sarek
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Output from ascat not stable
Description of the bug
When running the following test, which is also also part of the CI-test tests/test_tools_manually.yml
,
nextflow run main.nf -profile test,tools_somatic_ascat
@SusiJo found that the content (not just timestamps or something like that, but proper values!) of the output-files
results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourBAF.txt
results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourLogR.txt
change on reruns:
Command used and terminal output
nextflow run main.nf -profile test,tools_somatic_ascat
"unstable" output-files
results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourBAF.txt
results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourLogR.txt
Relevant files
sample4_vs_sample3.tumour_tumourBAF.txt
from consecutive runs of the test:
System information
No response
what did you use to run it? Docker?
what did you use to run it? Docker?
@SusiJo told me she used Docker.
Looking at the manual here: https://raw.githubusercontent.com/VanLoo-lab/ascat/master/man/ASCAT-manual.pdf looks like one can set seeds for a few functions. Haven't cross-checked them with the ones that are used, but seems like a good place to start.
So they fixed the issue on the master branch but we probably need to wait for the 3.1 release to make a new mulled container.
Hey! Let's keep this open until it is actually merged into the pipeline and added to the changelog or we will forget :)