Count check
- Input pipeline count: 141
- Output pipeline count (below): 141 ✅
- Categories: 16
- Sum of category counts: 141 ✅
Categorized pipelines (with counts)
1) Bulk RNA-seq & transcriptomics (19)
alleleexpression, cageseq, circrna, denovotranscript, differentialabundance, drop, dualrnaseq, evexplorer, isoseq, lncpipe, nanostring, nascent, rnafusion, rnaseq, rnasplice, rnavar, riboseq, slamseq, stableexpression
2) Small RNA-seq (1)
smrnaseq
3) Single-cell transcriptomics (6)
marsseq, scdownstream, scflow, scnanoseq, scrnaseq, smartseq2
4) Spatial omics (6)
molkart, panoramaseq, pixelator, sopa, spatialvi, spatialxe
5) Chromatin & regulation (10)
atacseq, callingcards, chipseq, clipseq, cutandrun, hic, hicar, mnaseseq, sammyseq, tfactivity
6) DNA methylation (3)
methylarray, methylong, methylseq
7) Human genomics, variants & disease (22)
abotyper, circdna, deepvariant, eager, exoseq, gwas, longraredisease, mitodetect, oncoanalyser, pacvar, phaseimpute, radseq, raredisease, rarevariantburden, rnadnavar, sarek, ssds, tumourevo, variantbenchmarking, variantcatalogue, variantprioritization, createpanelrefs
8) Viruses & pathogen surveillance (7)
pathogensurveillance, phageannotator, tbanalyzer, viralmetagenome, viralintegration, viralrecon, vipr
9) Metagenomics & microbiome (10)
ampliseq, coproid, createtaxdb, detaxizer, funcscan, mag, magmap, metapep, metatdenovo, taxprofiler
10) Genome assembly, annotation & comparative genomics (14)
bacass, bactmap, denovohybrid, genomeannotator, genomeassembler, genomeqc, genomeskim, hgtseq, multiplesequencealign, neutronstar, pangenome, pairgenomealign, phyloplace, reportho
11) Immunology & antigen presentation (4)
airrflow, epitopeprediction, hlatyping, mhcquant
12) Proteomics, metabolomics & protein informatics (11)
ddamsproteomics, diaproteomics, kmermaid, metaboigniter, proteinannotator, proteinfamilies, proteinfold, proteogenomicsdb, proteomicslfq, quantms, ribomsqc
13) Imaging & other experimental modalities (7)
cellpainting, imcyto, liverctanalysis, lsmquant, mcmicro, rangeland, troughgraph
14) Data acquisition, QC & ops / utilities (12)
bamtofastq, datasync, demo, demultiplex, fastqrepair, fastquorum, fetchngs, nanoseq, readsimulator, references, seqinspector, seqsubmit
15) Genome editing & screens (2)
crisprseq, crisprvar
16) Other methods / modelling / non-bioinformatics (7)
deepmodeloptim, deepmutscan, diseasemodulediscovery, drugresponseeval, meerpipe, omicsgenetraitassociation, spinningjenny
| Category | Name | Short description | 中文描述 | Released | Stars | Last release |
|---|---|---|---|---|---|---|
| Bulk RNA-seq & transcriptomics | alleleexpression | Allele-specific expression (ASE) analysis using STAR-WASP, UMI-tools, phaser | 等位基因特异性表达（ASE）分析：STAR-WASP 比对，UMI-tools 去重，phaser 单倍型分相与 ASE 检测 | 2 | – | |
| Bulk RNA-seq & transcriptomics | cageseq | CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags. | CAGE-seq 分析：剪切、比对并统计 CAGE 标签（转录起始相关）。 | 11 | 1.0.2 | |
| Bulk RNA-seq & transcriptomics | circrna | circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data | 环状 RNA（circRNA）定量、差异表达分析及 miRNA 靶标预测。 | 59 | – | |
| Bulk RNA-seq & transcriptomics | denovotranscript | de novo transcriptome assembly of paired-end short reads from bulk RNA-seq | 基于 bulk RNA-seq 双端短读长的从头转录组组装。 | 19 | 1.2.1 | |
| Bulk RNA-seq & transcriptomics | differentialabundance | Differential abundance analysis for feature/observation matrices (e.g., RNA-seq) | 对特征/观测矩阵做差异丰度分析（可用于表达矩阵等）。 | 87 | 1.5.0 | |
| Bulk RNA-seq & transcriptomics | drop | Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders | RNA-seq 异常事件检测流程（用于罕见病诊断等）。 | 7 | – | |
| Bulk RNA-seq & transcriptomics | dualrnaseq | Analysis of Dual RNA-seq data (host-pathogen interactions) | 宿主-病原双 RNA-seq 分析流程，用于研究宿主-病原相互作用。 | 25 | 1.0.0 | |
| Bulk RNA-seq & transcriptomics | evexplorer | Analyze RNA data from extracellular vesicles; QC, region detection, normalization, DRE | 胞外囊泡（EV）RNA 数据分析：质控、表达区域检测、归一化与差异 RNA 表达（DRE）。 | 1 | – | |
| Bulk RNA-seq & transcriptomics | isoseq | Genome annotation with PacBio Iso-Seq from raw subreads to FLNC and bed annotation | PacBio Iso-Seq 基因组注释：从 subreads 生成 FLNC 并产出 bed 注释。 | 50 | 2.0.0 | |
| Bulk RNA-seq & transcriptomics | lncpipe | Analysis of long non-coding RNAs from RNA-seq datasets (under development) | lncRNA（长链非编码 RNA）分析流程（开发中）。 | 34 | – | |
| Bulk RNA-seq & transcriptomics | nanostring | Analysis pipeline for Nanostring nCounter expression data. | Nanostring nCounter 表达数据分析流程。 | 16 | 1.3.1 | |
| Bulk RNA-seq & transcriptomics | nascent | Nascent Transcription Processing Pipeline | 新生转录（nascent RNA）处理与分析流程。 | 22 | 2.3.0 | |
| Bulk RNA-seq & transcriptomics | rnafusion | RNA-seq analysis pipeline for detection of gene-fusions | RNA-seq 融合基因检测流程。 | 170 | 4.0.0 | |
| Bulk RNA-seq & transcriptomics | rnaseq | RNA sequencing pipeline (STAR/RSEM/HISAT2/Salmon) with QC and counts | 常规 bulk RNA-seq 分析：比对/定量/计数与全面质控（多比对/定量器可选）。 | 1179 | 3.22.2 | |
| Bulk RNA-seq & transcriptomics | rnasplice | RNA-seq alternative splicing analysis | RNA-seq 可变剪接分析流程。 | 63 | 1.0.4 | |
| Bulk RNA-seq & transcriptomics | rnavar | gatk4 RNA variant calling pipeline | 基于 GATK4 的 RNA 变异检测（RNA variant calling）。 | 58 | 1.2.2 | |
| Bulk RNA-seq & transcriptomics | riboseq | Analysis of ribosome profiling (Ribo-seq) data | Ribo-seq（核糖体测序/核糖体 footprinting）分析流程。 | 21 | 1.2.0 | |
| Bulk RNA-seq & transcriptomics | slamseq | SLAMSeq processing and analysis pipeline | SLAM-seq（新生 RNA 标记）处理与分析流程。 | 10 | 1.0.0 | |
| Bulk RNA-seq & transcriptomics | stableexpression | Identify stable genes across datasets; useful for RT-qPCR reference genes | 寻找最稳定基因（适合作为 RT-qPCR 参考内参基因）。 | 5 | – | |
| Small RNA-seq | smrnaseq | A small-RNA sequencing analysis pipeline | 小 RNA 测序（如 miRNA 等）分析流程。 | 98 | 2.4.1 | |
| Single-cell transcriptomics | marsseq | MARS-seq v2 pre-processing pipeline with velocity | MARS-seq v2 预处理流程，支持 RNA velocity。 | 8 | 1.0.3 | |
| Single-cell transcriptomics | scdownstream | Single cell transcriptomics pipeline for QC, integration, presentation | 单细胞转录组下游：质控、整合与结果展示。 | 81 | – | |
| Single-cell transcriptomics | scflow | Please consider using/contributing to nf-core/scdownstream | 单细胞流程（建议转向/贡献 scdownstream）。 | 25 | – | |
| Single-cell transcriptomics | scnanoseq | Single-cell/nuclei pipeline for Oxford Nanopore + 10x Genomics | 单细胞/细胞核测序流程：结合 ONT 与 10x 数据。 | 52 | 1.2.1 | |
| Single-cell transcriptomics | scrnaseq | Single-cell RNA-Seq pipeline (10x/DropSeq/SmartSeq etc.) | 单细胞 RNA-seq 主流程：支持 10x、DropSeq、SmartSeq 等。 | 310 | 4.1.0 | |
| Single-cell transcriptomics | smartseq2 | Process single cell RNA-seq generated with SmartSeq2 | SmartSeq2 单细胞 RNA-seq 处理流程。 | 15 | – | |
| Spatial omics | molkart | Processing Molecular Cartography data (Resolve Bioscience combinatorial FISH) | Resolve Molecular Cartography（组合 FISH）数据处理流程。 | 14 | 1.2.0 | |
| Spatial omics | panoramaseq | Pipeline to process sequencing-based spatial transcriptomics data (in-situ arrays) | 测序型空间转录组（in-situ arrays）数据处理流程。 | 0 | – | |
| Spatial omics | pixelator | Pipeline to generate Molecular Pixelation data (Pixelgen) | Pixelgen 分子像素化（Molecular Pixelation）数据处理流程。 | 13 | 2.3.0 | |
| Spatial omics | sopa | Nextflow version of Sopa – spatial omics pipeline and analysis | Sopa 的 Nextflow 实现：空间组学流程与分析。 | 11 | – | |
| Spatial omics | spatialvi | Process spatial gene counts + spatial coordinates + image data (10x Visium) | 10x Visium 空间转录组处理：基因计数+空间坐标+图像数据。 | 70 | – | |
| Spatial omics | spatialxe | (no description shown) | 空间组学相关流程（原表未给出描述）。 | 24 | – | |
| Chromatin & regulation | atacseq | ATAC-seq peak-calling and QC analysis pipeline | ATAC-seq 峰识别与质控分析流程。 | 221 | 2.1.2 | |
| Chromatin & regulation | callingcards | A pipeline for processing calling cards data | Calling cards 实验数据处理流程。 | 6 | 1.0.0 | |
| Chromatin & regulation | chipseq | ChIP-seq peak-calling, QC and differential analysis | ChIP-seq 峰识别、质控与差异分析流程。 | 229 | 2.1.0 | |
| Chromatin & regulation | clipseq | CLIP-seq QC, mapping, UMI deduplication, peak-calling options | CLIP-seq 分析：质控、比对、UMI 去重与多种 peak calling。 | 24 | 1.0.0 | |
| Chromatin & regulation | cutandrun | CUT&RUN / CUT&TAG pipeline with QC, spike-ins, IgG controls, peak calling | CUT&RUN/CUT&TAG 分析：质控、spike-in、IgG 对照、峰识别与下游。 | 106 | 3.2.2 | |
| Chromatin & regulation | hic | Analysis of Chromosome Conformation Capture (Hi-C) data | Hi-C 染色体构象捕获数据分析流程。 | 105 | 2.1.0 | |
| Chromatin & regulation | hicar | HiCAR multi-omic co-assay pipeline | HiCAR 多组学共测（转录+染色质可及性+接触）分析流程。 | 12 | 1.0.0 | |
| Chromatin & regulation | mnaseseq | MNase-seq analysis pipeline using BWA and DANPOS2 | MNase-seq 分析流程（BWA + DANPOS2）。 | 12 | 1.0.0 | |
| Chromatin & regulation | sammyseq | SAMMY-seq pipeline to analyze chromatin state | SAMMY-seq 染色质状态分析流程。 | 5 | – | |
| Chromatin & regulation | tfactivity | Identify differentially active TFs using expression + open chromatin | 整合表达与开放染色质数据，识别差异活跃转录因子（TF）。 | 12 | – | |
| DNA methylation | methylarray | Illumina methylation array processing; QC, confounders, DMP/DMR, cell comp optional | Illumina 甲基化芯片分析：预处理、质控、混杂因素检查、DMP/DMR；可选细胞组成估计与校正。 | 6 | – | |
| DNA methylation | methylong | Extract methylation calls from long reads (ONT/PacBio) | 从长读长（ONT/PacBio）提取甲基化识别结果。 | 19 | 2.0.0 | |
| DNA methylation | methylseq | Bisulfite-seq methylation pipeline (Bismark/bwa-meth + MethylDackel/rastair) | 亚硫酸氢盐测序甲基化分析流程（Bismark/bwa-meth 等）。 | 185 | 4.2.0 | |
| Human genomics, variants & disease | abotyper | Characterise human blood group and red cell antigens using ONT | 基于 ONT 的人类血型与红细胞抗原分型/鉴定流程。 | 1 | – | |
| Human genomics, variants & disease | circdna | Identify extrachromosomal circular DNA (ecDNA) from Circle-seq/WGS/ATAC-seq | 从 Circle-seq/WGS/ATAC-seq 识别染色体外环状 DNA（ecDNA）。 | 31 | 1.1.0 | |
| Human genomics, variants & disease | createpanelrefs | Generate Panel of Normals / models / references from many samples | 从大量样本生成 PoN（Panel of Normals）/模型/参考资源。 | 11 | – | |
| Human genomics, variants & disease | deepvariant | Consider using/contributing to nf-core/sarek | DeepVariant 相关（建议使用/贡献至 sarek）。 | 40 | 1.0 | |
| Human genomics, variants & disease | eager | Ancient DNA analysis pipeline | 古 DNA（aDNA）分析流程（可重复、标准化）。 | 195 | 2.5.3 | |
| Human genomics, variants & disease | exoseq | Please consider using/contributing to nf-core/sarek | Exo-seq 相关（建议使用/贡献至 sarek）。 | 16 | – | |
| Human genomics, variants & disease | gwas | UNDER CONSTRUCTION: Genome Wide Association Studies | GWAS（全基因组关联分析）流程（建设中）。 | 27 | – | |
| Human genomics, variants & disease | longraredisease | Long-read sequencing pipeline for rare disease variant discovery | 长读长测序罕见病变异识别流程（神经发育障碍等）。 | 5 | v1.0.0-alpha | |
| Human genomics, variants & disease | mitodetect | A-Z analysis of mitochondrial NGS data | 线粒体 NGS 数据全流程分析。 | 7 | – | |
| Human genomics, variants & disease | oncoanalyser | Comprehensive cancer DNA/RNA analysis and reporting pipeline | 肿瘤 DNA/RNA 综合分析与报告生成流程。 | 97 | 2.3.0 | |
| Human genomics, variants & disease | pacvar | Long-read PacBio sequencing processing for WGS and PureTarget | PacBio 长读长 WGS/PureTarget 测序数据处理流程。 | 13 | 1.0.1 | |
| Human genomics, variants & disease | phaseimpute | Phase and impute genetic data | 遗传数据分相与基因型填补流程。 | 27 | 1.1.0 | |
| Human genomics, variants & disease | radseq | Variant-calling pipeline for RADseq | RADseq 变异检测流程。 | 7 | – | |
| Human genomics, variants & disease | raredisease | Call and score variants from WGS/WES of rare disease patients | 罕见病 WGS/WES 变异检测与打分流程。 | 112 | 2.6.0 | |
| Human genomics, variants & disease | rarevariantburden | Summary count based rare variant burden test (e.g., vs gnomAD) | 基于汇总计数的稀有变异负担检验（可与 gnomAD 等对照）。 | 0 | – | |
| Human genomics, variants & disease | rnadnavar | Integrated RNA+DNA somatic mutation detection | RNA+DNA 联合分析的体细胞突变检测流程。 | 14 | – | |
| Human genomics, variants & disease | sarek | Germline/somatic variant calling + annotation from WGS/targeted | WGS/靶向测序的生殖系/体细胞变异检测与注释（含预处理、calling、annotation）。 | 532 | 3.7.1 | |
| Human genomics, variants & disease | ssds | Single-stranded DNA Sequencing (SSDS) pipeline | SSDS（单链 DNA 测序）分析流程。 | 1 | – | |
| Human genomics, variants & disease | tumourevo | Model tumour clonal evolution from WGS (CN, subclones, signatures) | 基于 WGS 的肿瘤克隆进化建模（CN、亚克隆、突变签名等）。 | 20 | – | |
| Human genomics, variants & disease | variantbenchmarking | Evaluate/validate variant calling accuracy | 变异检测方法准确性评估与验证流程（benchmark）。 | 37 | 1.4.0 | |
| Human genomics, variants & disease | variantcatalogue | Generate population variant catalogues from WGS | 从 WGS 构建人群变异目录（变异列表及频率）。 | 13 | – | |
| Human genomics, variants & disease | variantprioritization | (no description shown) | 变异优先级筛选流程（原表未给出描述）。 | 12 | – | |
| Viruses & pathogen surveillance | pathogensurveillance | Surveillance of pathogens using population genomics and sequencing | 基于群体基因组与测序的病原体监测流程。 | 52 | 1.0.0 | |
| Viruses & pathogen surveillance | phageannotator | Identify, annotate, quantify phage sequences in (meta)genomes | 在（宏）基因组中识别、注释并定量噬菌体序列。 | 17 | – | |
| Viruses & pathogen surveillance | tbanalyzer | Pipeline for Mycobacterium tuberculosis complex analysis | 结核分枝杆菌复合群（MTBC）分析流程。 | 13 | – | |
| Viruses & pathogen surveillance | viralmetagenome | Untargeted viral genome reconstruction with iSNV detection from metagenomes | 宏基因组中无靶向病毒全基因组重建，并检测 iSNV。 | 28 | 1.0.1 | |
| Viruses & pathogen surveillance | viralintegration | Identify viral integration events using chimeric reads | 基于嵌合 reads 的病毒整合事件检测流程。 | 17 | 0.1.1 | |
| Viruses & pathogen surveillance | viralrecon | Viral assembly and intrahost/low-frequency variant calling | 病毒组装与宿主体内/低频变异检测流程。 | 151 | 3.0.0 | |
| Viruses & pathogen surveillance | vipr | Viral assembly and intrahost/low-frequency variant calling | 病毒组装与体内/低频变异检测流程（类似 viralrecon）。 | 14 | – | |
| Metagenomics & microbiome | ampliseq | Amplicon sequencing workflow using DADA2 and QIIME2 | 扩增子测序（如 16S/ITS）分析：DADA2 + QIIME2。 | 231 | 2.15.0 | |
| Metagenomics & microbiome | coproid | Coprolite host identification pipeline | 粪化石（coprolite）宿主鉴定流程。 | 13 | 2.0.0 | |
| Metagenomics & microbiome | createtaxdb | Automated construction of classifier databases for multiple tools | 自动化并行构建多种宏基因组分类工具的数据库。 | 20 | 2.0.0 | |
| Metagenomics & microbiome | detaxizer | Identify (and optionally remove) sequences; default remove human | 识别并（可选）去除特定序列（默认去除人源污染）。 | 22 | 1.3.0 | |
| Metagenomics & microbiome | funcscan | (Meta-)genome screening for functional and natural product genes | （宏）基因组功能基因与天然产物基因簇筛查。 | 99 | 3.0.0 | |
| Metagenomics & microbiome | mag | Assembly and binning of metagenomes | 宏基因组组装与分箱（MAG 构建）。 | 264 | 5.3.0 | |
| Metagenomics & microbiome | magmap | Mapping reads to large collections of genomes | 将 reads 比对到大型基因组集合的最佳实践流程。 | 10 | 1.0.0 | |
| Metagenomics & microbiome | metapep | From metagenomes to epitopes and beyond | 从宏基因组到表位（epitope）等免疫相关下游分析。 | 12 | 1.0.0 | |
| Metagenomics & microbiome | metatdenovo | De novo assembly/annotation of metatranscriptomic or metagenomic data | 宏转录组/宏基因组的从头组装与注释（支持原核/真核/病毒）。 | 34 | 1.3.0 | |
| Metagenomics & microbiome | taxprofiler | Multi-taxonomic profiling of shotgun short/long read metagenomics | shotgun 宏基因组多类群（多生物界）分类谱分析（短读长/长读长）。 | 175 | 1.2.5 | |
| Genome assembly, annotation & comparative genomics | bacass | Simple bacterial assembly and annotation pipeline | 简单的细菌组装与注释流程。 | 80 | 2.5.0 | |
| Genome assembly, annotation & comparative genomics | bactmap | Mapping-based pipeline for bacterial phylogeny from WGS | 基于比对的细菌 WGS 系统发育/建树流程。 | 61 | 1.0.0 | |
| Genome assembly, annotation & comparative genomics | denovohybrid | Hybrid genome assembly pipeline (under construction) | 混合组装流程（长+短读长）（建设中）。 | 8 | – | |
| Genome assembly, annotation & comparative genomics | genomeannotator | Identify (coding) gene structures in draft genomes | 草图基因组（draft genome）基因结构（编码基因）注释流程。 | 34 | – | |
| Genome assembly, annotation & comparative genomics | genomeassembler | Assembly and scaffolding from long ONT/PacBio HiFi reads | 长读长（ONT/PacBio HiFi）基因组组装与脚手架构建。 | 31 | 1.1.0 | |
| Genome assembly, annotation & comparative genomics | genomeqc | Compare quality of multiple genomes and annotations | 比较多个基因组及其注释质量。 | 19 | – | |
| Genome assembly, annotation & comparative genomics | genomeskim | QC/filter genome skims; organelle assembly and/or analysis | genome skim 数据质控/过滤，并进行细胞器组装或相关分析。 | 3 | – | |
| Genome assembly, annotation & comparative genomics | hgtseq | Investigate horizontal gene transfer from NGS data | 从 NGS 数据研究水平基因转移（HGT）。 | 26 | 1.1.0 | |
| Genome assembly, annotation & comparative genomics | multiplesequencealign | Systematically evaluate MSA methods | 多序列比对（MSA）方法系统评估流程。 | 40 | 1.1.1 | |
| Genome assembly, annotation & comparative genomics | neutronstar | De novo assembly for 10x linked-reads using Supernova | 10x linked-reads 从头组装流程（Supernova）。 | 3 | 1.0.0 | |
| Genome assembly, annotation & comparative genomics | pangenome | Render sequences into a pangenome graph | 将序列集合渲染为泛基因组图（pangenome graph）。 | 102 | 1.1.3 | |
| Genome assembly, annotation & comparative genomics | pairgenomealign | Pairwise genome comparison with LAST + plots | 基于 LAST 的两两基因组比对与可视化绘图。 | 10 | 2.2.1 | |
| Genome assembly, annotation & comparative genomics | phyloplace | Phylogenetic placement with EPA-NG | 使用 EPA-NG 的系统发育定位（placement）流程。 | 13 | 2.0.0 | |
| Genome assembly, annotation & comparative genomics | reportho | Comparative analysis of ortholog predictions | 直系同源（ortholog）预测结果的比较分析流程。 | 11 | 1.1.0 | |
| Immunology & antigen presentation | airrflow | AIRR-seq repertoire analysis using Immcantation | 免疫受体库（BCR/TCR，AIRR-seq）分析：基于 Immcantation。 | 73 | 4.3.1 | |
| Immunology & antigen presentation | epitopeprediction | Epitope prediction and annotation pipeline | 表位（epitope）预测与注释流程。 | 50 | 3.1.0 | |
| Immunology & antigen presentation | hlatyping | Precision HLA typing from NGS data | 基于 NGS 的高精度 HLA 分型流程。 | 76 | 2.1.0 | |
| Immunology & antigen presentation | mhcquant | Identify and quantify MHC eluted peptides from MS raw data | 从质谱原始数据识别并定量 MHC 洗脱肽段。 | 42 | 3.1.0 | |
| Proteomics, metabolomics & protein informatics | ddamsproteomics | Quantitative shotgun MS proteomics | 定量 shotgun 质谱蛋白组流程。 | 4 | – | |
| Proteomics, metabolomics & protein informatics | diaproteomics | Automated quantitative analysis of DIA proteomics MS measurements | DIA 蛋白组质谱数据自动化定量分析流程。 | 21 | 1.2.4 | |
| Proteomics, metabolomics & protein informatics | kmermaid | k-mer similarity analysis pipeline | k-mer 相似性分析流程。 | 23 | 0.1.0-alpha | |
| Proteomics, metabolomics & protein informatics | metaboigniter | Metabolomics MS pre-processing with identification/quantification (MS1/MS2) | 代谢组质谱预处理：基于 MS1/MS2 的鉴定与定量。 | 24 | 2.0.1 | |
| Proteomics, metabolomics & protein informatics | proteinannotator | Protein fasta → annotations | 蛋白序列（FASTA）到注释的自动化流程。 | 8 | – | |
| Proteomics, metabolomics & protein informatics | proteinfamilies | Generation and updating of protein families | 蛋白家族的生成与更新流程。 | 21 | 2.2.0 | |
| Proteomics, metabolomics & protein informatics | proteinfold | Protein 3D structure prediction pipeline | 蛋白三维结构预测流程。 | 94 | 1.1.1 | |
| Proteomics, metabolomics & protein informatics | proteogenomicsdb | Generate protein databases for proteogenomics analysis | 构建蛋白基因组学分析所需的蛋白数据库。 | 7 | 1.0.0 | |
| Proteomics, metabolomics & protein informatics | proteomicslfq | Proteomics label-free quantification (LFQ) analysis pipeline | 蛋白组无标记定量（LFQ）分析流程。 | 37 | 1.0.0 | |
| Proteomics, metabolomics & protein informatics | quantms | Quantitative MS workflow (DDA-LFQ, DDA-Isobaric, DIA-LFQ) | 定量蛋白组流程：支持 DDA-LFQ、等标记 DDA、DIA-LFQ 等。 | 34 | 1.2.0 | |
| Proteomics, metabolomics & protein informatics | ribomsqc | QC pipeline monitoring MS performance in ribonucleoside analysis | 核苷相关质谱分析的性能监控与质控流程。 | 0 | – | |
| Imaging & other modalities | cellpainting | (no description shown) | Cell Painting 相关流程（原表未给出描述）。 | 8 | – | |
| Imaging & other modalities | imcyto | Image Mass Cytometry analysis pipeline | 成像质谱细胞术（IMC）图像/数据分析流程。 | 26 | 1.0.0 | |
| Imaging & other modalities | liverctanalysis | UNDER CONSTRUCTION: pipeline for liver CT analysis | 肝脏 CT 影像分析流程（建设中）。 | 0 | – | |
| Imaging & other modalities | lsmquant | Process and analyze light-sheet microscopy images | 光片显微（light-sheet）图像处理与分析流程。 | 5 | – | |
| Imaging & other modalities | mcmicro | Whole-slide multi-channel image processing to single-cell data | 多通道全切片图像到单细胞数据的端到端处理流程。 | 29 | – | |
| Imaging & other modalities | rangeland | Remotely sensed imagery pipeline for land-cover trend files | 遥感影像处理流程：结合辅助数据生成土地覆盖变化趋势文件。 | 9 | 1.0.0 | |
| Imaging & other modalities | troughgraph | Quantitative assessment of permafrost landscapes and thaw level | 冻土景观与冻融程度的定量评估流程。 | 2 | – | |
| Data acquisition, QC & utilities | bamtofastq | Convert BAM/CRAM to FASTQ and perform QC | BAM/CRAM 转 FASTQ 并进行质控。 | 31 | 2.2.0 | |
| Data acquisition, QC & utilities | datasync | System operation / automation workflows | 系统运维/自动化工作流（数据同步与操作任务）。 | 10 | – | |
| Data acquisition, QC & utilities | demo | Simple nf-core style pipeline for workshops and demos | nf-core 风格的示例/教学演示流程。 | 10 | 1.0.2 | |
| Data acquisition, QC & utilities | demultiplex | Demultiplexing pipeline for sequencing data | 测序数据拆样/解复用流程。 | 52 | 1.7.0 | |
| Data acquisition, QC & utilities | fastqrepair | Recover corrupted FASTQ.gz, fix reads, remove unpaired, reorder | 修复损坏 FASTQ.gz：修正不合规 reads、移除未配对 reads、重排序等。 | 6 | 1.0.0 | |
| Data acquisition, QC & utilities | fastquorum | Produce consensus reads using UMIs/barcodes | 基于 UMI/条形码生成共识 reads 的流程。 | 27 | 1.2.0 | |
| Data acquisition, QC & utilities | fetchngs | Fetch metadata and raw FastQ files from public databases | 从公共数据库抓取元数据与原始 FASTQ。 | 185 | 1.12.0 | |
| Data acquisition, QC & utilities | nanoseq | Nanopore demultiplexing, QC and alignment pipeline | Nanopore 数据拆样、质控与比对流程。 | 218 | 3.1.0 | |
| Data acquisition, QC & utilities | readsimulator | Simulate sequencing reads (amplicon, metagenome, WGS, etc.) | 测序 reads 模拟流程（扩增子、靶向捕获、宏基因组、全基因组等）。 | 33 | 1.0.1 | |
| Data acquisition, QC & utilities | references | Build references for multiple use cases | 多用途参考资源构建流程。 | 19 | 0.1 | |
| Data acquisition, QC & utilities | seqinspector | QC-only pipeline producing global/group-specific MultiQC reports | 纯质控流程：运行多种 QC 工具并输出全局/分组 MultiQC 报告。 | 16 | – | |
| Data acquisition, QC & utilities | seqsubmit | Submit data to ENA | 向 ENA 提交数据的流程。 | 3 | – | |
| Genome editing & screens | crisprseq | CRISPR edited data analysis (targeted + screens) | CRISPR 编辑数据分析：靶向编辑质量评估与 pooled screen 关键基因发现。 | 53 | 2.3.0 | |
| Genome editing & screens | crisprvar | Evaluate outcomes from genome editing experiments (WIP) | 基因编辑实验结果评估流程（WIP）。 | 5 | – | |
| Other methods / modelling / non-bio | deepmodeloptim | Stochastic Testing and Input Manipulation for Unbiased Learning Systems | 无偏学习系统的随机测试与输入操控（机器学习相关）。 | 28 | – | |
| Other methods / modelling / non-bio | deepmutscan | Deep mutational scanning (DMS) analysis pipeline | 深度突变扫描（DMS）数据分析流程。 | 3 | – | |
| Other methods / modelling / non-bio | diseasemodulediscovery | Network-based disease module identification | 基于网络的疾病模块识别流程。 | 5 | – | |
| Other methods / modelling / non-bio | drugresponseeval | Evaluate drug response prediction models | 药物反应预测模型的评估流程（统计与生物学上更严谨）。 | 24 | 1.1.0 | |
| Other methods / modelling / non-bio | meerpipe | Astronomy pipeline for MeerKAT pulsar data | MeerKAT 脉冲星数据天文处理流程（成像与计时分析）。 | 10 | – | |
| Other methods / modelling / non-bio | omicsgenetraitassociation | Multi-omics integration and trait association analysis pipeline | 多组学整合并进行性状/表型关联分析的流程。 | 11 | – | |
| Other methods / modelling / non-bio | spinningjenny | Simulating the first industrial revolution using agent-based models | 基于主体（Agent-based）模型模拟第一次工业革命的流程。 | 4 | – |