ghga-de / nf-aceseq Goto Github PK

write unit tests for validations

CI/CD tests need to be prepared.

Naga reported recent changes in hg38-dev ACESEQ changes. It should be integrated

remove chrprefix from HDR estimation module

No multi-sample run is possible for now for no-control and fake-control samples. The problem is with the directory of fake controls and how it is handled. This should change.

remove from the configs

https://github.com/DKFZ-ODCF/sophia

"_tcn_distances_combined_star.png"

seems like 'star' plots are not moved from 'work' folders to 'plots'
and 'most_important' files are the final result files.. maybe you could move them out of the 'plots' folder to a 'result' folder..

rm ext.args from modules.config if it is not defined in the module.

• Update README.md
• Update docs/
• Update nextflow_schema.json

update nextflow_schema.json

this part only needed for out page

• no control
• fake control

Pipeline takes SV file from Sophia originally, experiment with different SV callers.

It is not straightforward to create a test dataset for ACEseq pipeline since the pipeline is primarily built using WGS data. There are multiple filtering steps, normalizations accordingly etc.

Note: talk to Gregor.

optimize cpu/memory per module

it should be HRD (Homologous Recombination Deficiency) everywhere, not HDR.

no-control pipeline is not working because of an unknown error in PSCBS segmentation module. pscbs_all.R is not working with --nocontrol TRUE option.

def snp_min_coverage = meta.iscontrol == "1" ? "${params.snp_min_coverage}" : "0"

fix