Add modules outlined in the pipeline proposal

Functionalities and modules

Mentioned in the pipeline proposal

primaryQC_pipeline_proposal.pdf

Pipeline proposal Slack thread

Standard QC

• FastQC Standard QC
• SeqKit histograms
  • I assume this refers to seqkit watch
  • Not available as a module currently, what I can see
• SeqFu
  • Not available as a module currently, what I can see
  • fastq integrity --> seqfu check
  • metadata --> seqfu metadata
  • merging lanes --> seqfu merge

Duplication + Complexity

• Preseq complexity
  • Which subtool?
• BBtools Clumpify
• UMI detection (stretch goal)

Adapter and Artifact detection

• Fastp
• BBtools
  • BBDuk
  • Testformat2
  • (RQCFilter2 is a corresponding subworkflow using multiple BBtools)
  • (For PacBio: Removesmartbell, Icecreamfinder)

Contamination detection

• FastQ screen
• Sylph
• Kraken2
• Mapping to reference

Mentioned in the pipeline Slack channel

• Mash screen
• checkQC

Start with primaryQC_pipeline_proposal.pdf and the linked pipeline proposal Slack thread, then compare their requested modules with the checked and unchecked items in this issue. Clarify which tools and subworkflows are in scope, including the unresolved Preseq, BBtools, SeqFu, UMI, Sylph, mapping, and Mash screen items; done means the agreed modules are added to the pipeline.