Optimisation: Drop samtools index processes

[matthdsm]

Description of feature

Most samtools tools now include the option to --write-index. By leveraging this we could omit a bunch of SAMTOOLS_INDEX processes, saving a lot of data shuffling and processes.

[FriederikeHanssen]

Good idea, I remember we considered this once and someone told me or tested it and at that point in time there was something of with this option. But I think it is a good idea to revisit this and test it.

[matthdsm]

I recently tested this with a modified SAMTOOLS_MARKDUP module and it worked like a charm!

[matthdsm]

https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/blob/dev/modules/local/samtools/sormadup/main.nf

[FriederikeHanssen]

awesome! (samtools markdup, we also want to add)