[2023-03-29]

Initial release of nf-core/viralintegration, created with the nf-core template. This pipeline is a re-implementation of CTAT-VirusIntegrationFinder v1.5.0. Main Contributors: (@alyssa-ab) (@Emiller88)

Pipeline Summary

1. Input Check
   • Input path to sample FASTAs in samplesheet.csv
   • Check that sample meets requirements (samplesheet_check)
2. Read QC (FastQC)
3. Align reads to human genome
   • Generate index and perform alignment (STAR)
4. Quality trimming for unaligned reads
   • Quality and adaptor trimming (Trimmomatic)
   • Remove polyAs from reads (PolyAStripper)
5. Identify chimeric reads
   • Combine human and virus FASTAs (cat_fasta)
   • Generate index and perform alignment to combined human + viral reference (STAR)
   • Sort and index alignments (SAMtools)
   • Determine potential insertion site candidates and optimize file (insertion_site_candidates, abridged_TSV)
6. Virus Report outputs:
   • Viral read counts in a tsv table and png plot
   • Preliminary genome wide abundance plot
   • Bam and bai for reads detected in potential viral insertion site
   • Web based interactive genome viewer for virus infection evidence (VirusDetect.igvjs.html)
7. Verify chimeric reads
   • Create chimeric FASTA and GTF extracts (extract_chimeric_genomic_targets)
   • Generate index and perform alignment to verify chimeric reads (STAR)
   • Sort and index validated alignments (SAMtools)
   • Remove duplicate alignments (remove_duplicates)
   • Generate evidence counts for chimeric reads (chimeric_contig_evidence_analyzer)
8. Summary Report outputs:
   • Refined genome wide abundance plog png
   • Insertion site candidates in tab-delimited format with gene annotations (vif.refined.wRefGeneAnnots.tsv)
   • Web based interactive genome viewer for virus insertion sites (vif.html)
9. Present quality checking and visualization for raw reads, adaptor trimming, and STAR alignments (MultiQC)

Added

• Add CTAT-VIF virus_db.fasta #1 (@alyssa-ab) (@Emiller88)
• Add small human test data set (chromosomes 6, 11, and 18 FASTA and GTF) #31 (@alyssa-ab)
• Write nf-test for full workflow #39 (@alyssa-ab) (@Emiller88)
• Add local module labels for resource management #35 (@alyssa-ab)
• Write documentation #50 (@alyssa-ab) (@Emiller88)