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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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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 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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Hi,
Thanks very much for sharing this tool to parse AmpliconArchitect (AA) results. My original understanding about AA's *cycles.txt file is that if a cycle include segment 0 at the start and at th…
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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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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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### 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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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
I ran
`nextflow run nf-core/circdna -r dev --input colo320dm_samplesheet.csv --outdir colo320dmlc_nftest --genome GRCh38 -profile docker --circle_identifier ampliconarchit…
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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/…