Nextflow Modules
Showing module(s) with keyword "qc"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| cellgeni/multiqc | Process | multiqc qc report custom content | Aggregates tool outputs and MultiQC custom content (*_mqc.* files) into a single HTML report, with a fixed output layout (multiqc_report.html and multiqc_data/) whatever the report title. |
| nf-core/ataqv/ataqv | Process | ATAC-seq qc ataqv | ataqv function of a corresponding ataqv tool |
| nf-core/ataqv/mkarv | Process | ataqv ATAC-seq qc mkarv | mkarv function of a corresponding ataqv tool |
| nf-core/bam_ngscheckmate | Workflow | ngscheckmate qc bam snp | Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs. |
| nf-core/bam_qc_rnaseq | Workflow | rnaseq bam qc quality_control preseq qualimap dupradar rseqc featurecounts biotype | Run post-alignment QC tools on RNA-seq BAM files including library complexity estimation (Preseq), biotype QC (featureCounts), RNA-seq-specific QC metrics (Qualimap), duplicate rate analysis (dupRadar), and comprehensive RSeQC analysis. |
| nf-core/bismark/report | Process | bismark qc methylation 5mC methylseq bisulphite bisulfite report | Collects bismark alignment reports |
| nf-core/bismark/summary | Process | bismark qc methylation 5mC methylseq bisulphite bisulfite report summary | Uses Bismark report files of several samples in a run folder to generate a graphical summary HTML report. |
| nf-core/chopper | Process | filter trimming fastq nanopore qc chopper pigz multi-tool | Filter and trim long read data. |
| nf-core/custom/collectstats | Process | stats collect summary qc | Collects per-sample read-processing statistics (trimming, decontamination, alignment, feature counting, and optionally taxonomy/function summaries) from a set of heterogeneous log/table files into a single overall-stats table per run. |
| nf-core/custom/multiqccustombiotype | Process | biotype featurecounts multiqc rnaseq qc | Generate MultiQC-compatible biotype count summaries from featureCounts output |
| nf-core/falco | Process | quality control qc adapters fastq | Run falco on sequenced reads |
| nf-core/fastaguard | Process | fasta assembly qc | FASTA preflight QC for assembly pipelines |
| nf-core/fastqc | Process | quality control qc adapters fastq | Run FastQC on sequenced reads |
| nf-core/fastq_complexity_filter | Workflow | fastq complexity filtering low complexity entropy qc | Perform low-complexity filtering of FASTQ reads using a selectable tool. One of PRINSEQ++, BBDuk, or fastp is executed based on the provided tool name. Only complexity filtering is applied; no adapter trimming, read merging, or quality trimming is performed. |
| nf-core/fastq_fastqc_umitools_fastp | Workflow | fastq fastqc qc UMI trimming fastp | Read QC, UMI extraction and trimming |
| nf-core/fastq_fastqc_umitools_trimgalore | Workflow | fastq fastqc qc UMI trimming trimgalore | Read QC, UMI extraction and trimming |
| nf-core/fastq_ngscheckmate |