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edited Aug 24, 2023 at 15:58

My hacktastic fix for this is to use basename to get the get the name of each file, then do

refName=`basename "${Ref}"`
ln -s "${Ref}" "$refName"

for each file. This puts aliases to each file in the executions dir, and then I pass "refName" to GATK rather than "${Ref}".

Not a good solution, but a solution

My hacktastic fix for this is to use basename to get the get the name of each file, then do

refName=`basename "${Ref}"`
ln -s "${Ref}" "$refName"

for each file. This puts aliases to each file in the executions dir, and then I pass "refName" to GATK rather than "${Ref}".

Not a good solution, but a solution

My hacktastic fix for this is to use basename to get the name of each file, then do

refName=`basename "${Ref}"`
ln -s "${Ref}" "$refName"

for each file. This puts aliases to each file in the executions dir, and then I pass "refName" to GATK rather than "${Ref}".

Not a good solution, but a solution

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created Jan 21, 2021 at 22:37

My hacktastic fix for this is to use basename to get the get the name of each file, then do

refName=`basename "${Ref}"`
ln -s "${Ref}" "$refName"

for each file. This puts aliases to each file in the executions dir, and then I pass "refName" to GATK rather than "${Ref}".

Not a good solution, but a solution