DSL2: preprocessing and mapping

[jfy133]

• FASTQC
• FASTP/ADAPTERREMOVAL
• FASTQC POST
• BWA ALN/BWA MEM/BOWTIE2/CIRCULAR MAPPING

Indexing

• BWA INDEX / BOWTIE2 INDEX (https://github.com/nf-core/eager/pull/926) / CIRCULARMAPPER
• SAMTOOLS FAIDX
• PICARD CREATESEQUENCEDICTIONARY

NEW

• Map by lane
• LEEHOM
• Multiple reference input

[jfy133]

Indexing Notes

• FASTA input only or TSV?

  • But what if need to specify chromosome?
  • Allow both?
  • If ending in {.fasta,.fna,.fas,.fa,.fasta.gz,.fna.gz,.fas.gz,.fa.gz} then just use that and make fake meta

  • If ending in .csv then make meta from TSV?

    ref_name,mt,fasta,fai,dict,mapindexdir,circulartarget,mt

  • May require patches to add meta? Or update meta?
  • Note: will need gunzip

  Modules

• gunzip

• bwa index (requires update: add meta)

• bowtie2 build (requires update: add meta)

• circular mapper

• samtools faidx

• picard dictionary

[TCLamnidis]

Add mapAD? NOTE: Cheristian mentioned in his Lab Seminar on 11/09/2023 that the map quality calculation between mapAD and BWA is a bit different. Might be good to note that when/if implementing mapAD