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replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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bump default container version for pangolin and nextclade #264

Closed MarieLataretu closed 7 months ago

MarieLataretu commented 7 months ago

bump to latest containers:

replikation commented 7 months ago

Could you also adjust this part and test on --update?

https://github.com/replikation/poreCov/blob/0ff536fe01c2c2410e1b666c74a3bd43bd8dc287/poreCov.nf#L260

replikation commented 7 months ago

@DataSpott can you validate the PR?

MarieLataretu commented 7 months ago

worked also w/ --update for me 👍

replikation commented 7 months ago

thank you @MarieLataretu

DataSpott commented 7 months ago

Tested 44 samples as I would rerun a routine batch. Once using the [--update]-flag and once omitting it, both runs were completed successfully. Also, with the [--update]-flag, the first attempt to create the final report-HTML failed, but completed on the 2nd try using [-resume].

Used command: nextflow run replikation/poreCov -r 5461df6 -profile ukj_cloud --primerV /path/to/nCoV-2019_V1200_dec-2022.bed --fastq "//path/to/poreCov_test_files/*.fastq.gz" --minLength 100 --maxLength 1500 --medaka_model "r941_min_sup_g507" --output /path/to/poreCov_test_without-update --rapid [--update]