Replace custom containers with seqera containers incl version upgrades

[verku]

No description provided.

[verku]

I wasn't able to find a container with the mlRho tools sam2pro or formatPro so will keep the custom container for now (samtools 1.9, mlRho 2.9, sam2pro and formatPro). All other custom containers have been replaced and tools have been upgraded as follows:

bedtools 2.29.2 > 2.31.1
htslib 1.15.1 > 1.20
samtools 1.9 > 1.20 (except for bam2pro and mlRho rules)

[verku]

None of the rules failed with an error message, but note that the results have not been doublechecked.