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
approved these changes
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
approved these changes
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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As discussed on Slack huddle: we don't need to embed in the module, just update the list of prefixes coming in via the new input channel for the module to add |
In the rare case that there are two samples with the same identifier and run accession, one being single-end and the other paired-end, this change makes the prefix and thus the KrakenUniq output filenames unique.
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Nice, OK I will test the following commands: Normal test, no run merging (about 4-6 profiles) nextflow run ../main.nf -profile test_krakenuniq,docker --outdir ./results_ku_testinputonly_runmerging --shortread_qc_mergepairs false --save_runmerged_readsNormal test, with run merging (2 profiles) nextflow run ../main.nf -profile test_krakenuniq,docker --outdir ./results_ku_testinputonly_norunmerging --shortread_qc_mergepairs false --save_runmerged_reads --perform_runmergingThen with dots with ids, no run merging nextflow run ../main.nf -profile test_krakenuniq,docker --outdir ./results_ku_dotsinname_norunmerging --input samplesheet_dots_in_ids.csv --shortread_qc_mergepairs false ---save_runmerged_reads Then with dots with ids, with run merging nextflow run ../main.nf -profile test_krakenuniq,docker --outdir ./results_ku_dotsinname_runmerging --input samplesheet_dots_in_ids.csv --shortread_qc_mergepairs false --perform_runmerging --save_runmerged_reads |
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I'll request you to re-review then. You can just approve when you are satisfied with the tests. |
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So those commands worked nicely with no crash as you see below. I need to try one more test where I merge pairs so SE/PE can be merged together (and considered SE) |
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And that look sgood too! nextflow run ../main.nf -profile test_krakenuniq,docker --outdir ./results_ku_testinputonly_runmerging_readmerge --shortread_qc_mergepairs true --save_runmerged_reads$ ls -l results_ku_testinputonly_runmerging_readmerge/krakenuniq/db6/
total 20
-rw-r--r-- 1 james james 427 Nov 21 12:47 2611.se.krakenuniq.report.txt
-rw-r--r-- 1 james james 421 Nov 21 12:47 2612.se.krakenuniq.report.txt
-rw-r--r-- 1 james james 432 Nov 21 12:47 2613.se.krakenuniq.report.txt
-rw-r--r-- 1 james james 414 Nov 21 12:47 2614.se.krakenuniq.report.txt
-rw-r--r-- 1 james james 445 Nov 21 12:47 ERR3201952.se.krakenuniq.report.txt |
jfy133
approved these changes
Nov 21, 2024
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Thanks @Midnighter ! |
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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