Add automatic shell detection if not provided in image/powderaverage #50
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AlexVCaron
reviewed
Nov 22, 2024
| @@ -21,7 +21,7 @@ process IMAGE_POWDERAVERAGE { | |||
| def prefix = task.ext.prefix ?: "${meta.id}" | |||
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| def b0_thr = task.ext.b0_thr ? "--b0_thr ${task.ext.b0_thr}" : '' | |||
| def shells = task.ext.shells ? "--shells ${task.ext.shells}" : '' | |||
| def shells = task.ext.shells ? "--shells ${task.ext.shells}" : "--shells \$(cut -d ' ' --output-delimiter=\$'\\n' -f 1- $bval | awk -F' ' '{v=int(\$1)}{print v}' | uniq)" | |||
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The scilpy script is doing this job itself, when no shell argument is supplied. It also controls for uneven bvalues, that is really hard to do in bash. Why do we need this ?
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I can't remember exactly why (I should have noted it somewhere), but this fix worked. I'll try to reproduce the error and see what happens. Let's wait for merging in the meantime!
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Well, I've tried to reproduce the error again, but it seems to run fine now. I reverted the change @AlexVCaron !
AlexVCaron
approved these changes
Nov 22, 2024
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LGTM ! |
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Add automatic shell detection in image/powderaverage. (#41)