Mapping can be removed

[DLBPointon]

Description of the bug

Mapping is resource-intensive and generates a lot of unnecessary data that BTK doesn't need. This adds a significant amount of time to the total run time.

Instead, the mapping should be removed from EAR and we allow the BTK to run its own mapping which only requires coverage information, not indels and CIGAR data.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[yumisims]

BTK can take aligned bam/cram or unaligned bam/cram, but in principle, giving an aligned one will save time to process BTK. The solution of mapping for EAR can be either: convert read fasta to unmapped bam/cram, but when running BTK should change the "align = true" in nextflow.config (https://github.com/sanger-tol/blobtoolkit/blob/dev/nextflow.config). solution B, using cram_filter to chunk the container as in readmapping : https://github.com/sanger-tol/readmapping/blob/dev/subworkflows/local/align_pacbio.nf, but will first convert fasta to cram (also in readmapping ).