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 194
  • fasta 180
  • genomics 165
  • vcf 138
  • fastq 134
  • metagenomics 99
  • genome 92
  • alignment 82
  • index 76
  • assembly 70
  • reference 70
  • bed 67
  • gatk4 64
  • cram 60
  • sort 53
  • sam 53
  • annotation 46
  • variant calling 44
  • filter 42
  • structural variants 42
  • align 40
  • database 39
  • gff 35
  • merge 35
  • bacteria 32
  • variants 31
  • download 31
  • coverage 31
  • map 30
  • statistics 30
  • quality control 27
  • classification 26
  • nanopore 25
  • qc 25
  • gtf 24
  • methylation 24
  • classify 23
  • taxonomy 22
  • k-mer 22
  • single-cell 22
  • cnv 21
  • pacbio 20
  • variant 20
  • somatic 20
  • split 20
  • clustering 19
  • proteomics 19
  • conversion 19
  • sentieon 19
  • MSA 19
  • convert 19
  • gfa 18
  • contamination 18
  • taxonomic profiling 18
  • bisulfite 18
  • binning 17
  • bisulphite 17
  • long-read 16
  • phylogeny 16
  • rnaseq 16
  • trimming 16
  • VCF 15
  • count 15
  • long reads 15
  • copy number 15
  • build 15
  • quality 15
  • ancient DNA 14
  • visualisation 14
  • imaging 14
  • protein 14
  • sv 14
  • imputation 13
  • contigs 13
  • phage 13
  • kmer 13
  • bcftools 13
  • metrics 13
  • mapping 13
  • bedtools 13
  • reporting 12
  • illumina 12
  • mags 12
  • plot 12
  • gvcf 12
  • segmentation 12
  • databases 12
  • variation graph 12
  • graph 12
  • table 12
  • cluster 12
  • bqsr 12
  • consensus 12
  • isoseq 12
  • picard 11
  • QC 11
  • virus 11
  • germline 11
  • rna 11
  • compression 11
  • wgs 11
  • cna 11
  • demultiplexing 11
  • indexing 11
  • tsv 11
  • depth 11
  • methylseq 11
  • taxonomic classification 11
  • histogram 10
  • plink2 10
  • stats 10
  • openms 10
  • demultiplex 10
  • 5mC 10
  • searching 10
  • protein sequence 10
  • antimicrobial resistance 10
  • sequences 10
  • expression 10
  • matrix 10
  • serotype 10
  • metagenome 9
  • neural network 9
  • amr 9
  • aDNA 9
  • validation 9
  • scWGBS 9
  • WGBS 9
  • DNA methylation 9
  • haplotype 9
  • structure 9
  • markduplicates 9
  • samtools 9
  • spatial 9
  • filtering 9
  • base quality score recalibration 9
  • sequence 9
  • sequencing 9
  • bcf 9
  • mmseqs2 9
  • repeat 9
  • pangenome graph 9
  • pairs 9
  • bins 9
  • low-coverage 8
  • gene 8
  • genotype 8
  • checkm 8
  • aligner 8
  • db 8
  • bisulfite sequencing 8
  • seqkit 8
  • mappability 8
  • iCLIP 8
  • biscuit 8
  • transcript 8
  • annotate 8
  • genotyping 8
  • palaeogenomics 8
  • cooler 8
  • LAST 8
  • machine learning 8
  • gzip 8
  • completeness 8
  • archaeogenomics 8
  • damage 8
  • umi 8
  • HMM 8
  • mag 8
  • phasing 8
  • transcriptome 8
  • splicing 8
  • bwa 8
  • ont 8
  • ncbi 7
  • ucsc 7
  • duplicates 7
  • newick 7
  • peaks 7
  • reads 7
  • gff3 7
  • csv 7
  • hmmer 7
  • kraken2 7
  • genomes 7
  • decompression 7
  • feature 7
  • bismark 7
  • snp 7
  • glimpse 7
  • msa 7
  • compare 7
  • complexity 7
  • evaluation 7
  • mkref 7
  • quantification 7
  • blast 7
  • population genetics 7
  • prediction 7
  • dedup 7
  • sketch 7
  • example 7
  • fusion 7
  • hmmsearch 7
  • transcripts 6
  • GPU-accelerated 6
  • pangenome 6
  • immunoinformatics 6
  • biosynthetic gene cluster 6
  • plasmid 6
  • dna 6
  • NCBI 6
  • prokaryote 6
  • json 6
  • scRNA-seq 6
  • BGC 6
  • report 6
  • transcriptomics 6
  • clipping 6
  • view 6
  • de novo 6
  • deduplication 6
  • extract 6
  • antimicrobial resistance genes 6
  • scaffold 6
  • differential 6
  • short-read 6
  • structural 6
  • profile 6
  • bigwig 6
  • kmers 6
  • mitochondria 6
  • bedGraph 6
  • antimicrobial peptides 6
  • RNA-seq 6
  • fungi 6
  • low frequency variant calling 6
  • call 6
  • mCtoT 6
  • cnvkit 6
  • C->T conversion 6
  • single 6
  • rastair 6
  • mirna 6
  • tumor-only 6
  • vsearch 6
  • multiple sequence alignment 6
  • indels 6
  • chromosome 6
  • ptr 5
  • preprocessing 5
  • deep learning 5
  • arg 5
  • parser 5
  • antibiotic resistance 5
  • benchmark 5
  • distance 5
  • eukaryotes 5
  • cat 5
  • text 5
  • regions 5
  • concatenate 5
  • de novo assembly 5
  • riboseq 5
  • kallisto 5
  • reference-free 5
  • hic 5
  • coptr 5
  • cool 5
  • isolates 5
  • prokaryotes 5
  • MAF 5
  • detection 5
  • tabular 5
  • deamination 5
  • summary 5
  • visualization 5
  • genome mining 5
  • hashing-based deconvolution 5
  • immunology 5
  • scanpy 5
  • fragment 5
  • microbiome 5
  • BCR 5
  • fastx 5
  • 3-letter genome 5
  • microscopy 5
  • diversity 5
  • wxs 5
  • amplicon 5
  • single cell 5
  • interval 5
  • amps 5
  • bgzip 5
  • idXML 5
  • mutect2 5
  • FASTQ 5
  • counts 5
  • sourmash 5
  • profiling 5
  • mpileup 5
  • svtk 5
  • merging 5
  • adapters 5
  • comparison 5
  • query 5
  • fgbio 5
  • rna-seq 5
  • gridss 5
  • contig 5
  • mem 5
  • rsem 5
  • enrichment 5
  • html 4
  • starfusion 4
  • haplotypecaller 4
  • sylph 4
  • antibiotics 4
  • HiFi 4
  • skani 4
  • typing 4
  • interval_list 4
  • phylogenetic placement 4
  • public datasets 4
  • microarray 4
  • STR 4
  • malt 4
  • ganon 4
  • antibody 4
  • ancestry 4
  • cut 4
  • embeddings 4
  • genome assembler 4
  • happy 4
  • antismash 4
  • bin 4
  • diamond 4
  • SV 4
  • decontamination 4
  • gsea 4
  • archaeogenetics 4
  • mask 4
  • palaeogenetics 4
  • miscoding lesions 4
  • secondary metabolites 4
  • structural-variant calling 4
  • CAZyme 4
  • ampir 4
  • dbCAN 4
  • CAZyme gene Cluster 4
  • peak-calling 4
  • ranking 4
  • parsing 4
  • ccs 4
  • snps 4
  • hmmcopy 4
  • genmod 4
  • reports 4
  • NRPS 4
  • compress 4
  • CRISPR 4
  • RiPP 4
  • krona chart 4
  • mtDNA 4
  • bedgraph 4
  • umitools 4
  • containment 4
  • DNA sequencing 4
  • add 4
  • lineage 4
  • mass spectrometry 4
  • propr 4
  • family 4
  • fai 4
  • bcl2fastq 4
  • image 4
  • nucleotide 4
  • retrotransposon 4
  • amplicon sequences 4
  • clean 4
  • telomere 4
  • scaffolding 4
  • union 4
  • copy number alteration calling 4
  • hybrid capture sequencing 4
  • targeted sequencing 4
  • benchmarking 4
  • redundancy 4
  • bedpe 4
  • sample 4
  • mzml 4
  • abundance 4
  • chunk 4
  • normalization 4
  • taxids 4
  • DNA sequence 4
  • WGS 4
  • logratio 4
  • circrna 4
  • arriba 4
  • isomir 4
  • pypgx 4
  • png 4
  • CLIP 4
  • RNA-Seq 4
  • paf 4
  • mbias 4
  • ATAC-seq 4
  • methylation bias 4
  • ngscheckmate 4
  • resistance 4
  • anndata 4
  • xeniumranger 4
  • microsatellite 4
  • matching 4
  • minimap2 3
  • duplication 3
  • untar 3
  • quantms-utils 3
  • genome assembly 3
  • short reads 3
  • windowmasker 3
  • rtg-tools 3
  • fusions 3
  • uLTRA 3
  • mapper 3
  • guide tree 3
  • fiberseq 3
  • npz 3
  • subclonal deconvolution 3
  • score 3
  • variant_calling 3
  • wastewater 3
  • m6A 3
  • align probes 3
  • zip 3
  • indel 3
  • realignment 3
  • diann 3
  • spaceranger 3
  • unzip 3
  • informative sites 3
  • SNP 3
  • uncompress 3
  • kinship 3
  • identity 3
  • relatedness 3
  • off-target probes 3
  • vrhyme 3
  • cancer genomics 3
  • opt 3
  • dictionary 3
  • dist 3
  • subsample 3
  • lossless 3
  • observations 3
  • gatk 3
  • shapeit 3
  • seqtk 3
  • tabix 3
  • archiving 3
  • survivor 3
  • spark 3
  • fcs-gx 3
  • somatic variants 3
  • amplicon sequencing 3
  • hidden Markov model 3
  • Pacbio 3
  • RNA 3
  • rna_structure 3
  • cfDNA 3
  • ambient RNA removal 3
  • population genomics 3
  • pangolin 3
  • maximum likelihood 3
  • covid 3
  • pan-genome 3
  • pairsam 3
  • popscle 3
  • notebook 3
  • ome-tif 3
  • miRNA 3
  • msisensor-pro 3
  • pseudoalignment 3
  • khmer 3
  • krona 3
  • interactive 3
  • mlst 3
  • polishing 3
  • long_read 3
  • small indels 3
  • genotype-based deconvoltion 3
  • amino acid 3
  • concordance 3
  • organelle 3
  • spatial transcriptomics 3
  • vizgen 3
  • vpt 3
  • ligate 3
  • polish 3
  • reformatting 3
  • gatk4spark 3
  • cutoff 3
  • panel 3
  • chimeras 3
  • prokka 3
  • long read 3
  • replace 3
  • transposons 3
  • retrotransposons 3
  • PacBio 3
  • kma 3
  • repeat expansion 3
  • subset 3
  • python 3
  • hla 3
  • fam 3
  • bim 3
  • insert 3
  • functional analysis 3
  • UMI 3
  • structural_variants 3
  • hi-c 3
  • microbes 3
  • ataqv 3
  • gene expression 3
  • roh 3
  • heatmap 3
  • host 3
  • das tool 3
  • metadata 3
  • entrez 3
  • das_tool 3
  • combine 3
  • comparisons 3
  • bacterial 3
  • deeparg 3
  • kraken 3
  • converter 3
  • complement 3
  • bakta 3
  • PCA 3
  • virulence 3
  • scores 3
  • intervals 3
  • checkv 3
  • highly_multiplexed_imaging 3
  • artic 3
  • wig 3
  • atac-seq 3
  • fingerprint 3
  • mcmicro 3
  • chip-seq 3
  • image_analysis 3
  • macrel 3
  • C to T 3
  • adapter trimming 3
  • remove 3
  • bwameth 3
  • neubi 3
  • fastk 3
  • dump 3
  • BAM 3
  • aln 3
  • mkfastq 3
  • read depth 3
  • cut up 3
  • fetch 3
  • pileup 3
  • angsd 3
  • cellranger 3
  • amplify 3
  • quality trimming 3
  • prefetch 3
  • bracken 3
  • bamtools 3
  • proteome 3
  • DRAMP 3
  • sequence analysis 2
  • simulate 2
  • pharmacogenetics 2
  • doublets 2
  • graph layout 2
  • dereplicate 2
  • adapter 2
  • nextclade 2
  • preseq 2
  • long-read sequencing 2
  • mirdeep2 2
  • genome bins 2
  • read-group 2
  • MCMICRO 2
  • demultiplexed reads 2
  • deletions 2
  • smrnaseq 2
  • repeats 2
  • immunoprofiling 2
  • vdj 2
  • bfiles 2
  • single cells 2
  • ped 2
  • variant pruning 2
  • aggregate 2
  • Pharmacogenetics 2
  • pbmerge 2
  • frame-shift correction 2
  • tags 2
  • RNA sequencing 2
  • import 2
  • UMIs 2
  • gene labels 2
  • serogroup 2
  • megan 2
  • checksum 2
  • find 2
  • pigz 2
  • CNV 2
  • tree 2
  • minhash 2
  • mash 2
  • haplotypes 2
  • calling 2
  • lofreq 2
  • barcode 2
  • GC content 2
  • primer 2
  • vep 2
  • drep 2
  • pair 2
  • microbial genomics 2
  • dereplication 2
  • enzyme 2
  • krakenuniq 2
  • krakentools 2
  • screen 2
  • pca 2
  • bustools 2
  • k-mer frequency 2
  • cvnkit 2
  • removal 2
  • parse 2
  • hostile 2
  • human removal 2
  • bioinformatics tools 2
  • screening 2
  • cleaning 2
  • trgt 2
  • micro-satellite-scan 2
  • tumor 2
  • library 2
  • instability 2
  • MSI 2
  • homoploymer 2
  • assembly evaluation 2
  • splice 2
  • eCLIP 2
  • recombination 2
  • split_kmers 2
  • corrupted 2
  • nacho 2
  • nanostring 2
  • estimation 2
  • mRNA 2
  • spatial_transcriptomics 2
  • resolve_bioscience 2
  • profiles 2
  • msi 2
  • blastn 2
  • cgMLST 2
  • COBS 2
  • transcriptomic 2
  • reheader 2
  • mudskipper 2
  • graft 2
  • xz 2
  • archive 2
  • taxon tables 2
  • otu tables 2
  • standardisation 2
  • standardise 2
  • taxonomic profile 2
  • k-mer index 2
  • norm 2
  • standardization 2
  • bloom filter 2
  • xenograft 2
  • pharokka 2
  • svdb 2
  • function 2
  • long terminal repeat 2
  • de novo assembler 2
  • small genome 2
  • parallel 2
  • long terminal retrotransposon 2
  • signature 2
  • scatter 2
  • normalize 2
  • join 2
  • tnhaplotyper2 2
  • registration 2
  • copyratios 2
  • mitochondrion 2
  • SimpleAF 2
  • proportionality 2
  • copy number alterations 2
  • cnvnator 2
  • nucleotides 2
  • multiallelic 2
  • small variants 2
  • rgfa 2
  • concat 2
  • rrna 2
  • BCF 2
  • tbi 2
  • bamUtil 2
  • vg 2
  • trim 2
  • yaml 2
  • vcflib 2
  • orthology 2
  • parallelized 2
  • downsample 2
  • upd 2
  • intersect 2
  • FracMinHash sketch 2
  • salmon 2
  • orthologs 2
  • check 2
  • soft-clipped clusters 2
  • interactions 2
  • readgroup 2
  • regression 2
  • taxon name 2
  • zlib 2
  • fixmate 2
  • dict 2
  • collate 2
  • bam2fq 2
  • differential expression 2
  • translation 2
  • variation 2
  • biological activity 2
  • awk 2
  • rtgtools 2
  • ampgram 2
  • amptransformer 2
  • junctions 2
  • version 2
  • runs_of_homozygosity 2
  • duplicate 2
  • Read depth 2
  • Duplication purging 2
  • purge duplications 2
  • quality check 2
  • prior knowledge 2
  • omics 2
  • quarto 2
  • Streptococcus pneumoniae 2
  • intersection 2
  • snpsift 2
  • snpeff 2
  • effect prediction 2
  • windows 2
  • CRAM 2
  • homologs 2
  • shigella 2
  • orf 2
  • switch 2
  • ancient dna 2
  • seqfu 2
  • sequenzautils 2
  • structural-variants 2
  • leviosam2 2
  • lift 2
  • metamaps 2
  • transformation 2
  • header 2
  • rename 2
  • region 2
  • sizes 2
  • salmonella 2
  • genetics 2
  • bases 2
  • varcal 2
  • correction 2
  • image_processing 2
  • bgc 2
  • methylkit 2
  • hlala 2
  • hla_typing 2
  • gwas 2
  • repeat_expansions 2
  • hlala_typing 2
  • expansionhunterdenovo 2
  • authentication 2
  • mapcounter 2
  • edit distance 2
  • secondary structure 2
  • cancer 2
  • deeptools 2
  • reformat 2
  • satellite data 2
  • emboss 2
  • random forest 2
  • eido 2
  • gene set 2
  • spectral library 2
  • annotations 2
  • datacube 2
  • format 2
  • microbial 2
  • nucleosome 2
  • samplesheet 2
  • validate 2
  • identifier 2
  • ChIP-seq 2
  • ichorcna 2
  • deconvolution 2
  • metagenomes 2
  • spatial_omics 2
  • ragtag 2
  • archaea 2
  • deseq2 2
  • zarr 2
  • gstama 2
  • tama 2
  • blastp 2
  • blobtoolkit 2
  • sawfish 2
  • trancriptome 2
  • gene set analysis 2
  • panelofnormals 2
  • CNV calling 2
  • allele 2
  • evidence 2
  • genome taxonomy database 2
  • sensitive search 2
  • allele-specific 2
  • filtermutectcalls 2
  • HOPS 2
  • MaltExtract 2
  • haplogroups 2
  • interval list 2
  • DNA 2
  • substrings 2
  • phase 2
  • coreutils 2
  • metacache 2
  • insilico 2
  • synteny 2
  • rearrangements 2
  • joint genotyping 2
  • tab 2
  • bayesian 2
  • slamseq 2
  • qualty 2
  • sra-tools 2
  • genomad 2
  • merge mate pairs 2
  • instrain 2
  • eigenstrat 2
  • fasterq-dump 2
  • reads merging 2
  • GEO 2
  • cancer evolution 2
  • refine 2
  • baf 2
  • settings 2
  • polyA_tail 2
  • mutational signatures 2
  • scanner 2
  • helitron 2
  • gem 2
  • duplex 2
  • unaligned 2
  • plant 2
  • Hi-C 2
  • iphop 2
  • detect 2
  • samples 2
  • minimizer 2
  • metagenomic 2
  • overlap-based merging 1
  • predict 1
  • enhancer 1
  • autofluorescence 1
  • metatranscriptomics 1
  • braker 1
  • formatting 1
  • tf_affinity 1
  • paired reads merging 1
  • hardy-weinberg 1
  • contact map 1
  • hwe statistics 1
  • hwe equilibrium 1
  • quality-control 1
  • reference-independent 1
  • genotype likelihood 1
  • collapse 1
  • abc_model 1
  • cycif 1
  • multi-tool 1
  • case/control 1
  • functional enrichment 1
  • scimap 1
  • ome-tiff 1
  • r 1
  • Bayesian 1
  • scrublet 1
  • coexpression 1
  • retrieval 1
  • transposable element 1
  • correlation 1
  • corpcor 1
  • assay 1
  • hashing-based deconvoltion 1
  • generic 1
  • gnu 1
  • doublet-detection 1
  • immunogenetics 1
  • phylogenetics 1
  • minimum_evolution 1
  • distance-based 1
  • nucleotide sequence 1
  • SBSs, DBSs, IDs 1
  • hamming-distance 1
  • gene_regulation 1
  • liftover 1
  • mkdssp 1
  • background 1
  • splitting 1
  • purity 1
  • principal-component-analysis 1
  • nanopore sequencing 1
  • single-stranded 1
  • fusion_report 1
  • structural bioinformatics 1
  • dssp 1
  • clahe 1
  • go 1
  • compartment signal 1
  • refresh 1
  • denovo assembly 1
  • association 1
  • fusioninspector 1
  • eigenvector 1
  • fusion report 1
  • mixed-genotype 1
  • pile up 1
  • sra 1
  • dimensionality-reduction 1
  • hashing 1
  • template 1
  • ena 1
  • feature table 1
  • probabilistic realignment 1
  • biom 1
  • grea 1
  • extension 1
  • n50 1
  • Fusion 1
  • cell_type_identification 1
  • cell_phenotyping 1
  • rna velocity 1
  • tag 1
  • cobra 1
  • machine_learning 1
  • spatial_neighborhoods 1
  • tumour contamination 1
  • normal 1
  • associations 1
  • cell_barcodes 1
  • mygene 1
  • GWAS 1
  • SINE 1
  • primer trimming 1
  • bamtools/split 1
  • cmaple 1
  • tree reconstruction 1
  • decoy 1
  • trimBam 1
  • htseq 1
  • phylogenetic tree 1
  • fna 1
  • faa 1
  • bigslice 1
  • sompy 1
  • gbk 1
  • clusters 1
  • peak picking 1
  • genome graph 1
  • site frequency spectrum 1
  • ancestral alleles 1
  • somatic mutations 1
  • derived alleles 1
  • tnfilter 1
  • clonal population 1
  • bamtools/convert 1
  • mbiasparser 1
  • array_cgh 1
  • cytosure 1
  • vector 1
  • quality assessment 1
  • tnseq 1
  • iqtree 1
  • adapterremoval 1
  • boxcox 1
  • modifications 1
  • groupby 1
  • tnscope 1
  • bgen 1
  • configuration 1
  • chloroplast 1
  • confidence 1
  • blat 1
  • alr 1
  • triqler 1
  • clr 1
  • background_correction 1
  • illumiation_correction 1
  • transmembrane 1
  • Escherichia coli 1
  • msstats 1
  • propd 1
  • Read coverage histogram 1
  • element 1
  • mztab 1
  • contiguate 1
  • reverse complement 1
  • simulation 1
  • hmmfetch 1
  • decompose 1
  • DIA 1
  • antimicrobial reistance 1
  • gprofiler2 1
  • skip malformed 1
  • plastid 1
  • phylogenetic-trees 1
  • traget transcriptome 1
  • install 1
  • joint-genotyping 1
  • opt track 1
  • genotypegvcf 1
  • bacphlip 1
  • virulent 1
  • binding predictions 1
  • opt stat 1
  • temperate 1
  • Staphylococcus aureus 1
  • opt flip 1
  • introns 1
  • lifestyle 1
  • resfinder 1
  • resistance genes 1
  • raw 1
  • mgf 1
  • parquet 1
  • dbsnp 1
  • standardize 1
  • genome editing 1
  • bkt 1
  • gzipped 1
  • splice-junctions 1
  • cancer-genomics 1
  • gaps 1
  • pbtk 1
  • airrseq 1
  • gost 1
  • star 1
  • dia 1
  • admixture 1
  • joint calling 1
  • rad 1
  • mouse 1
  • duplications 1
  • structural variant 1
  • bam2fastx 1
  • bam2fastq 1
  • immcantation 1
  • co-orthology 1
  • transform 1
  • homology 1
  • sequence similarity 1
  • spectral clustering 1
  • comparative genomics 1
  • reference panels 1
  • affy 1
  • strobemers 1
  • deep variant 1
  • mutect 1
  • idx 1
  • strobealign 1
  • clonal-evolution 1
  • cancer-evolution 1
  • summary stats 1
  • regulatory network 1
  • MMseqs2 1
  • long-reads 1
  • decomposeblocksub 1
  • block substitutions 1
  • pdb 1
  • run 1
  • updatedata 1
  • chip 1
  • metabolomics 1
  • spatialdata 1
  • partitioning 1
  • malformed 1
  • fix 1
  • iterative model refinement 1
  • paired reads re-pairing 1
  • TCR 1
  • regex 1
  • patterns 1
  • doublet 1
  • Immune Deconvolution 1
  • Bioinformatics Tools 1
  • Computational Immunology 1
  • catpack 1
  • prepare 1
  • mzML 1
  • references 1
  • taxonomic composition 1
  • modelsegments 1
  • missingness 1
  • identity-by-descent 1
  • nuclear contamination estimate 1
  • 16S 1
  • bnd-eval 1
  • ncbi taxonomy 1
  • import segmentation 1
  • nuclear segmentation 1
  • cell segmentation 1
  • utility 1
  • relabel 1
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