Nextflow Modules
Showing module(s) with keyword "rna"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/abra2 | Process | alignment realignment indels bam dna rna splice-junctions assembly | Assembly Based ReAligner for next-generation sequencing data |
| nf-core/circexplorer2/annotate | Process | rna circrna annotate | Annotate circRNAs detected in the output from CIRCexplorer2 parse |
| nf-core/ctatsplicing/prepgenomelib | Process | splicing cancer rna rnaseq | Reference preparation for CTAT-splicing |
| nf-core/ctatsplicing/startocancerintrons | Process | splicing cancer rna rnaseq | Detection and annotation of aberrant splicing isoforms in cancer transcriptomes |
| nf-core/fusioncatcher/build | Process | references fusions rna | Build references for fusioncatcher |
| nf-core/fusioncatcher/fusioncatcher | Process | fusion rna fastq | FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data |
| nf-core/parabricks/rnafq2bam | Process | align star rna | This tool is the equivalent of fq2bam for RNA-Seq samples, receiving inputs in FASTQ format, performing alignment with the splice-aware STAR algorithm, optionally marking of duplicate reads, and outputting an aligned BAM file ready for variant and fusion calling. |
| nf-core/parabricks/starfusion | Process | fusion starfusion rna | This tool uses the GPU to perform fusion calling for RNA-Seq samples, utilizing the STAR-Fusion algorithm. This requires input of a genome resource library, in accordance with the original STAR-Fusion tool, and outputs candidate fusion transcripts. |
| nf-core/picard/collectrnaseqmetrics | Process | rna bam metrics alignment statistics quality | Collect metrics from a RNAseq BAM file |
| nf-core/riker/multi | Process | bam qc metrics multi alignment insert size gc bias coverage rna | Run multiple riker collectors in a single BAM pass using riker multi. Specify tools via ext.args (e.g. '--tools alignment basic isize'). The wgs, gcbias, and error tools require a reference FASTA; the hybcap tool requires baits and targets. |
| nf-core/rrnatranscripts | Process | ribosomal rna genomics | Ribosomal RNA extraction from a GTF file. |
| nf-core/star/indexversion | Process | index version rna | Get the minimal allowed index version from STAR |