New version release

[SPPearce]

Hi ichorCNA team,

I've been using the most recent version, v0.3.2, for a while with good results.
I'm now trying to put ichorCNA into a nextflow module within the nf-core community framework, to make it easy for people to include ichorCNA within pipelines.

However, the most recent container on bioconda is still v0.2.0, with the runIchorCNA.R file dated 2018. This is missing the genomeBuild parameter for instance.

Can a new github release please be made so that I can use a v0.3.2 in bioconda.

Thanks, Simon

[SPPearce]

I have updated the container on bioconda to include the most recent v0.3.2, would be good for there to be a released tag.

[Salaheddinekacimi]

I want to use your nextflow script to run it on my cohort. Would you love to share it with me?

[SPPearce]

Hi Sala, There is a module on the nf-core community project: https://github.com/nf-core/modules/tree/master/modules/nf-core/ichorcna/run , along with modules for the hmmcopy prerequisites: https://github.com/nf-core/modules/tree/master/modules/nf-core/hmmcopy . There isn't currently an nf-core pipeline using it, but you'd want something like:

include { BAM_SORT_SAMTOOLS} from '../subworkflows/nf-core/bam_sort_samtools/main'
include { HMMCOPY_READCOUNTER } from '../modules/nf-core/hmmcopy/readcounter/main.nf'
include { ICHORCNA_RUN } from '../modules/ichorcna/run/main'

BAM_SORT_SAMTOOLS.out.bam.
            join(BAM_SORT_SAMTOOLS.out.bai, by :[0], remainder: true).
            set {ch_bam_bai}

HMMCOPY_READCOUNTER (ch_bam_bai)
ICHORCNA_RUN(HMMCOPY_READCOUNTER.out.wig, params.ichor_gc_wig, params.ichor_map_wig, params.ichor_pon, params.ichor_centromeres, params.ichor_seqinfo )

assuming you are using the nf-core tools to install modules.