CRAM Output support

[apeltzer]

We should have the possibility to output CRAM files

[apeltzer]

Issues with this:

• DeDup can't handle CRAM yet
• DamageProfiler can't handle CRAM yet

[jfy133]

@apeltzer I think it makes more sense to close this until fixed upstream ;) and we get more requests. Thoughts?

[apeltzer]

Maybe - damageprofiler though can do cram now :)

[jfy133]

Review of our tools that accepts CRAM format:

• samtools fastq ☑️
• samtools flagstat ☑️
• hostremoval 🟡 (but probably easily added, as uses pysam, which does)
• samtools view ☑️
• dedup ❌
• picard markDuplicates ☑️
• bedtools ☑️
• damageprofiler ☑️
• mtnucratio ❌
• preseq 🟡 (could just use bed format instead?)
• nuclear contamination ☑️
• qualimap ☑️ (not directly, but @FriederikeHanssen has made a sneaky nf-core module to make it 'supportable')
• PMDTools ☑️ not natively, but uses a pipe from samtools view
• BamUtils ❌
• mapDamage2 🟡 (uses pysam, seemingly without particular version? Maybe work...)
• GATK UnifiedGenotyper ❌
• GatkHaplotypeCaller ☑️
• sequenceTools ☑️
• Freebayes ❌
• ANGSD ☑️

So actually I guess most tools accept it, or at least there is a possible workaround...

The main blockers I would think are DeDup/MTNucRatio/UnifiedGenotyper

BamUtils I'm 99% we can find a different tool to do it for us.