[User Story] Clean up publishdirs

[fellen31]

Description of feature

At the moment everything is published, including intermediary files. We might have to think of more long-term solutions for some of these, but a fix in the near future is needed.

Suggest we publish:

Assembly:

• [x] Assembled haplotypes 1 and 2 as fasta.gz + assembly stats.
• [x] Assembled haplotypes aligned to reference genome as bam+bai.
  • [x] short-term this will have to include all dipcall files
  • [ ] #187

Read alignment:

• [x] Only the per sample merged aligned reads as bam+bai
  • [x] short term this will have to include both a set of phased and unphased
  • [x] #59

Phasing:

• [x] Only whatshap stats and haplotagged reads - no longer relevant since we don't use distrust genotypes
• [x] Output HiPhase reads (long or short-term don't have 3 parallel phasing programs)

Raw read QC:

• [x] All FastQC files - or is MultiQC-report enough?
• [x] Keep fqcrs for now, replace long-term, or make it an intermediary file)

Aligned QC:

• [x] All mosdepth files
  • [x] long term - make these into IGV-loadable tracks (not sure what I meant by that)
• [x] All cramino files
  • [x] short-term both phased and unphased

SNVs & SVs:

• [x] One SNV-calls per sample (as vcf.gz + g.vcf.gz), plus one additional where all samples are merged
  • [x] long term - index these
• [x] One SNV-calls per sample (as vcf) plus one additional where all samples are merged (as vcf)
  • [x] long term - index and compress these

Repeat calling (TRGT):

• [x] Sorted and indexed bcf.gz + spanning reads bam +bai
  • [x] long-term make bcf.gz-> vcf.gz

CNV:

• [x] Output all files (this includes depth tracks)

SNV-annotation:

• [x] Output all files
  • [x] long-term replace by #23

Methylation:

• [x] Methylation pileups
  • [x] short term both phased and unphased

General:

• [x] No tools should exist in the base output directory except maybe multiqc, which at the moment for example bcftools and tabix do.

[fellen31]

Break out the following more long-term changes into separate issues:

• If phasing is on, only output haplotagged alignments (#59)
• If phasing is on, only output run haplotagged cramino? (#61)
• Refactor assembly variant calling workflow (output aligned haplotypes) (#62)
• Make IGV visualisation files (#63)
• Output variant files as compressed and indexed vcf-files (#64)