search

madagiurgiu25 / decoil-pre

Reconstruct ecDNA from long-read data using Decoil tool
BSD 3-Clause "New" or "Revised" License
7 stars 0 forks source link

parameters #6

Closed eesiribloom closed 5 months ago

eesiribloom commented 6 months ago

I wasn't completely clear about all the parameters in the readme: --sv-caller and --dry-run were not accepted also, --dry-run (-n) and --name (-n) have the same input which wouldn't work?

madagiurgiu25 commented 6 months ago

Dear @eesiribloom,

Thank you for highlighting this. I will change for the future the -name (-n).

--dry-run is a snakemake command this is why it needs to go before the sv-reconstruct (run-mode) like in the example below:

docker run -it --platform=linux/amd64 \
    -v $PWD/test3:/output \
    -v $PWD/$GTFANNO:/annotation/anno.gtf \
    -v $PWD/$REFGENOME:/annotation/reference.fa \
    -t madagiurgiu25/decoil:1.1.1-slim-test \
decoil -f --dry-run sv-reconstruct \
    -b /examples/ecdna1/map.bam \
    -r /annotation/reference.fa \
    -g /annotation/anno.gtf \
    -o /output -n ecdna1

It works using both -n or --dry-run.

madagiurgiu25 commented 6 months ago

Dear @eesiribloom,

--sv-caller is currently deactivate and unvailable for this version. By default Decoil uses internally sniffles to call structural variants. The method will be fully functional after the paper is published.

madagiurgiu25 commented 5 months ago

Hi @eesiribloom,

I will close the issue due to inactivity. Please feel free to reopen if you have further questions.

Best, Madalina