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Update get_singularity.py #18

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2cd6a52
Update get_singularity.py
samir-watson Sep 29, 2025
5dbf378
fix dorado.nf
samir-watson Sep 29, 2025
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3 changes: 2 additions & 1 deletion scripts/get_singularity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,8 @@ def get_images(jsonfile, outdir):
newname = contname.replace('docker://', '')
newname = newname.replace('/', '-')
newname = outdir + "/" + newname.replace(':', '-') + ".img"
execDict[newname] = "singularity pull --name " + newname + " " + args.prefix + contname
uri = contname if contname.startswith("docker://") else args.prefix + contname
execDict[newname] = "singularity pull --name " + newname + " " + uri

for new_contname in execDict:
print("Downloading to " + new_contname)
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2 changes: 1 addition & 1 deletion subworkflows/basecalling/dorado.nf
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Expand Up @@ -11,7 +11,7 @@ params.EXTRAPARS_DEM = ""
params.OUTPUT = ""
params.OUTPUTMODE = "copy"
params.MOP = ""
params.CONTAINER = "docker pull ontresearch/dorado:shae423e761540b9d08b526a1eb32faf498f32e8f22"
params.CONTAINER = "ontresearch/dorado:shae423e761540b9d08b526a1eb32faf498f32e8f22"

params.GPU = ""
params.DUPLEX = ""
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