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Just pulled PAA down the other day and have running it, my run command is:
/data/PrepareAA/docker/run_paa_docker.py -o /data/output -s Colo -t 16 --bam /data/Data/Colo/cofinal.bam --run_AA --run_A…
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Hello,
Firts of all, I would like to express my appreciation for the development of AA. I have been using AA extensively, and it has been a crucial tool in my research.
I am planning to use Hi…
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Hi,
I have multiple 30X WGS data and want to try AA on it. As mentioned in other issues, 30X is too large for AA and downsampling is recommended. But I'm not sure which one is the right way for downs…
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Repro:
Running AS-p GroupedAnalysis mode via registry.hub.docker.com/jluebeck/prepareaa:v1.3.3: `python /home/programs/AmpliconSuite-pipeline-master/GroupedAnalysisAmpSuite.py --input input_file.tx…
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Hello,
I've been trying to run amplicon architect for several days now but the run reaches a certain point and does not progress further without giving any errors or terminating. I am running it …
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Dear @jluebeck:
Thank you for providing the research community for this application.
We would like to request a new docker image of ampliconarchitect with a slight change but makes it working to…
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Hi,
I am running AmpliconArchitect on WGS data (10x) and it has stalled at "plotting SV view" on a couple of samples without progressing for more than 4 days, but completed within a day for most of t…
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Hi there,
I used the end-to-end wrapper to process my data, but I didn't get any ecDNA. So, I want to check the steps one by one.
I reran the data following the log file generated by AmpliconSuite-p…
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### Description of feature
Thank you Daniel and the rest of the nf-circdna team for putting together this nextflow pipeline!
From my understanding of the nf-circdna workflow file, https://githu…
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### Description of the bug
The test profile is not working, appears to need samtools I think
### Command used and terminal output
```console
(base) [feshap@n102 ecdna]$ ~/raid/nextflow run nf-core/…