new module: ascat

[maxulysse]

I think it would be good to have a module for ascat

[lassefolkersen]

Maria and I are looking into this.

[lassefolkersen]

We have a very very early draft, but one issue that comes up is that it's not really ready for sequencing data

We are working on an integrated and automated whole genome, exome and targeted sequencing version that runs directly from BAM files.

ASCAT input files can also be derived from massively parallel sequencing data, through log-transformed normalised read depth (LogR) and allele frequencies (BAF) of selected SNP loci.

Is what it currently says. So it requires quite a lot of extra work up front to make it start from BAM files.

I've written the lab and ask if there's any updates I've missed.

[lassefolkersen]

Great news @aasNGC I talked to the vanLoo-lab people and they are releasing the 3.0 ASCAT version right now, and that does take bam input. I'll get it through with bioconda and such, and then we can proceed.

[lassefolkersen]

The v3.0.0 is now released. I've just put in a version-bump pull request at bioconda, so should be available as dockers and singularities from there soon. Once it is I'll go back to that old fork from @assNGC and finish up the module.