Fixed

• clusters on the negative strand were not included in the final output file
• bigwig export needs sorted input

Added

• Update template to nf-core/tools 1.12

v1.0.0 (Gold Lion) - [2020-10-16]

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

Pipeline summary

1. Input read QC (FastQC)
2. Adapter + EcoP15 + 5’G trimming (cutadapt)
3. (optional) rRNA filtering (SortMeRNA),
4. Trimmed and filtered read QC (FastQC)
5. Read alignment to a reference genome (STAR or bowtie1)
6. CAGE tag counting and clustering (paraclu)
7. CAGE tag clustering QC (RSeQC)
8. Present QC and visualisation for raw read, alignment and clustering results (MultiQC)