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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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Biosample overwrite names using lima errors as an unknown option #627

Closed kxr104 closed 9 months ago

kxr104 commented 9 months ago

Hi, I am having trouble using lima with the --overwrite-biosample-names to update the sample names. When I go to the lima help menu, it does not show as an option. Has this been implemented? Below is the error message. I have the most recent updates of all of the packages.

lima ERROR: [pbcopper] command line parser ERROR: unknown option 'overwrite-biosample-names'

This is the documentation on isoseq website:

If your sample is barcoded at the cDNA level, use --overwrite-biosample-names to update the sample names. $ lima movieX.hifi_reads.bam barcoded_primers.fasta movieX.fl.bam --isoseq --peek-guess --overwrite-biosample-names

kxr104 commented 9 months ago

loaded smrtcmd from modules which has the updated version of lima