vcffixup 1
  • peak-caller 1
  • cut&tag 1
  • chromatin 1
  • sequence headers 1
  • seacr 1
  • assembly-binning 1
  • scanpy 1
  • applyvarcal 1
  • VQSR 1
  • variant recalibration 1
  • AC/NS/AF 1
  • subseq 1
  • grep 1
  • lexogen 1
  • genetic sex 1
  • regulatory network 1
  • nanopore sequencing 1
  • dist 1
  • CRAM 1
  • relabel 1
  • SMN1 1
  • SMN2 1
  • cell segmentation 1
  • translation 1
  • POA 1
  • sniffles 1
  • core 1
  • snippy 1
  • cram-size 1
  • overlap-based merging 1
  • grea 1
  • size 1
  • dbnsfp 1
  • predictions 1
  • extension 1
  • SNPs 1
  • invariant 1
  • constant 1
  • cobra 1
  • rna velocity 1
  • selector 1
  • paraphase 1
  • transposable element 1
  • longread 1
  • generic 1
  • rare variants 1
  • decontamination 1
  • hostile 1
  • coreutils 1
  • error 1
  • morphology 1
  • gnu 1
  • transcription factors 1
  • de-novo 1
  • sha256 1
  • check 1
  • 256 bit 1
  • hashing-based deconvoltion 1
  • hamming-distance 1
  • shinyngs 1
  • exploratory 1
  • boxplot 1
  • density 1
  • features 1
  • resegment 1
  • sliding window 1
  • source tracking 1
  • downsample bam 1
  • prior knowledge 1
  • search engine 1
  • python 1
  • quarto 1
  • reverse complement 1
  • variant-calling 1
  • simulation 1
  • standardize 1
  • hmmfetch 1
  • poolseq 1
  • dbsnp 1
  • parser 1
  • parquet 1
  • stardist 1
  • mgf 1
  • decompose 1
  • multiallelic 1
  • raw 1
  • mass_error 1
  • small variants 1
  • transmembrane 1
  • resistance genes 1
  • genome graph 1
  • tnseq 1
  • resfinder 1
  • r 1
  • uniques 1
  • multiqc 1
  • chloroplast 1
  • ATACseq 1
  • nucleotide sequence 1
  • fastqfilter 1
  • distance-based 1
  • minimum_evolution 1
  • vsearch/fastqfilter 1
  • groupby 1
  • phylogenetics 1
  • tnscope 1
  • bgen 1
  • confidence 1
  • Read coverage histogram 1
  • blat 1
  • alr 1
  • clr 1
  • vsearch/dereplicate 1
  • boxcox 1
  • assay 1
  • corpcor 1
  • telseq 1
  • Escherichia coli 1
  • correlation 1
  • coexpression 1
  • decoy 1
  • htseq 1
  • shift 1
  • spectral clustering 1
  • standard 1
  • svg 1
  • xml 1
  • gost 1
  • idx 1
  • mutect 1
  • deep variant 1
  • rad 1
  • script 1
  • comparative genomics 1
  • sequence similarity 1
  • gprofiler2 1
  • tags 1
  • structural variant 1
  • bam2fastx 1
  • bam2fastq 1
  • immcantation 1
  • airrseq 1
  • java 1
  • rank 1
  • immunoinformatics 1
  • co-orthology 1
  • hashing-based deconvolution 1
  • impute-info 1
  • vector 1
  • rrna 1
  • parallel 1
  • microRNA 1
  • sompy 1
  • miRNA 1
  • Illumina 1
  • kma 1
  • reformatting 1
  • plastid 1
  • peak picking 1
  • Staging 1
  • site frequency spectrum 1
  • ancestral alleles 1
  • functional 1
  • cytosure 1
  • derived alleles 1
  • tnfilter 1
  • staging 1
  • genotypegvcf 1
  • joint-genotyping 1
  • install 1
  • introns 1
  • haplotag 1
  • gaps 1
  • transform 1
  • array_cgh 1
  • homologs 1
  • dnascope 1
  • cgMLST 1
  • case/control 1
  • spatial_neighborhoods 1
  • VCFtools 1
  • verifybamid 1
  • DNA contamination estimation 1
  • associations 1
  • genetics 1
  • construct 1
  • WGS 1
  • graph projection to vcf 1
  • AT content 1
  • GWAS 1
  • uniq 1
  • nucBed 1
  • bclconvert 1
  • extractunbinned 1
  • redundant 1
  • linkbins 1
  • association 1
  • refresh 1
  • sintax 1
  • clahe 1
  • vsearch/sort 1
  • usearch 1
  • deduplicate 1
  • vcfbreakmulti 1
  • pangenome-scale 1
  • uniparental 1
  • controlstatistics 1
  • pharmacogenetics 1
  • elprep 1
  • files 1
  • elfasta 1
  • functional analysis 1
  • biological activity 1
  • omics 1
  • structural-variants 1
  • upd 1
  • disomy 1
  • nucleotide content 1
  • snv 1
  • downsample 1
  • tag2tag 1
  • subsample bam 1
  • vcf2db 1
  • gemini 1
  • maf 1
  • lua 1
  • toml 1
  • Bayesian 1
  • scimap 1
  • long read alignment 1
  • targz 1
  • dnamodelapply 1
  • hwe statistics 1
  • liftover 1
  • readproteingroups 1
  • collapse 1
  • genotype likelihood 1
  • eigenvectors 1
  • hicPCA 1
  • sliding 1
  • reference-independent 1
  • hwe equilibrium 1
  • snakemake 1
  • workflow 1
  • seqfu 1
  • hardy-weinberg 1
  • workflow_mode 1
  • Read report 1
  • predict 1
  • drug categorization 1
  • multi-tool 1
  • ATACshift 1
  • createreadcountpanelofnormals 1
  • copyratios 1
  • denoisereadcounts 1
  • readwriter 1
  • probabilistic realignment 1
  • n50 1
  • tarball 1
  • cell_phenotyping 1
  • all versus all 1
  • cell_type_identification 1
  • wavefront 1
  • whamg 1
  • wham 1
  • tar 1
  • copy-number 1
  • copy number analysis 1
  • gender determination 1
  • machine_learning 1
  • translate 1
  • jvarkit 1
  • proteus 1
  • copy number alterations 1
  • nanoq 1
  • Read filters 1
  • copy number variation 1
  • yahs 1
  • geo 1
  • setgt 1
  • mapad 1
  • adna 1
  • c to t 1
  • Read trimming 1
  • mashmap 1
  • lofreq/call 1
  • readgroup 1
  • gene-calling 1
  • zipperbams 1
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