Currently we 'blindly' untar every row in the database samplesheet. If someone has submitted the same database but with different parameters, we will untar that database repeatedly. If we go to publish this, we we will repeatedly overwrite the same files - the latter causes an error with strict
We should improve the efficiency of untarring to only do it once per file - so likely we have to group by file name, untar, then spread again with the metas to separate the differnet parameters.
Picked up by setting nextflow.enabled.strict = true in test config and running the test_malt profile
jfy133
commented
6 months ago
Description of the bug
Currently we 'blindly' untar every row in the database samplesheet. If someone has submitted the same database but with different parameters, we will untar that database repeatedly. If we go to publish this, we we will repeatedly overwrite the same files - the latter causes an error with strict
We should improve the efficiency of untarring to only do it once per file - so likely we have to group by file name, untar, then spread again with the metas to separate the differnet parameters.
Picked up by setting
nextflow.enabled.strict = truein test config and running thetest_maltprofileCommand used and terminal output
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Relevant files
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System information
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