nf-core/clipseq 1.0.0 - Ianthine Pelican

Initial release of nf-core/clipseq, created with the nf-core template.

Pipeline summary

1. Adapter and quality trimming (Cutadapt)
2. Pre-mapping to e.g. rRNA and tRNA sequences (Bowtie 2)
3. Genome mapping (STAR)
4. UMI-based deduplication (UMI-tools)
5. Crosslink identification (BEDTools)
6. Bedgraph coverage track generation (BEDTools)
7. Peak calling (multiple options):
   • iCount
   • Paraclu
   • PureCLIP
   • Piranha
8. Motif detection (DREME)
9. Quality control:
   • Sequencing quality control (FastQC)
   • Library complexity (Preseq)
   • Regional distribution (RSeQC)
10. Overall pipeline run and QC summaries and peak calling comparisons (MultiQC)