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:

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

[jfy133]

Ping @apeltzer for DeDup/MTNucRatio ;)

[apeltzer]

Yeah supported, worst case I just bump the library used and it should work almost out of the box.

[jfy133]