Update krakenuniq #550
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Update krakenuniq #550
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The KrakenUniq module has a breaking change requiring a further input.
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jfy133
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Nov 5, 2024
Midnighter
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@jfy133 did you by any chance test this also without run merging? I'm still a bit in doubt about the |
jfy133
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Nov 6, 2024
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ONe thing I didn't check is if Taxpasta is still OK with this (no missing data), I'm assuming as it didn't fail it's OK but can you confirm from your tests @Midnighter ?
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Oh haha, just saw your question! will see if I can run again (DB wifi though) |
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How do you think taxpasta would be affected? I don't see a potential risk right now? |
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Same issue as you were referring to really - file names. I'm stuck on porechop_ABI for some reason, but suspect it's waiting for something to download still :grimace: |
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The taxpasta module uses a proper prefix definition, so I there should be no issues, there. def prefix = task.ext.prefix ?: "${meta.id}" |
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Currently doesn't work because of a file collision when there are SE and PE data in one run and run merging is not performed, as it results in file collisions. I think it needs a mdoules.conf update that a KrakenUniq SE run has |
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Unfortunately, can't use module config due to the batching :( but I'll update the pipeline channel logic. |
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Maybe embed it in the module? I think it it reasonable in this case |
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Please note that the module changes are currently copied over from a module update that I'm trying to get merged nf-core/modules#6912. That needs to be reverted later and the module updated properly.
This PR changes some of the channel plumbing to introduce a prefix for each sequencing reads file (or pairs).
Some doubt remains about the use of
meta.idas the prefix. I think, that refers to the sample identifier which may be non-unique if multiple runs are not merged. Potentially, that has to be changed to something else.I have run a local test and it seems to address #533